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Sang C, Li X, Liu J, Chen Z, Xia M, Yu M, Yu W. Reversible acetylation of HDAC8 regulates cell cycle. EMBO Rep 2024; 25:3925-3943. [PMID: 39043961 PMCID: PMC11387496 DOI: 10.1038/s44319-024-00210-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/28/2024] [Accepted: 07/05/2024] [Indexed: 07/25/2024] Open
Abstract
HDAC8, a member of class I HDACs, plays a pivotal role in cell cycle regulation by deacetylating the cohesin subunit SMC3. While cyclins and CDKs are well-established cell cycle regulators, our knowledge of other regulators remains limited. Here we reveal the acetylation of K202 in HDAC8 as a key cell cycle regulator responsive to stress. K202 acetylation in HDAC8, primarily catalyzed by Tip60, restricts HDAC8 activity, leading to increased SMC3 acetylation and cell cycle arrest. Furthermore, cells expressing the mutant form of HDAC8 mimicking K202 acetylation display significant alterations in gene expression, potentially linked to changes in 3D genome structure, including enhanced chromatid loop interactions. K202 acetylation impairs cell cycle progression by disrupting the expression of cell cycle-related genes and sister chromatid cohesion, resulting in G2/M phase arrest. These findings indicate the reversible acetylation of HDAC8 as a cell cycle regulator, expanding our understanding of stress-responsive cell cycle dynamics.
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Affiliation(s)
- Chaowei Sang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Xuedong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Jingxuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Ziyin Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Minhui Xia
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Miao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Wei Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, 200438, Shanghai, China.
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2
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Lou J, Deng Q, Zhang X, Bell CC, Das AB, Bediaga NG, Zlatic CO, Johanson TM, Allan RS, Griffin MDW, Paradkar P, Harvey KF, Dawson MA, Hinde E. Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture. Nucleic Acids Res 2024:gkae720. [PMID: 39193905 DOI: 10.1093/nar/gkae720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 07/29/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Our understanding of heterochromatin nanostructure and its capacity to mediate gene silencing in a living cell has been prevented by the diffraction limit of optical microscopy. Thus, here to overcome this technical hurdle, and directly measure the nucleosome arrangement that underpins this dense chromatin state, we coupled fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between histones core to the nucleosome, with molecular editing of heterochromatin protein 1 alpha (HP1α). Intriguingly, this super-resolved readout of nanoscale chromatin structure, alongside fluorescence fluctuation spectroscopy (FFS) and FLIM-FRET analysis of HP1α protein-protein interaction, revealed nucleosome arrangement to be differentially regulated by HP1α oligomeric state. Specifically, we found HP1α monomers to impart a previously undescribed global nucleosome spacing throughout genome architecture that is mediated by trimethylation on lysine 9 of histone H3 (H3K9me3) and locally reduced upon HP1α dimerisation. Collectively, these results demonstrate HP1α to impart a dual action on chromatin that increases the dynamic range of nucleosome proximity. We anticipate that this finding will have important implications for our understanding of how live cell heterochromatin structure regulates genome function.
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Affiliation(s)
- Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Qiji Deng
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Xiaomeng Zhang
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Andrew B Das
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Naiara G Bediaga
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Courtney O Zlatic
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - PrasadN Paradkar
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong3220, Australia
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
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3
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Das M, Semple JI, Haemmerli A, Volodkina V, Scotton J, Gitchev T, Annan A, Campos J, Statzer C, Dakhovnik A, Ewald CY, Mozziconacci J, Meister P. Condensin I folds the Caenorhabditis elegans genome. Nat Genet 2024; 56:1737-1749. [PMID: 39039278 DOI: 10.1038/s41588-024-01832-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/13/2024] [Indexed: 07/24/2024]
Abstract
The structural maintenance of chromosome (SMC) complexes-cohesin and condensins-are crucial for chromosome separation and compaction during cell division. During the interphase, mammalian cohesins additionally fold the genome into loops and domains. Here we show that, in Caenorhabditis elegans, a species with holocentric chromosomes, condensin I is the primary, long-range loop extruder. The loss of condensin I and its X-specific variant, condensin IDC, leads to genome-wide decompaction, chromosome mixing and disappearance of X-specific topologically associating domains, while reinforcing fine-scale epigenomic compartments. In addition, condensin I/IDC inactivation led to the upregulation of X-linked genes and unveiled nuclear bodies grouping together binding sites for the X-targeting loading complex of condensin IDC. C. elegans condensin I/IDC thus uniquely organizes holocentric interphase chromosomes, akin to cohesin in mammals, as well as regulates X-chromosome gene expression.
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Affiliation(s)
- Moushumi Das
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Jennifer I Semple
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Anja Haemmerli
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Valeriia Volodkina
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Janik Scotton
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Todor Gitchev
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Ahrmad Annan
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Julie Campos
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Cyril Statzer
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Switzerland
| | - Alexander Dakhovnik
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Switzerland
| | - Collin Y Ewald
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Switzerland
| | - Julien Mozziconacci
- Laboratoire Structure et Instabilité des Génomes UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Bern, Switzerland.
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4
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Do C, Jiang G, Cova G, Katsifis CC, Narducci DN, Yang J, Sakellaropoulos T, Vidal R, Lhoumaud P, Tsirigos A, Regis FFD, Kakabadze N, Nora EP, Noyes M, Cheng X, Hansen AS, Skok JA. Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer. RESEARCH SQUARE 2024:rs.3.rs-4670379. [PMID: 39070636 PMCID: PMC11275995 DOI: 10.21203/rs.3.rs-4670379/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Although only a fraction of CTCF motifs are bound in any cell type, and approximately half of the occupied sites overlap cohesin, the mechanisms underlying cell-type specific attachment and ability to function as a chromatin organizer remain unknown. To investigate the relationship between CTCF and chromatin we applied a combination of imaging, structural and molecular approaches, using a series of brain and cancer associated CTCF mutations that act as CTCF perturbations. We demonstrate that binding and the functional impact of WT and mutant CTCF depend not only on the unique properties of each protein, but also on the genomic context of bound sites. Our studies also highlight the reciprocal relationship between CTCF and chromatin, demonstrating that the unique binding properties of WT and mutant proteins have a distinct impact on accessibility, TF binding, cohesin overlap, chromatin interactivity and gene expression programs, providing insight into their cancer and brain related effects.
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Affiliation(s)
- Catherine Do
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Guimei Jiang
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Giulia Cova
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Christos C Katsifis
- MIT Department of Biological Engineering
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA
| | - Domenic N Narducci
- MIT Department of Biological Engineering
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA
| | - Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Theodore Sakellaropoulos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Raphael Vidal
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Priscillia Lhoumaud
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratories, Office of Science & Research, NYU Grossman School of Medicine, New York, NY, USA
| | - Faye Fara D Regis
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nata Kakabadze
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elphege P Nora
- Cardiovascular Research Institute, and Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
| | - Marcus Noyes
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Anders S Hansen
- MIT Department of Biological Engineering
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, 02139, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
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5
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Huang Z, Cui W, Ratnayake I, Tawil R, Pfeifer GP. SMCHD1 maintains heterochromatin and genome compartments in human myoblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602392. [PMID: 39026812 PMCID: PMC11257445 DOI: 10.1101/2024.07.07.602392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Mammalian genomes are subdivided into euchromatic A compartments that contain mostly active chromatin, and inactive, heterochromatic B compartments. However, it is unknown how A and B genome compartments are established and maintained. Here we studied SMCHD1, an SMC-like protein in human male myoblasts. SMCHD1 colocalizes with Lamin B1 and the heterochromatin mark H3K9me3. Loss of SMCHD1 leads to extensive heterochromatin depletion at the nuclear lamina and acquisition of active chromatin states along all chromosomes. In absence of SMCHD1, long range intra-chromosomal and inter-chromosomal contacts between B compartments are lost while many new TADs and loops are formed. Inactivation of SMCHD1 promotes numerous B to A compartment transitions accompanied by activation of silenced genes. SMCHD1 functions as an anchor for heterochromatin domains ensuring that these domains are inaccessible to epigenome modification enzymes that typically operate in active chromatin. Therefore, A compartments are formed by default when not prevented by SMCHD1.
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6
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An J, Brik Chaouche R, Pereyra-Bistraín LI, Zalzalé H, Wang Q, Huang Y, He X, Dias Lopes C, Antunez-Sanchez J, Bergounioux C, Boulogne C, Dupas C, Gillet C, Pérez-Pérez JM, Mathieu O, Bouché N, Fragkostefanakis S, Zhang Y, Zheng S, Crespi M, Mahfouz MM, Ariel F, Gutierrez-Marcos J, Raynaud C, Latrasse D, Benhamed M. An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution. Proc Natl Acad Sci U S A 2024; 121:e2400737121. [PMID: 38968127 PMCID: PMC11252963 DOI: 10.1073/pnas.2400737121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/21/2024] [Indexed: 07/07/2024] Open
Abstract
In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.
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Affiliation(s)
- Jing An
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Rim Brik Chaouche
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Leonardo I. Pereyra-Bistraín
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
| | - Hugo Zalzalé
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
| | - Qingyi Wang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Chloé Dias Lopes
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | | | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Claire Boulogne
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | - Cynthia Dupas
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | - Cynthia Gillet
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | | | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, Clermont-FerrandF-63000, France
| | - Nicolas Bouché
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles78000, France
| | | | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal23955-6900, Saudi Arabia
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, SantaFe 3000, Argentina
| | | | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
- Institut Universitaire de France, Orsay, Gif-sur-Yvette91190, France
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7
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Feng J, Chuah Y, Liang Y, Cipta N, Zeng Y, Warrier T, Elfar G, Yoon J, Grinchuk O, Tay E, Lok KZ, Zheng ZQ, Khong Z, Chong ZS, Teo J, Sanford E, Neo C, Chiu H, Leung J, Wang L, Lim Y, Zhao T, Sobota R, Crasta K, Tergaonkar V, Taneja R, Ng SY, Cheok C, Ling SC, Loh YH, Ong D. PHF2 regulates genome topology and DNA replication in neural stem cells via cohesin. Nucleic Acids Res 2024; 52:7063-7080. [PMID: 38808662 PMCID: PMC11229317 DOI: 10.1093/nar/gkae457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Cohesin plays a crucial role in the organization of topologically-associated domains (TADs), which influence gene expression and DNA replication timing. Whether epigenetic regulators may affect TADs via cohesin to mediate DNA replication remains elusive. Here, we discover that the histone demethylase PHF2 associates with RAD21, a core subunit of cohesin, to regulate DNA replication in mouse neural stem cells (NSC). PHF2 loss impairs DNA replication due to the activation of dormant replication origins in NSC. Notably, the PHF2/RAD21 co-bound genomic regions are characterized by CTCF enrichment and epigenomic features that resemble efficient, active replication origins, and can act as boundaries to separate adjacent domains. Accordingly, PHF2 loss weakens TADs and chromatin loops at the co-bound loci due to reduced RAD21 occupancy. The observed topological and DNA replication defects in PHF2 KO NSC support a cohesin-dependent mechanism. Furthermore, we demonstrate that the PHF2/RAD21 complex exerts little effect on gene regulation, and that PHF2's histone-demethylase activity is dispensable for normal DNA replication and proliferation of NSC. We propose that PHF2 may serve as a topological accessory to cohesin for cohesin localization to TADs and chromatin loops, where cohesin represses dormant replication origins directly or indirectly, to sustain DNA replication in NSC.
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Affiliation(s)
- Jia Feng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - You Heng Chuah
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Centre for Cancer Research Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yajing Liang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Nadia Omega Cipta
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Yingying Zeng
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Tushar Warrier
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Gamal Ahmed Rashed Elsayed Elfar
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, National University Hospital, Singapore 119074, Singapore
| | - Jeehyun Yoon
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Centre for Cancer Research Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Oleg V Grinchuk
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Centre for Cancer Research Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Emmy Xue Yun Tay
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Ker-Zhing Lok
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Zong-Qing Zheng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Zi Jian Khong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Zheng-Shan Chong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Jackie Teo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Emma May Sanford
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Healthy Longevity Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Cheryl Jia Yi Neo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Healthy Longevity Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hsin Yao Chiu
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Jia Yu Leung
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, National University Hospital, Singapore 119074, Singapore
| | - Loo Chien Wang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Yan Ting Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Karen Carmelina Crasta
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Centre for Cancer Research Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Healthy Longevity Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vinay Tergaonkar
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, MD7, Singapore 117596, Singapore
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Centre for Cancer Research Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Healthy Longevity Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shi-Yan Ng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- National Neuroscience Institute, 308433, Singapore
| | - Chit Fang Cheok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, National University Hospital, Singapore 119074, Singapore
| | - Shuo-Chien Ling
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Healthy Longevity Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yuin-Han Loh
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Centre for Cancer Research Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Healthy Longevity Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National Neuroscience Institute, 308433, Singapore
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8
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Sun D, Zhu Y, Peng W, Zheng S, Weng J, Dong S, Li J, Chen Q, Ge C, Liao L, Dong Y, Liu Y, Meng W, Jiang Y. SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells. Genome Biol 2024; 25:175. [PMID: 38961490 PMCID: PMC11221086 DOI: 10.1186/s13059-024-03327-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Transposable elements play a critical role in maintaining genome architecture during neurodevelopment. Short Interspersed Nuclear Elements (SINEs), a major subtype of transposable elements, are known to harbor binding sites for the CCCTC-binding factor (CTCF) and pivotal in orchestrating chromatin organization. However, the regulatory mechanisms controlling the activity of SINEs in the developing brain remains elusive. RESULTS In our study, we conduct a comprehensive genome-wide epigenetic analysis in mouse neural precursor cells using ATAC-seq, ChIP-seq, whole genome bisulfite sequencing, in situ Hi-C, and RNA-seq. Our findings reveal that the SET domain bifurcated histone lysine methyltransferase 1 (SETDB1)-mediated H3K9me3, in conjunction with DNA methylation, restricts chromatin accessibility on a selective subset of SINEs in neural precursor cells. Mechanistically, loss of Setdb1 increases CTCF access to these SINE elements and contributes to chromatin loop reorganization. Moreover, de novo loop formation contributes to differential gene expression, including the dysregulation of genes enriched in mitotic pathways. This leads to the disruptions of cell proliferation in the embryonic brain after genetic ablation of Setdb1 both in vitro and in vivo. CONCLUSIONS In summary, our study sheds light on the epigenetic regulation of SINEs in mouse neural precursor cells, suggesting their role in maintaining chromatin organization and cell proliferation during neurodevelopment.
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Affiliation(s)
- Daijing Sun
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yueyan Zhu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Wenzhu Peng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Shenghui Zheng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Jie Weng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Shulong Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiaqi Li
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Qi Chen
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Chuanhui Ge
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Liyong Liao
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yuhao Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yun Liu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Weida Meng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China.
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9
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Do C, Jiang G, Cova G, Katsifis CC, Narducci DN, Yang J, Sakellaropoulos T, Vidal R, Lhoumaud P, Tsirigos A, Regis FFD, Kakabadze N, Nora EP, Noyes M, Cheng X, Hansen AS, Skok JA. Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575070. [PMID: 38370764 PMCID: PMC10871189 DOI: 10.1101/2024.01.11.575070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Although only a fraction of CTCF motifs are bound in any cell type, and approximately half of the occupied sites overlap cohesin, the mechanisms underlying cell-type specific attachment and ability to function as a chromatin organizer remain unknown. To investigate the relationship between CTCF and chromatin we applied a combination of imaging, structural and molecular approaches, using a series of brain and cancer associated CTCF mutations that act as CTCF perturbations. We demonstrate that binding and the functional impact of WT and mutant CTCF depend not only on the unique properties of each protein, but also on the genomic context of bound sites. Our studies also highlight the reciprocal relationship between CTCF and chromatin, demonstrating that the unique binding properties of WT and mutant proteins have a distinct impact on accessibility, TF binding, cohesin overlap, chromatin interactivity and gene expression programs, providing insight into their cancer and brain related effects. Graphical abstract
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10
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Joosten SEP, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Yavuz K, Donaldson Collier M, Morova T, Altintaş UB, Kim Y, Canisius S, Moelans CB, van Diest PJ, Korkmaz G, Lack NA, Vermeulen M, Linn SC, Zwart W. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. Genome Res 2024; 34:539-555. [PMID: 38719469 PMCID: PMC11146591 DOI: 10.1101/gr.278680.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
Abstract
Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1+ breast cancers to explore inter-patient heterogeneity in ESR1 DNA binding to reveal a striking inter-tumor heterogeneity of ESR1 action. Of note, commonly shared ESR1 sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1 and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we can confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ESR1-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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Affiliation(s)
- Stacey E P Joosten
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Suzan Stelloo
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
| | - Elif Yapıcı
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Kerim Yavuz
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Maria Donaldson Collier
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tunç Morova
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Umut Berkay Altintaş
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Yongsoo Kim
- Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Gozde Korkmaz
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Nathan A Lack
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Michiel Vermeulen
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
- Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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11
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Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV, Xiao Y. Cooltools: Enabling high-resolution Hi-C analysis in Python. PLoS Comput Biol 2024; 20:e1012067. [PMID: 38709825 PMCID: PMC11098495 DOI: 10.1371/journal.pcbi.1012067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/16/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are now used to probe genome architecture across cell states, types, and organisms. Larger datasets add challenges at each step of computational analysis, from storage and memory constraints to researchers' time; however, analysis tools that meet these increased resource demands have not kept pace. Furthermore, existing tools offer limited support for customizing analysis for specific use cases or new biology. Here we introduce cooltools (https://github.com/open2c/cooltools), a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface (CLI) and Python application programming interface (API), which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments. In short, cooltools enables the effective use of the latest and largest genome folding datasets.
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Affiliation(s)
- Open2C
- https://open2c.github.io/
| | - Nezar Abdennur
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sameer Abraham
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Geoffrey Fudenberg
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Aleksandra A. Galitsyna
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Betul A. Oksuz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Yao Xiao
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
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12
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Tian H, Luan P, Liu Y, Li G. Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic Acids Res 2024; 52:3654-3666. [PMID: 38300758 DOI: 10.1093/nar/gkae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
DNA Methylation is a significant epigenetic modification that can modulate chromosome states, but its role in orchestrating chromosome organization has not been well elucidated. Here we systematically assessed the effects of DNA Methylation on chromosome organization with a multi-omics strategy to capture DNA Methylation and high-order chromosome interaction simultaneously on mouse embryonic stem cells with DNA methylation dioxygenase Tet triple knock-out (Tet-TKO). Globally, upon Tet-TKO, we observed weakened compartmentalization, corresponding to decreased methylation differences between CpG island (CGI) rich and poor domains. Tet-TKO could also induce hypermethylation for the CTCF binding peaks in TAD boundaries and chromatin loop anchors. Accordingly, CTCF peak generally weakened upon Tet-TKO, which results in weakened TAD structure and depletion of long-range chromatin loops. Genes that lost enhancer-promoter looping upon Tet-TKO showed DNA hypermethylation in their gene bodies, which may compensate for the disruption of gene expression. We also observed distinct effects of Tet1 and Tet2 on chromatin organization and increased DNA methylation correlation on spatially interacted fragments upon Tet inactivation. Our work showed the broad effects of Tet inactivation and DNA methylation dynamics on chromosome organization.
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Affiliation(s)
- Hao Tian
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Pengfei Luan
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yaping Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Guoqiang Li
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
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13
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Tang X, Zeng P, Liu K, Qing L, Sun Y, Liu X, Lu L, Wei C, Wang J, Jiang S, Sun J, Chang W, Yu H, Chen H, Zhou J, Xu C, Fan L, Miao YL, Ding J. The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation. Nat Commun 2024; 15:2813. [PMID: 38561336 PMCID: PMC10985093 DOI: 10.1038/s41467-024-47048-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
CCCTC-binding factor (CTCF), a ubiquitously expressed and highly conserved protein, is known to play a critical role in chromatin structure. Post-translational modifications (PTMs) diversify the functions of protein to regulate numerous cellular processes. However, the effects of PTMs on the genome-wide binding of CTCF and the organization of three-dimensional (3D) chromatin structure have not been fully understood. In this study, we uncovered the PTM profiling of CTCF and demonstrated that CTCF can be O-GlcNAcylated and arginine methylated. Functionally, we demonstrated that O-GlcNAcylation inhibits CTCF binding to chromatin. Meanwhile, deficiency of CTCF O-GlcNAcylation results in the disruption of loop domains and the alteration of chromatin loops associated with cellular development. Furthermore, the deficiency of CTCF O-GlcNAcylation increases the expression of developmental genes and negatively regulates maintenance and establishment of stem cell pluripotency. In conclusion, these results provide key insights into the role of PTMs for the 3D chromatin structure.
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Affiliation(s)
- Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Kezhi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yifei Sun
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Lizi Lu
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jia Wang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Jun Sun
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Wakam Chang
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Jiaguo Zhou
- Department of Pharmacology and Cardiac & Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Chengfang Xu
- The obstetric and gynecology Department of The third affiliated hospital of Sun Yat-Sen University, Guangzhou, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Junjun Ding
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China.
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14
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Otsuka A, Minami K, Higashi K, Kawaguchi A, Tamura S, Ide S, Hendzel MJ, Kurokawa K, Maeshima K. Chromatin organization and behavior in HRAS-transformed mouse fibroblasts. Chromosoma 2024; 133:135-148. [PMID: 38400910 DOI: 10.1007/s00412-024-00817-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
In higher eukaryotic cells, a string of nucleosomes, where long genomic DNA is wrapped around core histones, are rather irregularly folded into a number of condensed chromatin domains, which have been revealed by super-resolution imaging and Hi-C technologies. Inside these domains, nucleosomes fluctuate and locally behave like a liquid. The behavior of chromatin may be highly related to DNA transaction activities such as transcription and repair, which are often upregulated in cancer cells. To investigate chromatin behavior in cancer cells and compare those of cancer and non-cancer cells, we focused on oncogenic-HRAS (Gly12Val)-transformed mouse fibroblasts CIRAS-3 cells and their parental 10T1/2 cells. CIRAS-3 cells are tumorigenic and highly metastatic. First, we found that HRAS-induced transformation altered not only chromosome structure, but also nuclear morphology in the cell. Using single-nucleosome imaging/tracking in live cells, we demonstrated that nucleosomes are locally more constrained in CIRAS-3 cells than in 10T1/2 cells. Consistently, heterochromatin marked with H3K27me3 was upregulated in CIRAS-3 cells. Finally, Hi-C analysis showed enriched interactions of the B-B compartment in CIRAS-3 cells, which likely represents transcriptionally inactive chromatin. Increased heterochromatin may play an important role in cell migration, as they have been reported to increase during metastasis. Our study also suggests that single-nucleosome imaging provides new insights into how local chromatin is structured in living cells.
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Affiliation(s)
- Aoi Otsuka
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Koichi Higashi
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Akane Kawaguchi
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ken Kurokawa
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
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15
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Cheng G, Pratto F, Brick K, Li X, Alleva B, Huang M, Lam G, Camerini-Otero RD. High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586627. [PMID: 38903112 PMCID: PMC11188084 DOI: 10.1101/2024.03.25.586627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
When germ cells transition from the mitotic cycle into meiotic prophase I (MPI), chromosomes condense into an array of chromatin loops that are required to promote homolog pairing and genetic recombination. To identify the changes in chromosomal conformation, we isolated nuclei on a trajectory from spermatogonia to the end of MPI. At each stage along this trajectory, we built genomic interaction maps with the highest temporal and spatial resolution to date. The changes in chromatin folding coincided with a concurrent decline in mitotic cohesion and a rise in meiotic cohesin complexes. We found that the stereotypical large-scale A and B compartmentalization was lost during meiotic prophase I alongside the loss of topological associating domains (TADs). Still, local subcompartments were detected and maintained throughout meiosis. The enhanced Micro-C resolution revealed that, despite the loss of TADs, higher frequency contact sites between two loci were detectable during meiotic prophase I coinciding with CTCF bound sites. The pattern of interactions around these CTCF sites with their neighboring loci showed that CTCF sites were often anchoring the meiotic loops. Additionally, the localization of CTCF to the meiotic axes indicated that these anchors were at the base of loops. Strikingly, even in the face of the dramatic reconfiguration of interphase chromatin into a condensed loop-array, the interactions between regulatory elements remained well preserved. This establishes a potential mechanism for how the meiotic chromatin maintains active transcription within a highly structured genome. In summary, the high temporal and spatial resolution of these data revealed previously unappreciated aspects of mammalian meiotic chromatin organization.
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Affiliation(s)
- Gang Cheng
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Florencia Pratto
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Brick
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Xin Li
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Alleva
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD, USA
| | - Mini Huang
- Present address: Sun Yat-Sen University, School of Medicine, Shen Zhen, China
| | - Gabriel Lam
- Present address: RNA Regulation Section, NIA, National Institutes of Health, Baltimore, MD, USA
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16
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Choppavarapu L, Fang K, Liu T, Jin VX. Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity and tumor-specific looping-mediated biological pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584872. [PMID: 38559097 PMCID: PMC10979939 DOI: 10.1101/2024.03.13.584872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Current knowledge in three-dimensional (3D) chromatin regulation in normal and disease states was mostly accumulated through Hi-C profiling in in vitro cell culture system. The limitations include failing to recapitulate disease-specific physiological properties and often lacking clinically relevant disease microenvironment. In this study, we conduct tissue-specific Hi-C profiling in a pilot cohort of 12 breast tissues comprising of two normal tissues (NTs) and ten ER+ breast tumor tissues (TTs) including five primary tumors (PTs), and five tamoxifen-treated recurrent tumors (RTs). We find largely preserved compartments, highly heterogeneous topological associated domains (TADs) and intensively variable chromatin loops among breast tumors, demonstrating 3D chromatin-regulated breast tumor heterogeneity. Further cross-examination identifies RT-specific looping-mediated biological pathways and suggests CA2, an enhancer-promoter looping (EPL)-mediated target gene within the bicarbonate transport metabolism pathway, might play a role in driving the tamoxifen resistance. Remarkably, the inhibition of CA2 not only impedes tumor growth both in vitro and in vivo , but also reverses chromatin looping. Our study thus yields significant mechanistic insights into the role and clinical relevance of 3D chromatin architecture in breast cancer endocrine resistance.
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17
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Achinger-Kawecka J, Stirzaker C, Portman N, Campbell E, Chia KM, Du Q, Laven-Law G, Nair SS, Yong A, Wilkinson A, Clifton S, Milioli HH, Alexandrou S, Caldon CE, Song J, Khoury A, Meyer B, Chen W, Pidsley R, Qu W, Gee JMW, Schmitt A, Wong ES, Hickey TE, Lim E, Clark SJ. The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer. Nat Struct Mol Biol 2024; 31:498-512. [PMID: 38182927 PMCID: PMC10948365 DOI: 10.1038/s41594-023-01181-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
Three-dimensional (3D) epigenome remodeling is an important mechanism of gene deregulation in cancer. However, its potential as a target to counteract therapy resistance remains largely unaddressed. Here, we show that epigenetic therapy with decitabine (5-Aza-mC) suppresses tumor growth in xenograft models of pre-clinical metastatic estrogen receptor positive (ER+) breast tumor. Decitabine-induced genome-wide DNA hypomethylation results in large-scale 3D epigenome deregulation, including de-compaction of higher-order chromatin structure and loss of boundary insulation of topologically associated domains. Significant DNA hypomethylation associates with ectopic activation of ER-enhancers, gain in ER binding, creation of new 3D enhancer-promoter interactions and concordant up-regulation of ER-mediated transcription pathways. Importantly, long-term withdrawal of epigenetic therapy partially restores methylation at ER-enhancer elements, resulting in a loss of ectopic 3D enhancer-promoter interactions and associated gene repression. Our study illustrates the potential of epigenetic therapy to target ER+ endocrine-resistant breast cancer by DNA methylation-dependent rewiring of 3D chromatin interactions, which are associated with the suppression of tumor growth.
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Affiliation(s)
- Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia.
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Neil Portman
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Elyssa Campbell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Kee-Ming Chia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Qian Du
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Geraldine Laven-Law
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Shalima S Nair
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Aliza Yong
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ashleigh Wilkinson
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Samuel Clifton
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Heloisa H Milioli
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sarah Alexandrou
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - C Elizabeth Caldon
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jenny Song
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Amanda Khoury
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Braydon Meyer
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Wenhan Chen
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ruth Pidsley
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Wenjia Qu
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Julia M W Gee
- Breast Cancer Molecular Pharmacology Group, School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, UK
| | | | - Emily S Wong
- Victor Chang Cardiac Institute, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia.
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18
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Wahl N, Espeso-Gil S, Chietera P, Nagel A, Laighneach A, Morris DW, Rajarajan P, Akbarian S, Dechant G, Apostolova G. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol Cell 2024; 84:621-639.e9. [PMID: 38244545 PMCID: PMC10923151 DOI: 10.1016/j.molcel.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.
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Affiliation(s)
- Nico Wahl
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Sergio Espeso-Gil
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria; Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paola Chietera
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Amelie Nagel
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Prashanth Rajarajan
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
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19
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Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R. Orchestrating chromosome conformation capture analysis with Bioconductor. Nat Commun 2024; 15:1072. [PMID: 38316789 PMCID: PMC10844600 DOI: 10.1038/s41467-024-44761-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024] Open
Abstract
Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.
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Affiliation(s)
- Jacques Serizay
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France.
| | - Cyril Matthey-Doret
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Swiss Data Science Center, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lyam Baudry
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Université de Lausanne, Center for Integrative Genomics, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
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20
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Hou Y, Li Y, Xiang JF, Tilahun K, Jiang J, Corces VG, Yao B. TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk. Cell Rep 2024; 43:113662. [PMID: 38184854 PMCID: PMC10857847 DOI: 10.1016/j.celrep.2023.113662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
TDP-43 is an RNA/DNA-binding protein that forms aggregates in various brain disorders. TDP-43 engages in many aspects of RNA metabolism, but its molecular roles in regulating genes and transposable elements (TEs) have not been extensively explored. Chronic TDP-43 knockdown impairs cell proliferation and cellular responses to DNA damage. At the molecular level, TDP-43 chronic deficiency affects gene expression either locally or distally by concomitantly altering the crosstalk between R-loops and 5-hydroxymethylcytosine (5hmC) in gene bodies and long-range enhancer/promoter interactions. Furthermore, TDP-43 knockdown induces substantial disease-relevant TE activation by influencing their R-loop and 5hmC homeostasis in a locus-specific manner. Together, our findings highlight the genomic roles of TDP-43 in modulating R-loop-5hmC coordination in coding genes, distal regulatory elements, and TEs, presenting a general and broad molecular mechanism underlying the contributions of proteinopathies to the etiology of neurodegenerative disorders.
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Affiliation(s)
- Yingzi Hou
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jian-Feng Xiang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kedamawit Tilahun
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jie Jiang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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21
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Halasz L, Divoux A, Sandor K, Erdos E, Daniel B, Smith SR, Osborne TF. An Atlas of Promoter Chromatin Modifications and HiChIP Regulatory Interactions in Human Subcutaneous Adipose-Derived Stem Cells. Int J Mol Sci 2023; 25:437. [PMID: 38203607 PMCID: PMC10778978 DOI: 10.3390/ijms25010437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The genome of human adipose-derived stem cells (ADSCs) from abdominal and gluteofemoral adipose tissue depots are maintained in depot-specific stable epigenetic conformations that influence cell-autonomous gene expression patterns and drive unique depot-specific functions. The traditional approach to explore tissue-specific transcriptional regulation has been to correlate differential gene expression to the nearest-neighbor linear-distance regulatory region defined by associated chromatin features including open chromatin status, histone modifications, and DNA methylation. This has provided important information; nonetheless, the approach is limited because of the known organization of eukaryotic chromatin into a topologically constrained three-dimensional network. This network positions distal regulatory elements in spatial proximity with gene promoters which are not predictable based on linear genomic distance. In this work, we capture long-range chromatin interactions using HiChIP to identify remote genomic regions that influence the differential regulation of depot-specific genes in ADSCs isolated from different adipose depots. By integrating these data with RNA-seq results and histone modifications identified by ChIP-seq, we uncovered distal regulatory elements that influence depot-specific gene expression in ADSCs. Interestingly, a subset of the HiChIP-defined chromatin loops also provide previously unknown connections between waist-to-hip ratio GWAS variants with genes that are known to significantly influence ADSC differentiation and adipocyte function.
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Affiliation(s)
- Laszlo Halasz
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA (T.F.O.)
| | - Adeline Divoux
- Translational Research Institute, AdventHealth, Orlando, FL 32804, USA;
| | - Katalin Sandor
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA (T.F.O.)
| | - Edina Erdos
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA (T.F.O.)
| | - Bence Daniel
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA (T.F.O.)
| | - Steven R. Smith
- Translational Research Institute, AdventHealth, Orlando, FL 32804, USA;
| | - Timothy F. Osborne
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA (T.F.O.)
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22
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Qu Z, Batz Z, Singh N, Marchal C, Swaroop A. Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids. Cell Rep 2023; 42:113543. [PMID: 38048222 PMCID: PMC10790351 DOI: 10.1016/j.celrep.2023.113543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
We have generated a high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive stage-specific alterations in DNA topology and correlate these changes with transcription of cell-type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift toward A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression, respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages (i.e., TAD cliques) localize in active chromatin regions with binding sites for eye-field transcription factors. These genes gain chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.
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Affiliation(s)
- Zepeng Qu
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Zachary Batz
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Nivedita Singh
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Claire Marchal
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA; In silichrom Ltd, 15 Digby Road, Newbury RG14 1TS, UK
| | - Anand Swaroop
- Neurobiology, Neurodegeneration, and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
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23
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He J, Yan A, Chen B, Huang J, Kee K. 3D genome remodeling and homologous pairing during meiotic prophase of mouse oogenesis and spermatogenesis. Dev Cell 2023; 58:3009-3027.e6. [PMID: 37963468 DOI: 10.1016/j.devcel.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
During meiosis, the chromatin and transcriptome undergo prominent switches. Although recent studies have explored the genome reorganization during spermatogenesis, the chromatin remodeling in oogenesis and characteristics of homologous pairing remain largely elusive. We comprehensively compared chromatin structures and transcriptomes at successive substages of meiotic prophase in both female and male mice using low-input high-through chromosome conformation capture (Hi-C) and RNA sequencing (RNA-seq). Compartments and topologically associating domains (TADs) gradually disappeared and slowly recovered in both sexes. We found that homologs adopted different sex-conserved pairing strategies prior to and after the leptotene-to-zygotene transition, changing from long interspersed nuclear element (LINE)-enriched compartments B to short interspersed nuclear element (SINE)-enriched compartments A. We complemented marker genes and predicted the sex-specific meiotic sterile genes for each substage. This study provides valuable insights into the similarities and distinctions between sexes in chromosome architecture, homologous pairing, and transcriptome during meiotic prophase of both oogenesis and spermatogenesis.
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Affiliation(s)
- Jing He
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - An Yan
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Bo Chen
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Jiahui Huang
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Kehkooi Kee
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China.
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24
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Bsteh D, Moussa HF, Michlits G, Yelagandula R, Wang J, Elling U, Bell O. Loss of cohesin regulator PDS5A reveals repressive role of Polycomb loops. Nat Commun 2023; 14:8160. [PMID: 38071364 PMCID: PMC10710464 DOI: 10.1038/s41467-023-43869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) are conserved epigenetic regulators that promote transcriptional gene silencing. PRC1 and PRC2 converge on shared targets, catalyzing repressive histone modifications. Additionally, a subset of PRC1/PRC2 targets engage in long-range interactions whose functions in gene silencing are poorly understood. Using a CRISPR screen in mouse embryonic stem cells, we found that the cohesin regulator PDS5A links transcriptional silencing by Polycomb and 3D genome organization. PDS5A deletion impairs cohesin unloading and results in derepression of a subset of endogenous PRC1/PRC2 target genes. Importantly, derepression is not linked to loss of Polycomb chromatin domains. Instead, PDS5A removal causes aberrant cohesin activity leading to ectopic insulation sites, which disrupt the formation of ultra-long Polycomb loops. We show that these loops are important for robust silencing at a subset of PRC1/PRC2 target genes and that maintenance of cohesin-dependent genome architecture is critical for Polycomb regulation.
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Affiliation(s)
- Daniel Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Medical Oncology, Department of Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hagar F Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- JLP Health GmbH, Himmelhofgasse 62, 1130, Vienna, Austria
| | - Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, 500039, India
| | - Jingkui Wang
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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25
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Xie B, Dean A. Noncoding function of super enhancer derived mRNA in modulating neighboring gene expression and TAD interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570115. [PMID: 38105946 PMCID: PMC10723268 DOI: 10.1101/2023.12.05.570115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Super enhancers are important regulators of gene expression that often overlap with protein-coding genes. However, it is unclear whether the overlapping protein-coding genes and the mRNA derived from them contribute to enhancer activity. Using an erythroid-specific super enhancer that overlaps the Cpox gene as a model, we found that Cpox mRNA has a non-coding function in regulating neighboring protein-coding genes, eRNA expression and TAD interactions. Depletion of Cpox mRNA leads to accumulation of H3K27me3 and release of p300 from the Cpox locus, activating an intra-TAD enhancer and gene expression. Additionally, we identified a head-to-tail interaction between the TAD boundary genes Cpox and Dcbld2 that is facilitated by a novel type of repressive loop anchored by p300 and PRC2/H3K27me3. Our results uncover a regulatory role for mRNA transcribed within a super enhancer context and provide insight into head-to-tail inter-gene interaction in the regulation of gene expression and oncogene activation.
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Affiliation(s)
- Bingning Xie
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
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26
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Hu Y, Salgado Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark MR, Morgan BA, Ay F, Georgopoulos K. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell 2023; 186:5269-5289.e22. [PMID: 37995656 PMCID: PMC10895928 DOI: 10.1016/j.cell.2023.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS' ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.
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Affiliation(s)
- Yeguang Hu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Daniela Salgado Figueroa
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Bioinformatics and Systems Biology Program, La Jolla, CA, USA
| | - Zhihong Zhang
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Margaret Veselits
- Gwen Knapp Center for Lupus and Immunology Research, Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Sourya Bhattacharyya
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Mariko Kashiwagi
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Marcus R Clark
- Gwen Knapp Center for Lupus and Immunology Research, Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Bruce A Morgan
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ferhat Ay
- Centers for Autoimmunity, Inflammation and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Bioinformatics and Systems Biology Program, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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27
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Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Estrogen Receptor alpha (ERα) is the main driver and prime drug target in luminal breast. ERα chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ERα chromatin action, along with its biological implications. Here, we use a large set of ERα ChIP-seq data from 70 ERα+ breast cancers to explore inter-patient heterogeneity in ERα DNA binding, to reveal a striking inter-tumor heterogeneity of ERα action. Interestingly, commonly-shared ERα sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERα-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ERα and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ERα-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERα landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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28
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Youngblood MW, Erson-Omay Z, Li C, Najem H, Coșkun S, Tyrtova E, Montejo JD, Miyagishima DF, Barak T, Nishimura S, Harmancı AS, Clark VE, Duran D, Huttner A, Avşar T, Bayri Y, Schramm J, Boetto J, Peyre M, Riche M, Goldbrunner R, Amankulor N, Louvi A, Bilgüvar K, Pamir MN, Özduman K, Kilic T, Knight JR, Simon M, Horbinski C, Kalamarides M, Timmer M, Heimberger AB, Mishra-Gorur K, Moliterno J, Yasuno K, Günel M. Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas. Nat Commun 2023; 14:6279. [PMID: 37805627 PMCID: PMC10560290 DOI: 10.1038/s41467-023-41926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/25/2023] [Indexed: 10/09/2023] Open
Abstract
Hedgehog signaling mediates embryologic development of the central nervous system and other tissues and is frequently hijacked by neoplasia to facilitate uncontrolled cellular proliferation. Meningiomas, the most common primary brain tumor, exhibit Hedgehog signaling activation in 6.5% of cases, triggered by recurrent mutations in pathway mediators such as SMO. In this study, we find 35.6% of meningiomas that lack previously known drivers acquired various types of somatic structural variations affecting chromosomes 2q35 and 7q36.3. These cases exhibit ectopic expression of Hedgehog ligands, IHH and SHH, respectively, resulting in Hedgehog signaling activation. Recurrent tandem duplications involving IHH permit de novo chromatin interactions between super-enhancers within DIRC3 and a locus containing IHH. Our work expands the landscape of meningioma molecular drivers and demonstrates enhancer hijacking of Hedgehog ligands as a route to activate this pathway in neoplasia.
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Affiliation(s)
- Mark W Youngblood
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neurological Surgery, Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zeynep Erson-Omay
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Chang Li
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P. R. China
| | - Hinda Najem
- Department of Neurological Surgery, Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Süleyman Coșkun
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Evgeniya Tyrtova
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, University of Washington, Seattle, WA, USA
| | - Julio D Montejo
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Section of Neurosurgery, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Danielle F Miyagishima
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Tanyeri Barak
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Sayoko Nishimura
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Akdes Serin Harmancı
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Victoria E Clark
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Daniel Duran
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Anita Huttner
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Timuçin Avşar
- Department of Neurosurgery, Bahcesehir University, School of Medicine, Istanbul, Turkey
| | - Yasar Bayri
- Department of Neurosurgery, Marmara University School of Medicine, 34854, Istanbul, Turkey
| | | | - Julien Boetto
- Department of Neurosurgery, Hopital Pitie-Salpetriere, AP-HP & Sorbonne Université, F-75103, Paris, France
- Department of Neurosurgery, Gui de Chauliac Hospital, Montpellier University Medical Center, Montpellier, France
| | - Matthieu Peyre
- Department of Neurosurgery, Hopital Pitie-Salpetriere, AP-HP & Sorbonne Université, F-75103, Paris, France
| | - Maximilien Riche
- Department of Neurosurgery, Hopital Pitie-Salpetriere, AP-HP & Sorbonne Université, F-75103, Paris, France
| | - Roland Goldbrunner
- Center for Neurosurgery, University Hospital of Cologne, 50937, Cologne, Germany
| | - Nduka Amankulor
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Angeliki Louvi
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Kaya Bilgüvar
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale University West Campus, Orange, CT, USA
- Department of Medical Genetics Acibadem Mehmet Ali Aydınlar University, School of Medicine, Istanbul, 34848, Turkey
| | - M Necmettin Pamir
- Department of Neurosurgery, Acibadem Mehmet Ali Aydınlar University, School of Medicine, Istanbul, 34848, Turkey
| | - Koray Özduman
- Department of Neurosurgery, Acibadem Mehmet Ali Aydınlar University, School of Medicine, Istanbul, 34848, Turkey
| | - Türker Kilic
- Department of Neurosurgery, Bahcesehir University, School of Medicine, Istanbul, Turkey
| | - James R Knight
- Yale Center for Genome Analysis, Yale University West Campus, Orange, CT, USA
| | - Matthias Simon
- University of Bonn Medical School, 53105, Bonn, Germany
- Department of Neurosurgery, Bethel Clinic, University of Bielefeld Medical Center OWL, Bielefeld, Germany
| | - Craig Horbinski
- Department of Neurological Surgery, Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Michel Kalamarides
- Department of Neurosurgery, Hopital Pitie-Salpetriere, AP-HP & Sorbonne Université, F-75103, Paris, France
| | - Marco Timmer
- Center for Neurosurgery, University Hospital of Cologne, 50937, Cologne, Germany
| | - Amy B Heimberger
- Department of Neurological Surgery, Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ketu Mishra-Gorur
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jennifer Moliterno
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Katsuhito Yasuno
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
| | - Murat Günel
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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29
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Dai R, Zhu Y, Li Z, Qin L, Liu N, Liao S, Hao B. Three-way contact analysis characterizes the higher order organization of the Tcra locus. Nucleic Acids Res 2023; 51:8987-9000. [PMID: 37534534 PMCID: PMC10516640 DOI: 10.1093/nar/gkad641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during rearrangements of the T-cell antigen receptor gene Tcra. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multiway contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely to be responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.
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Affiliation(s)
- Ranran Dai
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Yongchang Zhu
- Department of Immunology, School of Basic Medical, Zhengzhou University, Zhengzhou 450001, China
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Zhaoqiang Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Litao Qin
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Nan Liu
- Division of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Bingtao Hao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
- Department of Immunology, School of Basic Medical, Zhengzhou University, Zhengzhou 450001, China
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30
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Nakato R, Sakata T, Wang J, Nagai LAE, Nagaoka Y, Oba GM, Bando M, Shirahige K. Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors. Nat Commun 2023; 14:5647. [PMID: 37726281 PMCID: PMC10509244 DOI: 10.1038/s41467-023-41316-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datasets are compared systematically. To validate our methodology, we generated 3D genome, transcriptome, and epigenome data before and after depletion of cohesin and related factors and compared the effects of depletion. We observed diverse effects on the 3D genome and transcriptome, and gene expression changes were correlated with the splitting of TADs caused by cohesin loss. We also observed variations in long-range interactions across TADs, which correlated with their epigenomic states. These computational tools and datasets will be valuable for 3D genome and epigenome studies.
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Affiliation(s)
- Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan.
| | - Toyonori Sakata
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
- Karolinska Institutet, Department of Biosciences and Nutrition, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden
| | - Jiankang Wang
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Luis Augusto Eijy Nagai
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Yuya Nagaoka
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Gina Miku Oba
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Masashige Bando
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan.
- Karolinska Institutet, Department of Biosciences and Nutrition, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden.
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Quarter A6, 171 77, Stockholm, Sweden.
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31
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Qu J, Sun J, Zhao C, Liu X, Zhang X, Jiang S, Wei C, Yu H, Zeng X, Fan L, Ding J. Simultaneous profiling of chromatin architecture and transcription in single cells. Nat Struct Mol Biol 2023; 30:1393-1402. [PMID: 37580628 DOI: 10.1038/s41594-023-01066-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/12/2023] [Indexed: 08/16/2023]
Abstract
The three-dimensional structure of chromatin plays a crucial role in development and disease, both of which are associated with transcriptional changes. However, given the heterogeneity in single-cell chromatin architecture and transcription, the regulatory relationship between the three-dimensional chromatin structure and gene expression is difficult to explain based on bulk cell populations. Here we develop a single-cell, multimodal, omics method allowing the simultaneous detection of chromatin architecture and messenger RNA expression by sequencing (single-cell transcriptome sequencing (scCARE-seq)). Applying scCARE-seq to examine chromatin architecture and transcription from 2i to serum single mouse embryonic stem cells, we observe improved separation of cell clusters compared with single-cell chromatin conformation capture. In addition, after defining the cell-cycle phase of each cell through chromatin architecture extracted by scCARE-seq, we find that periodic changes in chromatin architecture occur in parallel with transcription during the cell cycle. These findings highlight the potential of scCARE-seq to facilitate comprehensive analyses that may boost our understanding of chromatin architecture and transcription in the same single cell.
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Affiliation(s)
- Jiale Qu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jun Sun
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Cai Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinyao Zhang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoxi Zeng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
| | - Junjun Ding
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China.
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.
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Poonperm R, Ichihara S, Miura H, Tanigawa A, Nagao K, Obuse C, Sado T, Hiratani I. Replication dynamics identifies the folding principles of the inactive X chromosome. Nat Struct Mol Biol 2023; 30:1224-1237. [PMID: 37563439 PMCID: PMC10442229 DOI: 10.1038/s41594-023-01052-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/28/2023] [Indexed: 08/12/2023]
Abstract
Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase during X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization for heterochromatin stability and gene regulation.
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Affiliation(s)
- Rawin Poonperm
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Saya Ichihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Shizuoka, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Akie Tanigawa
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
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Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.
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Affiliation(s)
- Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Yuxin Cao
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yi Liu
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xiaochang Yin
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
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Zhang G, Li Y, Wei G. Multi-omic analysis reveals dynamic changes of three-dimensional chromatin architecture during T cell differentiation. Commun Biol 2023; 6:773. [PMID: 37488215 PMCID: PMC10366224 DOI: 10.1038/s42003-023-05141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/13/2023] [Indexed: 07/26/2023] Open
Abstract
Cell differentiation results in widespread changes in transcriptional programs as well as multi-level remodeling of three-dimensional genome architecture. Nonetheless, few synthetically investigate the chromatin higher-order landscapes in different T helper (Th) cells. Using RNA-Seq, ATAC-Seq and Hi-C assays, we characterize dynamic changes in chromatin organization at different levels during Naive CD4+ T cells differentiation into T helper 17 (Th17) and T helper 1 (Th1) cells. Upon differentiation, we observe decreased short-range and increased extra-long-range chromatin interactions. Although there is no apparent global switch in the A/B compartments, Th cells display the weaker compartmentalization. A portion of topologically associated domains are rearranged. Furthermore, we identify cell-type specific enhancer-promoter loops, many of which are associated with functional genes in Th cells, such as Rorc facilitating Th17 differentiation and Hif1a responding to intracellular oxygen levels in Th1. Taken together, these results uncover the general patterns of chromatin reorganization and epigenetic landscapes of gene regulation during T helper cell differentiation.
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Affiliation(s)
- Ge Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ying Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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Fukuda K, Shimi T, Shimura C, Ono T, Suzuki T, Onoue K, Okayama S, Miura H, Hiratani I, Ikeda K, Okada Y, Dohmae N, Yonemura S, Inoue A, Kimura H, Shinkai Y. Epigenetic plasticity safeguards heterochromatin configuration in mammals. Nucleic Acids Res 2023; 51:6190-6207. [PMID: 37178005 PMCID: PMC10325917 DOI: 10.1093/nar/gkad387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Heterochromatin is a key architectural feature of eukaryotic chromosomes critical for cell type-specific gene expression and genome stability. In the mammalian nucleus, heterochromatin segregates from transcriptionally active genomic regions and exists in large, condensed, and inactive nuclear compartments. However, the mechanisms underlying the spatial organization of heterochromatin need to be better understood. Histone H3 lysine 9 trimethylation (H3K9me3) and lysine 27 trimethylation (H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Mammals have at least five H3K9 methyltransferases (SUV39H1, SUV39H2, SETDB1, G9a and GLP) and two H3K27 methyltransferases (EZH1 and EZH2). In this study, we addressed the role of H3K9 and H3K27 methylation in heterochromatin organization using a combination of mutant cells for five H3K9 methyltransferases and an EZH1/2 dual inhibitor, DS3201. We showed that H3K27me3, which is normally segregated from H3K9me3, was redistributed to regions targeted by H3K9me3 after the loss of H3K9 methylation and that the loss of both H3K9 and H3K27 methylation resulted in impaired condensation and spatial organization of heterochromatin. Our data demonstrate that the H3K27me3 pathway safeguards heterochromatin organization after the loss of H3K9 methylation in mammalian cells.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
- School of Biosciences, The University of Melbourne, Royal Parade, 3010 Parkville, Australia
| | - Takeshi Shimi
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
| | - Takao Ono
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako 351-0198, Japan
| | - Kenta Onoue
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Satoko Okayama
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Kazuho Ikeda
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
- Universal Biology Institute (UBI) and International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo113-0033, Japan
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka565-0874, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako 351-0198, Japan
| | - Shigenobu Yonemura
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
- Department of Cell Biology, Tokushima University Graduate School of Medicine, Tokushima770-8503, Japan
| | - Azusa Inoue
- Laboratory for Epigenome Inheritance, RIKEN Center for Integrative Medical Sciences, Yokohama230-0045, Japan
- Tokyo Metropolitan University, Hachioji192-0397, Japan
| | - Hiroshi Kimura
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
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36
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Sun Y, Xu X, Zhao W, Zhang Y, Chen K, Li Y, Wang X, Zhang M, Xue B, Yu W, Hou Y, Wang C, Xie W, Li C, Kong D, Wang S, Sun Y. RAD21 is the core subunit of the cohesin complex involved in directing genome organization. Genome Biol 2023; 24:155. [PMID: 37381036 DOI: 10.1186/s13059-023-02982-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND The ring-shaped cohesin complex is an important factor for the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesin and chromatin is poorly understood. In this study, we use super-resolution imaging to reveal the unique role of cohesin subunit RAD21 in cohesin loading and chromatin structure regulation. RESULTS We directly visualize that up-regulation of RAD21 leads to excessive chromatin loop extrusion into a vermicelli-like morphology with RAD21 clustered into foci and excessively loaded cohesin bow-tying a TAD to form a beads-on-a-string-type pattern. In contrast, up-regulation of the other four cohesin subunits results in even distributions. Mechanistically, we identify that the essential role of RAD21 is attributed to the RAD21-loader interaction, which facilitates the cohesin loading process rather than increasing the abundance of cohesin complex upon up-regulation of RAD21. Furthermore, Hi-C and genomic analysis reveal how RAD21 up-regulation affects genome-wide higher-order chromatin structure. Accumulated contacts are shown at TAD corners while inter-TAD interactions increase after vermicelli formation. Importantly, we find that in breast cancer cells, the expression of RAD21 is aberrantly high with poor patient survival and RAD21 forms beads in the nucleus. Up-regulated RAD21 in HeLa cells leads to compartment switching and up-regulation of cancer-related genes. CONCLUSIONS Our results provide key insights into the molecular mechanism by which RAD21 facilitates the cohesin loading process and provide an explanation to how cohesin and loader work cooperatively to promote chromatin extrusion, which has important implications in construction of three-dimensional genome organization.
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Affiliation(s)
- Yuao Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Xin Xu
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Wenxue Zhao
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, 100871, China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing, 100084, China
| | - Keyang Chen
- Yuanpei College, Peking University, Beijing, 100871, China
| | - Yongzheng Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Xiaotian Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Wanting Yu
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Chaobin Wang
- Breast Center, Peking University People's Hospital, Beijing, 100044, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing, 100084, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, 100871, China
| | - Daochun Kong
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Shu Wang
- Breast Center, Peking University People's Hospital, Beijing, 100044, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
- Breast Center, Peking University People's Hospital, Beijing, 100044, China.
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, 100871, China.
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Kiefer L, Chiosso A, Langen J, Buckley A, Gaudin S, Rajkumar SM, Servito GIF, Cha ES, Vijay A, Yeung A, Horta A, Mui MH, Canzio D. WAPL functions as a rheostat of Protocadherin isoform diversity that controls neural wiring. Science 2023; 380:eadf8440. [PMID: 37347873 DOI: 10.1126/science.adf8440] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/07/2023] [Indexed: 06/24/2023]
Abstract
Neural type-specific expression of clustered Protocadherin (Pcdh) proteins is essential for the establishment of connectivity patterns during brain development. In mammals, deterministic expression of the same Pcdh isoform promotes minimal overlap of tiled projections of serotonergic neuron axons throughout the brain, while stochastic expression of Pcdh genes allows for convergence of tightly packed, overlapping olfactory sensory neuron axons into targeted structures. How can the same gene locus generate opposite transcriptional programs that orchestrate distinct spatial arrangements of axonal patterns? Here, we reveal that cell type-specific Pcdh expression and axonal behavior depend on the activity of cohesin and its unloader, WAPL (wings apart-like protein homolog). While cohesin erases genomic-distance biases in Pcdh choice, WAPL functions as a rheostat of cohesin processivity that determines Pcdh isoform diversity.
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Affiliation(s)
- Lea Kiefer
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anna Chiosso
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Langen
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alex Buckley
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simon Gaudin
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Ecole Normale Superieure de Lyon, 69432 Lyon, France
| | - Sandy M Rajkumar
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gabrielle Isabelle F Servito
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth S Cha
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Akshara Vijay
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albert Yeung
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adan Horta
- Pura Vida Investments, New York, NY 10106, USA
| | - Michael H Mui
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniele Canzio
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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38
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Gregoricchio S, Zwart W. snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis. BIOINFORMATICS ADVANCES 2023; 3:vbad080. [PMID: 37397353 PMCID: PMC10307938 DOI: 10.1093/bioadv/vbad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Summary Genome-wide chromosome conformation capture (Hi-C) is a technique that allows the study of 3D genome organization. Despite being widely used, analysis of Hi-C data is technically challenging and involves several time-consuming steps that often require manual involvement making it error prone, potentially affecting data reproducibility. In order to facilitate and simplify these analyses we implemented snHiC, a snakemake-based pipeline that allows for the generation of contact matrices at multiple resolutions in one single run, aggregation of individual samples into user-specified groups, detection of domains, compartments, loops and stripes and performance of differential compartment and chromatin interaction analyses. Availability and implementation Source code is freely available at https://github.com/sebastian-gregoricchio/snHiC. A yaml-formatted file (snHiC/workflow/envs/snHiC_conda_env_stable.yaml) is available to build a compatible conda environment. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Shi Y, Niu Y, Zhang P, Luo H, Liu S, Zhang S, Wang J, Li Y, Liu X, Song T, Xu T, He S. Characterization of genome-wide STR variation in 6487 human genomes. Nat Commun 2023; 14:2092. [PMID: 37045857 PMCID: PMC10097659 DOI: 10.1038/s41467-023-37690-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Short tandem repeats (STRs) are abundant and highly mutagenic in the human genome. Many STR loci have been associated with a range of human genetic disorders. However, most population-scale studies on STR variation in humans have focused on European ancestry cohorts or are limited by sequencing depth. Here, we depicted a comprehensive map of 366,013 polymorphic STRs (pSTRs) constructed from 6487 deeply sequenced genomes, comprising 3983 Chinese samples (~31.5x, NyuWa) and 2504 samples from the 1000 Genomes Project (~33.3x, 1KGP). We found that STR mutations were affected by motif length, chromosome context and epigenetic features. We identified 3273 and 1117 pSTRs whose repeat numbers were associated with gene expression and 3'UTR alternative polyadenylation, respectively. We also implemented population analysis, investigated population differentiated signatures, and genotyped 60 known disease-causing STRs. Overall, this study further extends the scale of STR variation in humans and propels our understanding of the semantics of STRs.
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Affiliation(s)
- Yirong Shi
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiwei Niu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuai Liu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sijia Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiajia Wang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanyan Li
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinyue Liu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingrui Song
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China.
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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40
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Kalluchi A, Harris HL, Reznicek TE, Rowley MJ. Considerations and caveats for analyzing chromatin compartments. Front Mol Biosci 2023; 10:1168562. [PMID: 37091873 PMCID: PMC10113542 DOI: 10.3389/fmolb.2023.1168562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023] Open
Abstract
Genomes are organized into nuclear compartments, separating active from inactive chromatin. Chromatin compartments are readily visible in a large number of species by experiments that map chromatin conformation genome-wide. When analyzing these maps, a common step is the identification of genomic intervals that interact within A (active) and B (inactive) compartments. It has also become increasingly common to identify and analyze subcompartments. We review different strategies to identify A/B and subcompartment intervals, including a discussion of various machine-learning approaches to predict these features. We then discuss the strengths and limitations of current strategies and examine how these aspects of analysis may have impacted our understanding of chromatin compartments.
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Affiliation(s)
| | | | | | - M. Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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41
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Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023; 13:5420. [PMID: 37012431 PMCID: PMC10070455 DOI: 10.1038/s41598-023-32568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| | - Maggie A Marshall
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aaron Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kavita Murthy
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Abhijit Chakraborty
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joaquin Reyna
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Daniela Salgado Figueroa
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Laura Hinojosa-Gonzalez
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Erika Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Brittany A Baur
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Ferhat Ay
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Pediatrics, UC San Diego-School of Medicine, La Jolla, CA, 92093, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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42
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de Wit E, Nora EP. New insights into genome folding by loop extrusion from inducible degron technologies. Nat Rev Genet 2023; 24:73-85. [PMID: 36180596 DOI: 10.1038/s41576-022-00530-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2022] [Indexed: 01/24/2023]
Abstract
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically wire distant loci together for gene regulation. These loops are continuously created, extended and positioned by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin, and their regulators, including CTCF, in a highly dynamic process known as loop extrusion. Genetic loss of extrusion factors is lethal, complicating their study. Inducible protein degradation technologies enable the depletion of loop extrusion factors within hours, leading to the rapid reconfiguration of chromatin folding. Here, we review how these technologies have changed our understanding of genome organization, upsetting long-held beliefs on its role in transcription. Finally, we examine recent models that attempt to reconcile observations after chronic versus acute perturbations, and discuss future developments in this rapidly developing field of research.
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Affiliation(s)
- Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Amsterdam, the Netherlands.
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Elphège P Nora
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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43
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Kato H, Tateishi K, Iwadate D, Yamamoto K, Fujiwara H, Nakatsuka T, Kudo Y, Hayakawa Y, Ijichi H, Otsuka M, Kishikawa T, Takahashi R, Miyabayashi K, Nakai Y, Hirata Y, Toyoda A, Morishita S, Fujishiro M. HNF1B-driven three-dimensional chromatin structure for molecular classification in pancreatic cancers. Cancer Sci 2022; 114:1672-1685. [PMID: 36511816 PMCID: PMC10067390 DOI: 10.1111/cas.15690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/09/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
The molecular subtypes of pancreatic cancer (PC), either classical/progenitor-like or basal/squamous-like, are currently a major topic of research because of their direct association with clinical outcomes. Some transcription factors (TFs) have been reported to be associated with these subtypes. However, the mechanisms by which these molecular signatures of PCs are established remain unknown. Epigenetic regulatory processes, supported by dynamic changes in the chromatin structure, are essential for transcriptional profiles. Previously, we reported the importance of open chromatin profiles in the biological features and transcriptional status of PCs. Here, we aimed to analyze the relationships between three-dimensional (3D) genome structures and the molecular subtypes of human PCs using Hi-C analysis. We observed a correlation of the specific elements of 3D genome modules, including compartments, topologically associating domains, and enhancer-promoter loops, with the expression of related genes. We focused on HNF1B, a TF that is implicated in the progenitor subtype. Forced expression of HNF1B in squamous-type PC organoids induced the upregulation and downregulation of genes associated with progenitor and squamous subtypes, respectively. Long-range genomic interactions induced by HNF1B were accompanied by compartment modulation and H3K27ac redistribution. We also found that these HNF1B-induced changes in subtype-related gene expression required an intrinsically disordered region, suggesting a possible involvement of phase separation in compartment modulation. Thus, mapping of 3D structural changes induced by TFs, such as HNF1B, may become a useful resource for further understanding the molecular features of PCs.
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Affiliation(s)
- Hiroyuki Kato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Tateishi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Gastroenterology, Department of Internal Medicine, St Marianna University School of Medicine, Kawasaki, Japan
| | - Dosuke Iwadate
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Yamamoto
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Fujiwara
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Gastroenterology, The Institute of Medical Science, Asahi Life Foundation, Tokyo, Japan
| | - Takuma Nakatsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yotaro Kudo
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideaki Ijichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Kishikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryota Takahashi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koji Miyabayashi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yousuke Nakai
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Endoscopy and Endoscopic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoshihiro Hirata
- Division of Advanced Genome Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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44
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Lyu H, Liu E, Wu Z, Li Y, Liu Y, Yin X. scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data. Bioinformatics 2022; 38:5151-5159. [PMID: 36205615 DOI: 10.1093/bioinformatics/btac670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/25/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The emerging single-cell Hi-C technology provides opportunities to study dynamics of chromosomal organization. How to construct a pseudotime path using single-cell Hi-C contact matrices to order cells along developmental trajectory is a challenging topic, since these matrices produced by the technology are inherently high dimensional and sparse, they suffer from noises and biases, and the topology of trajectory underlying them may be diverse. RESULTS We present scHiCPTR, an unsupervised graph-based pipeline to infer pseudotime from single-cell Hi-C contact matrices. It provides a workflow consisting of imputation and embedding, graph construction, dual graph refinement, pseudotime calculation and result visualization. Beyond the few existing methods, scHiCPTR ties to optimize graph structure by two parallel procedures of graph pruning, which help reduce the spurious cell links resulted from noises and determine a global developmental directionality. Besides, it has an ability to handle developmental trajectories with multiple topologies, including linear, bifurcated and circular ones, and is competitive with methods developed for single-cell RNA-seq data. The comparative results tell that our scHiCPTR can achieve higher performance in pseudotime inference, and the inferred developmental trajectory exhibit a reasonable biological significance. AVAILABILITY AND IMPLEMENTATION scHiCPTR is freely available at https://github.com/lhqxinghun/scHiCPTR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hongqiang Lyu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi 710049, China
| | - Erhu Liu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi 710049, China
| | - Zhifang Wu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi 710049, China
| | - Yao Li
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi 710049, China
| | - Yuan Liu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Shaanxi 710049, China
| | - Xiaoran Yin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi 710004, China
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45
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Zelenka T, Klonizakis A, Tsoukatou D, Papamatheakis DA, Franzenburg S, Tzerpos P, Tzonevrakis IR, Papadogkonas G, Kapsetaki M, Nikolaou C, Plewczynski D, Spilianakis C. The 3D enhancer network of the developing T cell genome is shaped by SATB1. Nat Commun 2022; 13:6954. [PMID: 36376298 PMCID: PMC9663569 DOI: 10.1038/s41467-022-34345-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout mouse which allows us to infer the molecular mechanisms responsible for the deregulation of its immune system. H3K27ac HiChIP and Hi-C experiments indicate that SATB1-dependent promoter-enhancer loops regulate expression of master regulator genes (such as Bcl6), the T cell receptor locus and adhesion molecule genes, collectively being critical for cell lineage specification and immune system homeostasis. SATB1-dependent regulatory chromatin loops represent a more refined layer of genome organization built upon a high-order scaffold provided by CTCF and other factors. Overall, our findings unravel the function of a tissue-specific factor that controls transcription programs, via spatial chromatin arrangements complementary to the chromatin structure imposed by ubiquitously expressed genome organizers.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Despina Tsoukatou
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, HU-4032, Hungary
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Centre "Alexander Fleming", 16672, Vari, Greece
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece.
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece.
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46
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van Schaik T, Manzo SG, Vouzas AE, Liu NQ, Teunissen H, de Wit E, Gilbert DM, van Steensel B. Dynamic chromosomal interactions and control of heterochromatin positioning by Ki-67. EMBO Rep 2022; 23:e55782. [PMID: 36245428 PMCID: PMC9724667 DOI: 10.15252/embr.202255782] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Ki-67 is a chromatin-associated protein with a dynamic distribution pattern throughout the cell cycle and is thought to be involved in chromatin organization. The lack of genomic interaction maps has hampered a detailed understanding of its roles, particularly during interphase. By pA-DamID mapping in human cell lines, we find that Ki-67 associates with large genomic domains that overlap mostly with late-replicating regions. Early in interphase, when Ki-67 is present in pre-nucleolar bodies, it interacts with these domains on all chromosomes. However, later in interphase, when Ki-67 is confined to nucleoli, it shows a striking shift toward small chromosomes. Nucleolar perturbations indicate that these cell cycle dynamics correspond to nucleolar maturation during interphase, and suggest that nucleolar sequestration of Ki-67 limits its interactions with larger chromosomes. Furthermore, we demonstrate that Ki-67 does not detectably control chromatin-chromatin interactions during interphase, but it competes with the nuclear lamina for interaction with late-replicating DNA, and it controls replication timing of (peri)centromeric regions. Together, these results reveal a highly dynamic choreography of genome interactions and roles for Ki-67 in heterochromatin organization.
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Affiliation(s)
- Tom van Schaik
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Stefano G Manzo
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Athanasios E Vouzas
- Department of Biological ScienceThe Florida State UniversityTallahasseeFLUSA,San Diego Biomedical Research InstituteSan DiegoCAUSA
| | - Ning Qing Liu
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Hans Teunissen
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Elzo de Wit
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - David M Gilbert
- Department of Biological ScienceThe Florida State UniversityTallahasseeFLUSA,San Diego Biomedical Research InstituteSan DiegoCAUSA
| | - Bas van Steensel
- Division of Gene Regulation and Oncode InstituteNetherlands Cancer InstituteAmsterdamThe Netherlands,Department of Cell BiologyErasmus University Medical CentreRotterdamThe Netherlands
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47
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Dimitrova E, Feldmann A, van der Weide RH, Flach KD, Lastuvkova A, de Wit E, Klose RJ. Distinct roles for CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction. Nat Struct Mol Biol 2022; 29:1000-1010. [PMID: 36220895 PMCID: PMC9568430 DOI: 10.1038/s41594-022-00840-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 08/22/2022] [Indexed: 11/20/2022]
Abstract
Precise control of gene expression underpins normal development. This relies on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs), the cyclin-dependent kinase module Mediator complex (CKM-Mediator) has been reported to physically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here, we show that CKM-Mediator contributes little to three-dimensional genome organization in ESCs, but it has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by Polycomb repressive complexes (PRCs). These interactions are established by the canonical PRC1 (cPRC1) complex but rely on CKM-Mediator, which facilitates binding of cPRC1 to its target sites. Importantly, through separation-of-function experiments, we reveal that this collaboration between CKM-Mediator and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on an interaction-independent mechanism whereby the CKM supports core Mediator engagement with gene promoters during differentiation to enable gene activation.
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Affiliation(s)
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robin H van der Weide
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Hubrecht Institute KNAW, Utrecht, The Netherlands
| | - Koen D Flach
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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48
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Zhao X, Peng T, Cao X, Hou Y, Li R, Han T, Fan Z, Zhao M, Chang Y, Chen H, Li C, Huang X. In vivo G-CSF treatment activates the GR-SOCS1 axis to suppress IFN-γ secretion by natural killer cells. Cell Rep 2022; 40:111342. [PMID: 36103837 DOI: 10.1016/j.celrep.2022.111342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 12/15/2022] Open
Abstract
Natural killer (NK) cells are lymphocytes that are involved in controlling tumors or microbial infections through the production of interferon gamma (IFN-γ). Granulocyte colony-stimulating factor (G-CSF) inhibits IFN-γ secretion by NK cells, but the mechanism underlying this effect remains unclear. Here, by comparing the multi-omics profiles of human NK cells before and after in vivo G-CSF treatment, we identify a pathway that is activated in response to G-CSF treatment, which suppresses IFN-γ secretion in NK cells. Specifically, glucocorticoid receptors (GRs) activated by G-CSF inhibit secretion of IFN-γ by promoting interactions between SOCS1 promoters and enhancers, as well as increasing the expression of SOCS1. Experiments in mice confirm that G-CSF treatment significantly downregulates IFN-γ secretion and upregulates GR and SOCS1 expression in NK cells. In addition, GR blockade by the antagonist RU486 significantly reverses the effects of G-CSF, demonstrating that GRs upregulate SOCS1 and inhibit the production of IFN-γ by NK cells.
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Affiliation(s)
- Xiangyu Zhao
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Ting Peng
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Xunhong Cao
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yingping Hou
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Ruifeng Li
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Tingting Han
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Zeying Fan
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Ming Zhao
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yingjun Chang
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Hebin Chen
- Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Xiaojun Huang
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China.
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49
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Cheng N, Li G, Kanchwala M, Evers BM, Xing C, Yu H. STAG2 promotes the myelination transcriptional program in oligodendrocytes. eLife 2022; 11:e77848. [PMID: 35959892 PMCID: PMC9439679 DOI: 10.7554/elife.77848] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Cohesin folds chromosomes via DNA loop extrusion. Cohesin-mediated chromosome loops regulate transcription by shaping long-range enhancer-promoter interactions, among other mechanisms. Mutations of cohesin subunits and regulators cause human developmental diseases termed cohesinopathy. Vertebrate cohesin consists of SMC1, SMC3, RAD21, and either STAG1 or STAG2. To probe the physiological functions of cohesin, we created conditional knockout (cKO) mice with Stag2 deleted in the nervous system. Stag2 cKO mice exhibit growth retardation, neurological defects, and premature death, in part due to insufficient myelination of nerve fibers. Stag2 cKO oligodendrocytes exhibit delayed maturation and downregulation of myelination-related genes. Stag2 loss reduces promoter-anchored loops at downregulated genes in oligodendrocytes. Thus, STAG2-cohesin generates promoter-anchored loops at myelination-promoting genes to facilitate their transcription. Our study implicates defective myelination as a contributing factor to cohesinopathy and establishes oligodendrocytes as a relevant cell type to explore the mechanisms by which cohesin regulates transcription.
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Affiliation(s)
- Ningyan Cheng
- Department of Pharmacology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Guanchen Li
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
- School of Life Sciences, Westlake UniversityHangzhouChina
- Institute of Biology, Westlake Institute for Advanced StudyHangzhouChina
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
| | - Bret M Evers
- Division of Neuropathology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Bioinformatics, Department of Population and Data Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Hongtao Yu
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouChina
- School of Life Sciences, Westlake UniversityHangzhouChina
- Institute of Biology, Westlake Institute for Advanced StudyHangzhouChina
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50
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Warrier T, El Farran C, Zeng Y, Ho B, Bao Q, Zheng Z, Bi X, Ng HH, Ong D, Chu J, Sanyal A, Fullwood MJ, Collins J, Li H, Xu J, Loh YH. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Res 2022; 50:7326-7349. [PMID: 35776115 PMCID: PMC9303280 DOI: 10.1093/nar/gkac531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
SETDB1 is a key regulator of lineage-specific genes and endogenous retroviral elements (ERVs) through its deposition of repressive H3K9me3 mark. Apart from its H3K9me3 regulatory role, SETDB1 has seldom been studied in terms of its other potential regulatory roles. To investigate this, a genomic survey of SETDB1 binding in mouse embryonic stem cells across multiple libraries was conducted, leading to the unexpected discovery of regions bereft of common repressive histone marks (H3K9me3, H3K27me3). These regions were enriched with the CTCF motif that is often associated with the topological regulator Cohesin. Further profiling of these non-H3K9me3 regions led to the discovery of a cluster of non-repeat loci that were co-bound by SETDB1 and Cohesin. These regions, which we named DiSCs (domains involving SETDB1 and Cohesin) were seen to be proximal to the gene promoters involved in embryonic stem cell pluripotency and lineage development. Importantly, it was found that SETDB1-Cohesin co-regulate target gene expression and genome topology at these DiSCs. Depletion of SETDB1 led to localized dysregulation of Cohesin binding thereby locally disrupting topological structures. Dysregulated gene expression trends revealed the importance of this cluster in ES cell maintenance as well as at gene 'islands' that drive differentiation to other lineages. The 'unearthing' of the DiSCs thus unravels a unique topological and transcriptional axis of control regulated chiefly by SETDB1.
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Affiliation(s)
- Tushar Warrier
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chadi El Farran
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Benedict Shao Quan Ho
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Qiuye Bao
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zi Hao Zheng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Xuezhi Bi
- Proteomics Group, Bioprocessing Technology Institute, A*STAR, Singapore 138668, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Infectious Disease Translational Research Programme, National University of Singapore, Singapore 117597, Singapore
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Melissa Jane Fullwood
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - James J Collins
- Howard Hughes Medical Institute, Boston, MA 02114, USA
- Institute for Medical Engineering and Science Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 MedicalDrive, Singapore 117456, Singapore
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