1
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Bing X, Ke W, Fujioka M, Kurbidaeva A, Levitt S, Levine M, Schedl P, Jaynes JB. Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. eLife 2024; 13:RP94070. [PMID: 39110499 PMCID: PMC11305675 DOI: 10.7554/elife.94070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Two different models have been proposed to explain how the endpoints of chromatin looped domains ('TADs') in eukaryotic chromosomes are determined. In the first, a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop. In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of MicroC to analyze how TADs are organized, and experimental manipulations of the even skipped TAD boundary, homie, to test the predictions of the 'loop-extrusion' and the 'boundary-pairing' models. Our findings are incompatible with the loop-extrusion model, and instead suggest that the endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their partners, either head-to-head or head-to-tail, with varying degrees of specificity. Although our experiments do not address how partners find each other, the mechanism is unlikely to require loop extrusion.
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Affiliation(s)
- Xinyang Bing
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Wenfan Ke
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Amina Kurbidaeva
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Sarah Levitt
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Mike Levine
- Lewis Sigler Institute, Princeton UniversityPrincetonUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
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2
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Ke W, Fujioka M, Schedl P, Jaynes JB. Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties. eLife 2024; 13:RP94114. [PMID: 39110491 PMCID: PMC11305674 DOI: 10.7554/elife.94114] [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] [Indexed: 08/10/2024] Open
Abstract
The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT orientation), and homie forward (same orientation as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: in MicroC experiments, the eve TAD is a 'volcano' triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the 'new' eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve triangle peak is converted to a pair of 'clouds' of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.
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Affiliation(s)
- Wenfan Ke
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Paul Schedl
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
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3
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Went M, Duran-Lozano L, Halldorsson GH, Gunnell A, Ugidos-Damboriena N, Law P, Ekdahl L, Sud A, Thorleifsson G, Thodberg M, Olafsdottir T, Lamarca-Arrizabalaga A, Cafaro C, Niroula A, Ajore R, Lopez de Lapuente Portilla A, Ali Z, Pertesi M, Goldschmidt H, Stefansdottir L, Kristinsson SY, Stacey SN, Love TJ, Rognvaldsson S, Hajek R, Vodicka P, Pettersson-Kymmer U, Späth F, Schinke C, Van Rhee F, Sulem P, Ferkingstad E, Hjorleifsson Eldjarn G, Mellqvist UH, Jonsdottir I, Morgan G, Sonneveld P, Waage A, Weinhold N, Thomsen H, Försti A, Hansson M, Juul-Vangsted A, Thorsteinsdottir U, Hemminki K, Kaiser M, Rafnar T, Stefansson K, Houlston R, Nilsson B. Deciphering the genetics and mechanisms of predisposition to multiple myeloma. Nat Commun 2024; 15:6644. [PMID: 39103364 DOI: 10.1038/s41467-024-50932-7] [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: 01/03/2024] [Accepted: 07/24/2024] [Indexed: 08/07/2024] Open
Abstract
Multiple myeloma (MM) is an incurable malignancy of plasma cells. Epidemiological studies indicate a substantial heritable component, but the underlying mechanisms remain unclear. Here, in a genome-wide association study totaling 10,906 cases and 366,221 controls, we identify 35 MM risk loci, 12 of which are novel. Through functional fine-mapping and Mendelian randomization, we uncover two causal mechanisms for inherited MM risk: longer telomeres; and elevated levels of B-cell maturation antigen (BCMA) and interleukin-5 receptor alpha (IL5RA) in plasma. The largest increase in BCMA and IL5RA levels is mediated by the risk variant rs34562254-A at TNFRSF13B. While individuals with loss-of-function variants in TNFRSF13B develop B-cell immunodeficiency, rs34562254-A exerts a gain-of-function effect, increasing MM risk through amplified B-cell responses. Our results represent an analysis of genetic MM predisposition, highlighting causal mechanisms contributing to MM development.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Laura Duran-Lozano
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | | | - Andrea Gunnell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Nerea Ugidos-Damboriena
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Philip Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ludvig Ekdahl
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Malte Thodberg
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | | | - Antton Lamarca-Arrizabalaga
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Caterina Cafaro
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Abhishek Niroula
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Ram Ajore
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Aitzkoa Lopez de Lapuente Portilla
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Zain Ali
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Maroulio Pertesi
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Sigurdur Y Kristinsson
- Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Simon N Stacey
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
| | - Thorvardur J Love
- Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Saemundur Rognvaldsson
- Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Roman Hajek
- University Hospital Ostrava and University of Ostrava, Ostrava, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - Florentin Späth
- Department of Radiation Sciences, Umeå University, SE-901 87, Umeå, Sweden
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Frits Van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Patrick Sulem
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
| | | | | | | | | | - Gareth Morgan
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491, Trondheim, Norway
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, 69120, Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
| | | | - Asta Försti
- German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Hopp Children's Cancer Center, Heidelberg, Germany
| | - Markus Hansson
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
- Section of Hematology, Sahlgrenska University Hospital, Gothenburg, SE-413 45, Sweden
- Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Annette Juul-Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen, Denmark
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Kari Hemminki
- German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
- Faculty of Medicine in Pilsen, Charles University, 30605, Pilsen, Czech Republic
| | - Martin Kaiser
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Thorunn Rafnar
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Sturlugata 8, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
| | - Björn Nilsson
- Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.
- Lund Stem Cell Center, Lund University, SE-221 84, Lund, Sweden.
- Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.
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4
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Li W, Hu J, Song F, Yu J, Peng X, Zhang S, Wang L, Hu M, Liu JC, Wei Y, Xiao X, Li Y, Li D, Wang H, Zhou BR, Dai L, Mou Z, Zhou M, Zhang H, Zhou Z, Zhang H, Bai Y, Zhou JQ, Li W, Li G, Zhu P. Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction. Cell Res 2024:10.1038/s41422-024-01009-z. [PMID: 39103524 DOI: 10.1038/s41422-024-01009-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/20/2024] [Indexed: 08/07/2024] Open
Abstract
The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo.
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Affiliation(s)
- Wenyan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Hu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Song
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shangdong, China
| | - Juan Yu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xin Peng
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuming Zhang
- Department of Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Lin Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingli Hu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yu Wei
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Xiao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dongyu Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Linchang Dai
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zongjun Mou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haonan Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Zhou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huidong Zhang
- Research Center for Environment and Female Reproductive Health, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Guohong Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
| | - Ping Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Chang LH, Noordermeer D. Permeable TAD boundaries and their impact on genome-associated functions. Bioessays 2024:e2400137. [PMID: 39093600 DOI: 10.1002/bies.202400137] [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: 06/05/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024]
Abstract
TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer-promoter loop formation and other genomic processes.
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Affiliation(s)
- Li-Hsin Chang
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Blood and Transplant Research Unit in Precision Cellular Therapeutics, National Institute of Health Research, Oxford, UK
| | - Daan Noordermeer
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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6
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Dong P, Zhang S, Gandin V, Xie L, Wang L, Lemire AL, Li W, Otsuna H, Kawase T, Lander AD, Chang HY, Liu ZJ. Cohesin prevents cross-domain gene coactivation. Nat Genet 2024:10.1038/s41588-024-01852-1. [PMID: 39048795 DOI: 10.1038/s41588-024-01852-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The contrast between the disruption of genome topology after cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome and chromatin accessibility at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic coexpression tendencies of cis-linked genes in single cells. Notably, cohesin loss induces widespread gene coactivation and chromatin co-opening tens of million bases apart in cis. Spatial genome and protein imaging reveals that cohesin prevents gene co-bursting along the chromosome and blocks spatial mixing of transcriptional hubs. Single-molecule imaging shows that cohesin confines the exploration of diverse enhancer and core promoter binding transcriptional regulators. Together, these results support that cohesin arranges nuclear topology to control gene coexpression in single cells.
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Affiliation(s)
- Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Shu Zhang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Valentina Gandin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Cancer Biology and Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Wenhong Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Hideo Otsuna
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Takashi Kawase
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Zhe J Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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7
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Jensen CL, Chen LF, Swigut T, Crocker OJ, Yao D, Bassik MC, Ferrell JE, Boettiger AN, Wysocka J. Long range regulation of transcription scales with genomic distance in a gene specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604327. [PMID: 39071420 PMCID: PMC11275926 DOI: 10.1101/2024.07.19.604327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
While critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here we bypass the need for sequence-specific transcription factors and recruit activators directly using CARGO-VPR, an approach for targeting dCas9-VPR using a multiplexed array of RNA guides. We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible by single dCas9. We utilize CARGO-VPR across the Prdm8-Fgf5 locus in mESCs, where neither gene is expressed. We demonstrate that while activator recruitment to any tested region results in transcriptional induction of at least one gene, the expression level strongly depends on the genomic distance between the promoter and activator recruitment site. However, the expression-distance relationship for each gene scales distinctly in a manner not attributable to differences in 3D contact frequency, promoter DNA sequence or presence of the repressive chromatin marks at the locus.
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8
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Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. SCIENCE ADVANCES 2024; 10:eado6406. [PMID: 38996012 PMCID: PMC11244446 DOI: 10.1126/sciadv.ado6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention and its genomic consequences are still poorly understood. Here, we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, hypermethylated genomic regions in Amoebidium derive from viral insertions, including hundreds of endogenized giant viruses, contributing 14% of the proteome. Using a combination of inhibitors and genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenization, and purging. Our results indicate that 5mC is critical for the controlled coexistence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic DNA.
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Affiliation(s)
- Luke A. Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Iana V. Kim
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Vladimir Ovchinnikov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Arnau Sebé-Pedrós
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- ICREA, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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9
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Brahmachari S, Tripathi S, Onuchic JN, Levine H. Nucleosomes play a dual role in regulating transcription dynamics. Proc Natl Acad Sci U S A 2024; 121:e2319772121. [PMID: 38968124 PMCID: PMC11252751 DOI: 10.1073/pnas.2319772121] [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: 11/10/2023] [Accepted: 05/31/2024] [Indexed: 07/07/2024] Open
Abstract
Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a possible regulator of eukaryotic transcription, however, the modes and mechanisms of this regulation are elusive. Here, we first take a statistical mechanics approach to model the torsional response of topology-constrained chromatin. Our model recapitulates the experimentally observed weaker torsional stiffness of chromatin compared to bare DNA and proposes structural transitions of nucleosomes into chirally distinct states as the driver of the contrasting torsional mechanics. Coupling chromatin mechanics with RNAP translocation in stochastic simulations, we reveal a complex interplay of DNA supercoiling and nucleosome dynamics in governing RNAP velocity. Nucleosomes play a dual role in controlling the transcription dynamics. The steric barrier aspect of nucleosomes in the gene body counteracts transcription via hindering RNAP motion, whereas the chiral transitions facilitate RNAP motion via driving a low restoring torque upon twisting the DNA. While nucleosomes with low dissociation rates are typically transcriptionally repressive, highly dynamic nucleosomes offer less of a steric barrier and enhance the transcription elongation dynamics of weakly transcribed genes via buffering DNA twist. We use the model to predict transcription-dependent levels of DNA supercoiling in segments of the budding yeast genome that are in accord with available experimental data. The model unveils a paradigm of DNA supercoiling-mediated interaction between genes and makes testable predictions that will guide experimental design.
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Affiliation(s)
| | - Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX77005
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Physics and Astronomy, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of Biosciences, Rice University, Houston, TX77005
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
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10
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Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE. Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation. CELL GENOMICS 2024:100606. [PMID: 38991604 DOI: 10.1016/j.xgen.2024.100606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/11/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024]
Abstract
DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.
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Affiliation(s)
- Katelyn R Titus
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Simandi
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Harshini Chandrashekar
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Lucini F, Petrini C, Salviato E, Pal K, Rosti V, Gorini F, Santarelli P, Quadri R, Lembo G, Graziano G, Di Patrizio Soldateschi E, Tagliaferri I, Pinatel E, Sebestyén E, Rotta L, Gentile F, Vaira V, Lanzuolo C, Ferrari F. Biochemical properties of chromatin domains define genome compartmentalization. Nucleic Acids Res 2024; 52:e54. [PMID: 38808669 PMCID: PMC11229364 DOI: 10.1093/nar/gkae454] [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: 03/15/2024] [Revised: 04/22/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10 000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their compartmentalization in one single experiment.
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Affiliation(s)
- Federica Lucini
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Cristiano Petrini
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Elisa Salviato
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Koustav Pal
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Valentina Rosti
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Francesca Gorini
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Philina Santarelli
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Roberto Quadri
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Giovanni Lembo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Giulia Graziano
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Emanuele Di Patrizio Soldateschi
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | | | - Eva Pinatel
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Endre Sebestyén
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Luca Rotta
- IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Francesco Gentile
- Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Lanzuolo
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Francesco Ferrari
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
- IGM-CNR, Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Pavia 27100, Italy
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12
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Oguchi A, Suzuki A, Komatsu S, Yoshitomi H, Bhagat S, Son R, Bonnal RJP, Kojima S, Koido M, Takeuchi K, Myouzen K, Inoue G, Hirai T, Sano H, Takegami Y, Kanemaru A, Yamaguchi I, Ishikawa Y, Tanaka N, Hirabayashi S, Konishi R, Sekito S, Inoue T, Kere J, Takeda S, Takaori-Kondo A, Endo I, Kawaoka S, Kawaji H, Ishigaki K, Ueno H, Hayashizaki Y, Pagani M, Carninci P, Yanagita M, Parrish N, Terao C, Yamamoto K, Murakawa Y. An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science 2024; 385:eadd8394. [PMID: 38963856 DOI: 10.1126/science.add8394] [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: 07/17/2022] [Accepted: 05/01/2024] [Indexed: 07/06/2024]
Abstract
Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5' single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4+ T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type-specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type-resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.
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Affiliation(s)
- Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuichiro Komatsu
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Hiroyuki Yoshitomi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shruti Bhagat
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiro Takeuchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiko Myouzen
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Gyo Inoue
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomoya Hirai
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Hiromi Sano
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | | | | | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nao Tanaka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shigeki Hirabayashi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Riyo Konishi
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sho Sekito
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Takahiro Inoue
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Shinpei Kawaoka
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Integrative Bioanalytics, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Science, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hideki Ueno
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihide Hayashizaki
- K.K. DNAFORM, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Massimiliano Pagani
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi, Milan, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Motoko Yanagita
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nicholas Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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13
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Stasevich EM, Simonova AV, Bogomolova EA, Murashko MM, Uvarova AN, Zheremyan EA, Korneev KV, Schwartz AM, Kuprash DV, Demin DE. Cut from the same cloth: RNAs transcribed from regulatory elements. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195049. [PMID: 38964653 DOI: 10.1016/j.bbagrm.2024.195049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases.
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Affiliation(s)
- E M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A V Simonova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Bogomolova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - M M Murashko
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - A N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - K V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A M Schwartz
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - D V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D E Demin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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14
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Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024; 25:574-591. [PMID: 38413840 DOI: 10.1038/s41580-024-00710-6] [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] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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15
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Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024; 20:799-824. [PMID: 38745107 PMCID: PMC11220090 DOI: 10.1038/s44320-024-00038-5] [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: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
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Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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16
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Fang T, Liu Y, Woicik A, Lu M, Jha A, Wang X, Li G, Hristov B, Liu Z, Xu H, Noble WS, Wang S. Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model. Bioinformatics 2024; 40:i471-i480. [PMID: 38940142 PMCID: PMC11211821 DOI: 10.1093/bioinformatics/btae211] [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] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION High-resolution Hi-C contact matrices reveal the detailed three-dimensional architecture of the genome, but high-coverage experimental Hi-C data are expensive to generate. Simultaneously, chromatin structure analyses struggle with extremely sparse contact matrices. To address this problem, computational methods to enhance low-coverage contact matrices have been developed, but existing methods are largely based on resolution enhancement methods for natural images and hence often employ models that do not distinguish between biologically meaningful contacts, such as loops and other stochastic contacts. RESULTS We present Capricorn, a machine learning model for Hi-C resolution enhancement that incorporates small-scale chromatin features as additional views of the input Hi-C contact matrix and leverages a diffusion probability model backbone to generate a high-coverage matrix. We show that Capricorn outperforms the state of the art in a cross-cell-line setting, improving on existing methods by 17% in mean squared error and 26% in F1 score for chromatin loop identification from the generated high-coverage data. We also demonstrate that Capricorn performs well in the cross-chromosome setting and cross-chromosome, cross-cell-line setting, improving the downstream loop F1 score by 14% relative to existing methods. We further show that our multiview idea can also be used to improve several existing methods, HiCARN and HiCNN, indicating the wide applicability of this approach. Finally, we use DNA sequence to validate discovered loops and find that the fraction of CTCF-supported loops from Capricorn is similar to those identified from the high-coverage data. Capricorn is a powerful Hi-C resolution enhancement method that enables scientists to find chromatin features that cannot be identified in the low-coverage contact matrix. AVAILABILITY AND IMPLEMENTATION Implementation of Capricorn and source code for reproducing all figures in this paper are available at https://github.com/CHNFTQ/Capricorn.
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Affiliation(s)
- Tangqi Fang
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
| | - Yifeng Liu
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
| | - Addie Woicik
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
| | - Minsi Lu
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anupama Jha
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, United States
| | - Gang Li
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
- eScience Institute, University of Washington, Seattle, WA 98195, United States
| | - Borislav Hristov
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
| | - Zixuan Liu
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
| | - Hanwen Xu
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
| | - William S Noble
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States
| | - Sheng Wang
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States
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17
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Salari H, Fourel G, Jost D. Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization. Nat Commun 2024; 15:5393. [PMID: 38918438 PMCID: PMC11199603 DOI: 10.1038/s41467-024-49727-7] [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: 07/24/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Although our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
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Affiliation(s)
- Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007, Lyon, France.
| | - Geneviève Fourel
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007, Lyon, France.
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18
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Makino S, Fukaya T. Dynamic modulation of enhancer-promoter and promoter-promoter connectivity in gene regulation. Bioessays 2024:e2400101. [PMID: 38922969 DOI: 10.1002/bies.202400101] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Enhancers are short segments of regulatory DNA that control when and in which cell-type genes should be turned on in response to a variety of extrinsic and intrinsic signals. At the molecular level, enhancers serve as a genomic scaffold that recruits sequence-specific transcription factors and co-activators to facilitate transcription from linked promoters. However, it remains largely unclear how enhancers communicate with appropriate target promoters in the context of higher-order genome topology. In this review, we discuss recent progress in our understanding of the functional interplay between enhancers, genome topology, and the molecular properties of transcription machineries in gene regulation. We suggest that the activities of transcription hubs are highly regulated through the dynamic rearrangement of enhancer-promoter and promoter-promoter connectivity during animal development.
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Affiliation(s)
- Shiho Makino
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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19
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Kocher AA, Dutrow EV, Uebbing S, Yim KM, Rosales Larios MF, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. Genome Biol 2024; 25:156. [PMID: 38872220 PMCID: PMC11170920 DOI: 10.1186/s13059-024-03300-z] [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: 06/01/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. CpG islands (CGIs) have recently been shown to influence enhancer activity, and here we test how their turnover across species contributes to enhancer evolution. RESULTS We integrate maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and find that CGI content in enhancers is strongly associated with increased histone modification levels. CGIs show widespread turnover across species and species-specific CGIs are strongly enriched for enhancers exhibiting species-specific activity across all tissues and species. Genes associated with enhancers with species-specific CGIs show concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. CONCLUSIONS Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
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Affiliation(s)
- Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Division of Molecular Genetics and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Zoetis, Inc, 333 Portage St, Kalamazoo, MI, 49007, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kristina M Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, 06510, USA.
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20
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Fouziya S, Krietenstein N, Mir US, Mieczkowski J, Khan MA, Baba A, Dar MA, Altaf M, Wani AH. Genome wide nucleosome landscape shapes 3D chromatin organization. SCIENCE ADVANCES 2024; 10:eadn2955. [PMID: 38848364 PMCID: PMC11160460 DOI: 10.1126/sciadv.adn2955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
The hierarchical chromatin organization begins with formation of nucleosomes, which fold into chromatin domains punctuated by boundaries and ultimately chromosomes. In a hierarchal organization, lower levels shape higher levels. However, the dependence of higher-order 3D chromatin organization on the nucleosome-level organization has not been studied in cells. We investigated the relationship between nucleosome-level organization and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation SWItch (ISWI) and Chromodomain Helicase DNA-binding (CHD1) chromatin remodeling factors in budding yeast. We find that changes in nucleosome-level properties are accompanied by changes in 3D chromatin organization. Short-range chromatin contacts up to a few kilo-base pairs decrease, chromatin domains weaken, and boundary strength decreases. Boundary strength scales with accessibility and moderately with width of nucleosome-depleted region. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical "bottom-up" mechanism by which nucleosome distribution across genome shapes 3D chromatin organization.
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Affiliation(s)
- Shah Fouziya
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Nils Krietenstein
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Ulfat Syed Mir
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Jakub Mieczkowski
- International Research Agenda 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Masood A. Khan
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Aemon Baba
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohmmad Abaas Dar
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohammad Altaf
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Ajazul H. Wani
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
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21
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Gonzalez-Avalos E, Onodera A, Samaniego-Castruita D, Rao A, Ay F. Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome Biol 2024; 25:142. [PMID: 38825692 PMCID: PMC11145787 DOI: 10.1186/s13059-024-03273-z] [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: 04/03/2023] [Accepted: 05/11/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC, generated through the action of TET dioxygenases at gene bodies of actively-transcribed genes and at active or lineage-specific enhancers. Although such enrichments are reported for 5hmC, to date, predictive models of gene expression state or putative regulatory regions for genes using 5hmC have not been developed. RESULTS Here, by using only 5hmC enrichment in genic regions and their vicinity, we develop neural network models that predict gene expression state across 49 cell types. We show that our deep neural network models distinguish high vs low expression state utilizing only 5hmC levels and these predictive models generalize to unseen cell types. Further, in order to leverage 5hmC signal in distal enhancers for expression prediction, we employ an Activity-by-Contact model and also develop a graph convolutional neural network model with both utilizing Hi-C data and 5hmC enrichment to prioritize enhancer-promoter links. These approaches identify known and novel putative enhancers for key genes in multiple immune cell subsets. CONCLUSIONS Our work highlights the importance of 5hmC in gene regulation through proximal and distal mechanisms and provides a framework to link it to genome function. With the recent advances in 6-letter DNA sequencing by short and long-read techniques, profiling of 5mC and 5hmC may be done routinely in the near future, hence, providing a broad range of applications for the methods developed here.
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Affiliation(s)
- Edahi Gonzalez-Avalos
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Atsushi Onodera
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Daniela Samaniego-Castruita
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anjana Rao
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Ferhat Ay
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
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22
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Wong EWP, Sahin M, Yang R, Lee U, Zhan YA, Misra R, Tomas F, Alomran N, Polyzos A, Lee CJ, Trieu T, Fundichely AM, Wiesner T, Rosowicz A, Cheng S, Liu C, Lallo M, Merghoub T, Hamard PJ, Koche R, Khurana E, Apostolou E, Zheng D, Chen Y, Leslie CS, Chi P. TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596845. [PMID: 38895201 PMCID: PMC11185511 DOI: 10.1101/2024.05.31.596845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.
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23
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Brandani GB, Gu C, Gopi S, Takada S. Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci. PNAS NEXUS 2024; 3:pgae226. [PMID: 38881841 PMCID: PMC11179106 DOI: 10.1093/pnasnexus/pgae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024]
Abstract
Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1 kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, we identify diverse tetranucleosome folding motifs with a characteristic distribution along the genome, predominantly open at cis-regulatory elements and compact in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive internucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure-function relationships.
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Affiliation(s)
- Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Chenyang Gu
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Soundhararajan Gopi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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24
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Zhao Y, Yang M, Gong F, Pan Y, Hu M, Peng Q, Lu L, Lyu X, Sun K. Accelerating 3D genomics data analysis with Microcket. Commun Biol 2024; 7:675. [PMID: 38824179 PMCID: PMC11144199 DOI: 10.1038/s42003-024-06382-4] [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: 03/27/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024] Open
Abstract
The three-dimensional (3D) organization of genome is fundamental to cell biology. To explore 3D genome, emerging high-throughput approaches have produced billions of sequencing reads, which is challenging and time-consuming to analyze. Here we present Microcket, a package for mapping and extracting interacting pairs from 3D genomics data, including Hi-C, Micro-C, and derivant protocols. Microcket utilizes a unique read-stitch strategy that takes advantage of the long read cycles in modern DNA sequencers; benchmark evaluations reveal that Microcket runs much faster than the current tools along with improved mapping efficiency, and thus shows high potential in accelerating and enhancing the biological investigations into 3D genome. Microcket is freely available at https://github.com/hellosunking/Microcket .
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Affiliation(s)
- Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Department of Chemical and Biological Engineering, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, 999077, China
| | - Fanglei Gong
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Yuqi Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Minghui Hu
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Leina Lu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaowen Lyu
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Reproductive Health Research, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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25
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Magnitov M, de Wit E. Attraction and disruption: how loop extrusion and compartmentalisation shape the nuclear genome. Curr Opin Genet Dev 2024; 86:102194. [PMID: 38636335 PMCID: PMC11190842 DOI: 10.1016/j.gde.2024.102194] [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: 10/01/2023] [Revised: 03/21/2024] [Accepted: 03/31/2024] [Indexed: 04/20/2024]
Abstract
Chromatin loops, which bring two distal loci of the same chromosome into close physical proximity, are the ubiquitous units of the three-dimensional genome. Recent advances in understanding the spatial organisation of chromatin suggest that several distinct mechanisms control chromatin interactions, such as loop extrusion by cohesin complexes, compartmentalisation by phase separation, direct protein-protein interactions and others. Here, we review different types of chromatin loops and highlight the factors and processes involved in their regulation. We discuss how loop extrusion and compartmentalisation shape chromatin interactions and how these two processes can either positively or negatively influence each other.
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Affiliation(s)
- Mikhail Magnitov
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. https://twitter.com/@MMagnitov
| | - Elzo de Wit
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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26
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Harris HL, Rowley MJ. Mechanistic drivers of chromatin organization into compartments. Curr Opin Genet Dev 2024; 86:102193. [PMID: 38626581 DOI: 10.1016/j.gde.2024.102193] [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: 02/12/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024]
Abstract
The human genome is not just a simple string of DNA, it is a complex and dynamic entity intricately folded within the cell's nucleus. This three-dimensional organization of chromatin, the combination of DNA and proteins in the nucleus, is crucial for many biological processes and has been prominently studied for its intricate relationship to gene expression. Indeed, the transcriptional machinery does not operate in isolation but interacts intimately with the folded chromatin structure. Techniques for chromatin conformation capture, including genome-wide sequencing approaches, have revealed key organizational features of chromatin, such as the formation of loops by CCCTC-binding factor (CTCF) and the division of loci into chromatin compartments. While much of the recent research and reviews have focused on CTCF loops, we discuss several new revelations that have emerged concerning chromatin compartments, with a particular focus on what is known about mechanistic drivers of compartmentalization. These insights challenge the traditional views of chromatin organization and reveal the complexity behind the formation and maintenance of chromatin compartments.
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Affiliation(s)
- Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA.
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27
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Kabirova E, Ryzhkova A, Lukyanchikova V, Khabarova A, Korablev A, Shnaider T, Nuriddinov M, Belokopytova P, Smirnov A, Khotskin NV, Kontsevaya G, Serova I, Battulin N. TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene. Nat Commun 2024; 15:4521. [PMID: 38806452 PMCID: PMC11133455 DOI: 10.1038/s41467-024-48523-7] [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: 01/16/2023] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
Topologically associated domains (TADs) restrict promoter-enhancer interactions, thereby maintaining the spatiotemporal pattern of gene activity. However, rearrangements of the TADs boundaries do not always lead to significant changes in the activity pattern. Here, we investigated the consequences of the TAD boundaries deletion on the expression of developmentally important genes encoding tyrosine kinase receptors: Kit, Kdr, Pdgfra. We used genome editing in mice to delete the TADs boundaries at the Kit locus and characterized chromatin folding and gene expression in pure cultures of fibroblasts, mast cells, and melanocytes. We found that although Kit is highly active in both mast cells and melanocytes, deletion of the TAD boundary between the Kit and Kdr genes results in ectopic activation only in melanocytes. Thus, the epigenetic landscape, namely the mutual arrangement of enhancers and actively transcribing genes, is important for predicting the consequences of the TAD boundaries removal. We also found that mice without a TAD border between the Kit and Kdr genes have a phenotypic manifestation of the mutation - a lighter coloration. Thus, the data obtained shed light on the principles of interaction between the 3D chromatin organization and epigenetic marks in the regulation of gene activity.
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Affiliation(s)
- Evelyn Kabirova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | | | - Anna Khabarova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Alexey Korablev
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | | | - Polina Belokopytova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | - Irina Serova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
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28
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Zhu H, Liu T, Wang Z. C2c: Predicting Micro-C from Hi-C. Genes (Basel) 2024; 15:673. [PMID: 38927609 PMCID: PMC11203216 DOI: 10.3390/genes15060673] [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: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
MOTIVATION High-resolution Hi-C data, capable of detecting chromatin features below the level of Topologically Associating Domains (TADs), significantly enhance our understanding of gene regulation. Micro-C, a variant of Hi-C incorporating a micrococcal nuclease (MNase) digestion step to examine interactions between nucleosome pairs, has been developed to overcome the resolution limitations of Hi-C. However, Micro-C experiments pose greater technical challenges compared to Hi-C, owing to the need for precise MNase digestion control and higher-resolution sequencing. Therefore, developing computational methods to derive Micro-C data from existing Hi-C datasets could lead to better usage of a large amount of existing Hi-C data in the scientific community and cost savings. RESULTS We developed C2c ("high" or upper case C to "micro" or lower case c), a computational tool based on a residual neural network to learn the mapping between Hi-C and Micro-C contact matrices and then predict Micro-C contact matrices based on Hi-C contact matrices. Our evaluation results show that the predicted Micro-C contact matrices reveal more chromatin loops than the input Hi-C contact matrices, and more of the loops detected from predicted Micro-C match the promoter-enhancer interactions. Furthermore, we found that the mutual loops from real and predicted Micro-C better match the ChIA-PET data compared to Hi-C and real Micro-C loops, and the predicted Micro-C leads to more TAD-boundaries detected compared to the Hi-C data. The website URL of C2c can be found in the Data Availability Statement.
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Affiliation(s)
| | | | - Zheng Wang
- Department of Computer Science, University of Miami, 330M Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33124-4245, USA; (H.Z.); (T.L.)
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29
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Xu J, Xu X, Huang D, Luo Y, Lin L, Bai X, Zheng Y, Yang Q, Cheng Y, Huang A, Shi J, Bo X, Gu J, Chen H. A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains. Nat Commun 2024; 15:4376. [PMID: 38782890 PMCID: PMC11116433 DOI: 10.1038/s41467-024-48593-7] [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: 09/18/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.
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Affiliation(s)
- Jingxuan Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiang Xu
- Academy of Military Medical Science, Beijing, 100850, China
| | - Dandan Huang
- Department of Oncology, Peking University Shougang Hospital, Beijing, China
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China
| | - Yawen Luo
- Academy of Military Medical Science, Beijing, 100850, China
| | - Lin Lin
- Academy of Military Medical Science, Beijing, 100850, China
- School of Computer Science and Information Technology& KLAS, Northeast Normal University, Changchun, China
| | - Xuemei Bai
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yang Zheng
- Academy of Military Medical Science, Beijing, 100850, China
| | - Qian Yang
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yu Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - An Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jingyi Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaochen Bo
- Academy of Military Medical Science, Beijing, 100850, China.
| | - Jin Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Department of Oncology, Peking University Shougang Hospital, Beijing, China.
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
| | - Hebing Chen
- Academy of Military Medical Science, Beijing, 100850, China.
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30
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Li Y, Lee J, Bai L. DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions. Nat Commun 2024; 15:4358. [PMID: 38778058 PMCID: PMC11111806 DOI: 10.1038/s41467-024-48718-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: 09/13/2023] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra- and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that (1) most long-distance chromosomal interactions detected by MTAC reflect tethering by the nuclear pore complexes (NPCs), (2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, (3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and (4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization.
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Affiliation(s)
- Yi Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - James Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA.
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31
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression. Proc Natl Acad Sci U S A 2024; 121:e2401494121. [PMID: 38753513 PMCID: PMC11127048 DOI: 10.1073/pnas.2401494121] [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: 01/26/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross-over between two and four at contour lengths on the order of 30 kilo-base pairs. The anomalously high fractal dimension [Formula: see text] is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ([Formula: see text]) longer than tens of minutes to be proportional to [Formula: see text]. We validate our results with hybrid molecular dynamics-Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, NC27708
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, NC27708
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
- Department of Physics, Duke University, Durham, NC27708
- Department of Chemistry, Duke University, Durham, NC27708
- World Premier International Research Center Initiative–Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
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32
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Kant A, Guo Z, Vinayak V, Neguembor MV, Li WS, Agrawal V, Pujadas E, Almassalha L, Backman V, Lakadamyali M, Cosma MP, Shenoy VB. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nat Commun 2024; 15:4338. [PMID: 38773126 PMCID: PMC11109243 DOI: 10.1038/s41467-024-48698-z] [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: 04/24/2023] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, histone modifications, and chromatin extrusion. We predict that the size of heterochromatic domains is governed by a balance among the diffusive flux of methylated histones sustaining them and the acetylation reactions in the domains and the process of loop extrusion via supercoiling by RNAPII at their periphery, which contributes to size reduction. Super-resolution and nano-imaging of five distinct cell lines confirm the predictions indicating that the absence of transcription leads to larger heterochromatin domains. Furthermore, the model accurately reproduces the findings regarding how transcription-mediated supercoiling loss can mitigate the impacts of excessive cohesin loading. Our findings shed light on the role of transcription in genome organization, offering insights into chromatin dynamics and potential therapeutic targets.
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Affiliation(s)
- Aayush Kant
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zixian Guo
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vinayak Vinayak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Wing Shun Li
- Department of Applied Physics, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Vasundhara Agrawal
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Emily Pujadas
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Luay Almassalha
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA
| | - Vadim Backman
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- ICREA, Barcelona, 08010, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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33
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Gómez Acuña LI, Flyamer I, Boyle S, Friman ET, Bickmore WA. Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity. PLoS Genet 2024; 20:e1011277. [PMID: 38781242 DOI: 10.1371/journal.pgen.1011277] [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: 11/27/2023] [Revised: 06/05/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
How enhancers regulate their target genes in the context of 3D chromatin organization is extensively studied and models which do not require direct enhancer-promoter contact have recently emerged. Here, we use the activation of estrogen receptor-dependent enhancers in a breast cancer cell line to study enhancer-promoter communication at two loci. This allows high temporal resolution tracking of molecular events from hormone stimulation to efficient gene activation. We examine how both enhancer-promoter spatial proximity assayed by DNA fluorescence in situ hybridization, and contact frequencies resulting from chromatin in situ fragmentation and proximity ligation, change dynamically during enhancer-driven gene activation. These orthogonal methods produce seemingly paradoxical results: upon enhancer activation enhancer-promoter contact frequencies increase while spatial proximity decreases. We explore this apparent discrepancy using different estrogen receptor ligands and transcription inhibitors. Our data demonstrate that enhancer-promoter contact frequencies are transcription independent whereas altered enhancer-promoter proximity depends on transcription. Our results emphasize that the relationship between contact frequencies and physical distance in the nucleus, especially over short genomic distances, is not always a simple one.
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Affiliation(s)
- Luciana I Gómez Acuña
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Ilya Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
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34
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Lee KH, Kim J, Kim JH. 3D epigenomics and 3D epigenopathies. BMB Rep 2024; 57:216-231. [PMID: 38627948 PMCID: PMC11139681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 03/18/2024] [Indexed: 05/25/2024] Open
Abstract
Mammalian genomes are intricately compacted to form sophisticated 3-dimensional structures within the tiny nucleus, so called 3D genome folding. Despite their shapes reminiscent of an entangled yarn, the rapid development of molecular and next-generation sequencing technologies (NGS) has revealed that mammalian genomes are highly organized in a hierarchical order that delicately affects transcription activities. An increasing amount of evidence suggests that 3D genome folding is implicated in diseases, giving us a clue on how to identify novel therapeutic approaches. In this review, we will study what 3D genome folding means in epigenetics, what types of 3D genome structures there are, how they are formed, and how the technologies have developed to explore them. We will also discuss the pathological implications of 3D genome folding. Finally, we will discuss how to leverage 3D genome folding and engineering for future studies. [BMB Reports 2024; 57(5): 216-231].
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Affiliation(s)
- Kyung-Hwan Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jungyu Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Ji Hun Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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35
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Liu T, Zhu H, Wang Z. Learning Micro-C from Hi-C with diffusion models. PLoS Comput Biol 2024; 20:e1012136. [PMID: 38758956 PMCID: PMC11139321 DOI: 10.1371/journal.pcbi.1012136] [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: 11/11/2023] [Revised: 05/30/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024] Open
Abstract
In the last few years, Micro-C has shown itself as an improved alternative to Hi-C. It replaced the restriction enzymes in Hi-C assays with micrococcal nuclease (MNase), resulting in capturing nucleosome resolution chromatin interactions. The signal-to-noise improvement of Micro-C allows it to detect more chromatin loops than high-resolution Hi-C. However, compared with massive Hi-C datasets available in the literature, there are only a limited number of Micro-C datasets. To take full advantage of these Hi-C datasets, we present HiC2MicroC, a computational method learning and then predicting Micro-C from Hi-C based on the denoising diffusion probabilistic models (DDPM). We trained our DDPM and other regression models in human foreskin fibroblast (HFFc6) cell line and evaluated these methods in six different cell types at 5-kb and 1-kb resolution. Our evaluations demonstrate that both HiC2MicroC and regression methods can markedly improve Hi-C towards Micro-C, and our DDPM-based HiC2MicroC outperforms regression in various terms. First, HiC2MicroC successfully recovers most of the Micro-C loops even those not detected in Hi-C maps. Second, a majority of the HiC2MicroC-recovered loops anchor CTCF binding sites in a convergent orientation. Third, HiC2MicroC loops share genomic and epigenetic properties with Micro-C loops, including linking promoters and enhancers, and their anchors are enriched for structural proteins (CTCF and cohesin) and histone modifications. Lastly, we find our recovered loops are also consistent with the loops identified from promoter capture Micro-C (PCMicro-C) and Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET). Overall, HiC2MicroC is an effective tool for further studying Hi-C data with Micro-C as a template. HiC2MicroC is publicly available at https://github.com/zwang-bioinformatics/HiC2MicroC/.
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Affiliation(s)
- Tong Liu
- Department of Computer Science, University of Miami, Coral Gables, Florida, United States of America
| | - Hao Zhu
- Department of Computer Science, University of Miami, Coral Gables, Florida, United States of America
| | - Zheng Wang
- Department of Computer Science, University of Miami, Coral Gables, Florida, United States of America
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36
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Lando D, Ma X, Cao Y, Jartseva A, Stevens TJ, Boucher W, Reynolds N, Montibus B, Hall D, Lackner A, Ragheb R, Leeb M, Hendrich BD, Laue ED. Enhancer-promoter interactions are reconfigured through the formation of long-range multiway hubs as mouse ES cells exit pluripotency. Mol Cell 2024; 84:1406-1421.e8. [PMID: 38490199 PMCID: PMC7616059 DOI: 10.1016/j.molcel.2024.02.015] [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: 02/02/2023] [Revised: 12/19/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
Enhancers bind transcription factors, chromatin regulators, and non-coding transcripts to modulate the expression of target genes. Here, we report 3D genome structures of single mouse ES cells as they are induced to exit pluripotency and transition through a formative stage prior to undergoing neuroectodermal differentiation. We find that there is a remarkable reorganization of 3D genome structure where inter-chromosomal intermingling increases dramatically in the formative state. This intermingling is associated with the formation of a large number of multiway hubs that bring together enhancers and promoters with similar chromatin states from typically 5-8 distant chromosomal sites that are often separated by many Mb from each other. In the formative state, genes important for pluripotency exit establish contacts with emerging enhancers within these multiway hubs, suggesting that the structural changes we have observed may play an important role in modulating transcription and establishing new cell identities.
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Affiliation(s)
- David Lando
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Xiaoyan Ma
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Yang Cao
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Nicola Reynolds
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Bertille Montibus
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Dominic Hall
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Andreas Lackner
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Ramy Ragheb
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Brian D Hendrich
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
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37
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Zhang Y, Dong Q, Wang Z, Liu Q, Yu H, Sun W, Cheema J, You Q, Ding L, Cao X, He C, Ding Y, Zhang H. A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics. Nat Commun 2024; 15:3253. [PMID: 38627396 PMCID: PMC11021422 DOI: 10.1038/s41467-024-47678-7] [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: 03/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transcriptional reprogramming in response to cold stress remains unclear. Here, we apply a chemical-crosslinking assisted proximity capture (CAP-C) method to elucidate the fine-scale chromatin landscape, revealing chromatin interactions within gene bodies closely associated with RNA polymerase II (Pol II) densities across initiation, pausing, and termination sites. We observe dynamic changes in chromatin interactions alongside Pol II activity alterations during cold stress, suggesting local chromatin dynamics may regulate Pol II activity. Notably, cold stress does not affect large-scale chromatin conformations. We further identify a comprehensive promoter-promoter interaction (PPI) network across the genome, potentially facilitating co-regulation of gene expression in response to cold stress. Our study deepens the understanding of chromatin conformation-associated gene regulation in plant response to cold.
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Affiliation(s)
- Yueying Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Qianli Dong
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Zhen Wang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Qinzhe Liu
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Haopeng Yu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wenqing Sun
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jitender Cheema
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Qiancheng You
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Ling Ding
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Chuan He
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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38
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Golov AK, Gavrilov AA. Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:601-625. [PMID: 38831499 DOI: 10.1134/s0006297924040023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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39
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Palikyras S, Sofiadis K, Stavropoulou A, Danieli‐Mackay A, Varamogianni‐Mamatsi V, Hörl D, Nasiscionyte S, Zhu Y, Papadionysiou I, Papadakis A, Josipovic N, Zirkel A, O'Connell A, Loughran G, Keane J, Michel A, Wagner W, Beyer A, Harz H, Leonhardt H, Lukinavicius G, Nikolaou C, Papantonis A. Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor. Aging Cell 2024; 23:e14083. [PMID: 38196311 PMCID: PMC11019153 DOI: 10.1111/acel.14083] [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: 10/06/2023] [Revised: 12/07/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Cellular senescence is acknowledged as a key contributor to organismal ageing and late-life disease. Though popular, the study of senescence in vitro can be complicated by the prolonged and asynchronous timing of cells committing to it and by its paracrine effects. To address these issues, we repurposed a small molecule inhibitor, inflachromene (ICM), to induce senescence to human primary cells. Within 6 days of treatment with ICM, senescence hallmarks, including the nuclear eviction of HMGB1 and -B2, are uniformly induced across IMR90 cell populations. By generating and comparing various high throughput datasets from ICM-induced and replicative senescence, we uncovered a high similarity of the two states. Notably though, ICM suppresses the pro-inflammatory secretome associated with senescence, thus alleviating most paracrine effects. In summary, ICM rapidly and synchronously induces a senescent-like phenotype thereby allowing the study of its core regulatory program without confounding heterogeneity.
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Affiliation(s)
- Spiros Palikyras
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Konstantinos Sofiadis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Oncode InstituteHubrecht Institute‐KNAW and University Medical Center UtrechtUtrechtThe Netherlands
| | - Athanasia Stavropoulou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Adi Danieli‐Mackay
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
| | | | - David Hörl
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Yajie Zhu
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | | | - Antonis Papadakis
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Natasa Josipovic
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Present address:
Single Cell DiscoveriesUtrechtThe Netherlands
| | - Anne Zirkel
- Center for Molecular Medicine CologneUniversity and University Hospital of CologneCologneGermany
| | | | | | | | | | - Wolfgang Wagner
- Helmholtz‐Institute for Biomedical EngineeringRWTH Aachen University Medical SchoolAachenGermany
- Institute for Stem Cell BiologyRWTH Aachen University Medical SchoolAachenGermany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Hartmann Harz
- Faculty of BiologyLudwig Maximilians University MunichMunichGermany
| | | | - Grazvydas Lukinavicius
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Christoforos Nikolaou
- Institute for BioinnovationBiomedical Sciences Research Center “Alexander Fleming”VariGreece
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Center GöttingenGöttingenGermany
- Clinical Research Unit 5002University Medical Center GöttingenGöttingenGermany
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40
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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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41
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Liu R, Xu R, Yan S, Li P, Jia C, Sun H, Sheng K, Wang Y, Zhang Q, Guo J, Xin X, Li X, Guo D. Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells. Front Genet 2024; 15:1377238. [PMID: 38586584 PMCID: PMC10995239 DOI: 10.3389/fgene.2024.1377238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianhao Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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42
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Jeong D, Shi G, Li X, Thirumalai D. Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion. eLife 2024; 12:RP88564. [PMID: 38502563 PMCID: PMC10950330 DOI: 10.7554/elife.88564] [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] [Indexed: 03/21/2024] Open
Abstract
Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer-promoter/promoter-promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.
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Affiliation(s)
- Davin Jeong
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Guang Shi
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Xin Li
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - D Thirumalai
- Department of Chemistry, University of Texas at AustinAustinUnited States
- Department of Physics, University of Texas at AustinAustinUnited States
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43
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Shin S, Shi G, Cho HW, Thirumalai D. Transcription-induced active forces suppress chromatin motion. Proc Natl Acad Sci U S A 2024; 121:e2307309121. [PMID: 38489381 PMCID: PMC10963020 DOI: 10.1073/pnas.2307309121] [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: 05/02/2023] [Accepted: 02/06/2024] [Indexed: 03/17/2024] Open
Abstract
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of chromatin. Some experiments have shown that the motility of individual loci in human interphase chromosome decreases during transcription and increases upon inhibiting transcription. This is a counterintuitive finding because it is thought that the active mechanical force (F) on the order of ten piconewtons, generated by RNA polymerase II (RNAPII) that is presumably transmitted to the gene-rich region of the chromatin, would render it more open, thus enhancing the mobility. We developed a minimal active copolymer model for interphase chromosomes to investigate how F affects the dynamical properties of chromatin. The movements of the loci in the gene-rich region are suppressed in an intermediate range of F and are enhanced at small F values, which has also been observed in experiments. In the intermediate F, the bond length between consecutive loci increases, becoming commensurate with the distance at the minimum of the attractive interaction between nonbonded loci. This results in a transient disorder-to-order transition, leading to a decreased mobility during transcription. Strikingly, the F-dependent change in the locus dynamics preserves the organization of the chromosome at [Formula: see text]. Transient ordering of the loci, which is not found in the polymers with random epigenetic profiles, in the gene-rich region might be a plausible mechanism for nucleating a dynamic network involving transcription factors, RNAPII, and chromatin.
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Affiliation(s)
- Sucheol Shin
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
| | - Guang Shi
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Materials Science, University of Illinois, Urbana, IL61801
| | - Hyun Woo Cho
- Department of Fine Chemistry and Center for Functional Biomaterials, Seoul National University of Science and Technology, Seoul01811, Republic of Korea
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Physics, The University of Texas at Austin, Austin, TX78712
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Daniel B, Chen AY, Sandor K, Zhang W, Miao Z, Lareau CA, Yost KE, Chang HY, Satpathy AT. Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582872. [PMID: 38496446 PMCID: PMC10942375 DOI: 10.1101/2024.02.29.582872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.
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Affiliation(s)
- Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
- Present address: Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Andy Y. Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Wenxi Zhang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zhuang Miao
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Caleb A. Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Present address: Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Present address: Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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45
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Busby T, Misteli T. Building chromatin from the ground up. Nat Genet 2024; 56:360-361. [PMID: 38351384 DOI: 10.1038/s41588-024-01666-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024]
Affiliation(s)
- Theodore Busby
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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46
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Bignaud A, Cockram C, Borde C, Groseille J, Allemand E, Thierry A, Marbouty M, Mozziconacci J, Espéli O, Koszul R. Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes. Nat Struct Mol Biol 2024; 31:489-497. [PMID: 38177686 PMCID: PMC10948358 DOI: 10.1038/s41594-023-01178-2] [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: 08/29/2022] [Accepted: 11/10/2023] [Indexed: 01/06/2024]
Abstract
Transcription generates local topological and mechanical constraints on the DNA fiber, leading to the generation of supercoiled chromosome domains in bacteria. However, the global impact of transcription on chromosome organization remains elusive, as the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~5-10 kb). Here we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units. We show that transcriptional units form discrete three-dimensional transcription-induced domains that impose mechanical and topological constraints on their neighboring sequences at larger scales, modifying their localization and dynamics. These results show that transcriptional domains constitute primary building blocks of bacterial chromosome folding and locally impose structural and dynamic constraints.
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Affiliation(s)
- Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Charlotte Cockram
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Céline Borde
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Justine Groseille
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Allemand
- INSERM-U1163, Unité mécanismes cellulaires et moléculaires des désordres hématologiques et implications thérapeutiques, Institut Imagine, Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Martial Marbouty
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Julien Mozziconacci
- Laboratoire Structure et Instabilité des Génomes, UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
| | - Olivier Espéli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France.
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France.
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47
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Marie P, Bazire M, Ladet J, Ameur LB, Chahar S, Fontrodona N, Sexton T, Auboeuf D, Bourgeois CF, Mortreux F. Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation. Nucleic Acids Res 2024; 52:1527-1543. [PMID: 38272542 PMCID: PMC10899780 DOI: 10.1093/nar/gkae015] [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: 06/10/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
The NF-κB protein p65/RelA plays a pivotal role in coordinating gene expression in response to diverse stimuli, including viral infections. At the chromatin level, p65/RelA regulates gene transcription and alternative splicing through promoter enrichment and genomic exon occupancy, respectively. The intricate ways in which p65/RelA simultaneously governs these functions across various genes remain to be fully elucidated. In this study, we employed the HTLV-1 Tax oncoprotein, a potent activator of NF-κB, to investigate its influence on the three-dimensional organization of the genome, a key factor in gene regulation. We discovered that Tax restructures the 3D genomic landscape, bringing together genes based on their regulation and splicing patterns. Notably, we found that the Tax-induced gene-gene contact between the two master genes NFKBIA and RELA is associated with their respective changes in gene expression and alternative splicing. Through dCas9-mediated approaches, we demonstrated that NFKBIA-RELA interaction is required for alternative splicing regulation and is caused by an intragenic enrichment of p65/RelA on RELA. Our findings shed light on new regulatory mechanisms upon HTLV-1 Tax and underscore the integral role of p65/RelA in coordinated regulation of NF-κB-responsive genes at both transcriptional and splicing levels in the context of the 3D genome.
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Affiliation(s)
- Paul Marie
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Matéo Bazire
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Julien Ladet
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Lamya Ben Ameur
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Sanjay Chahar
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Nicolas Fontrodona
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Franck Mortreux
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
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48
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Contreras A, Perea-Resa C. Transcriptional repression across mitosis: mechanisms and functions. Biochem Soc Trans 2024; 52:455-464. [PMID: 38372373 PMCID: PMC10903446 DOI: 10.1042/bst20231071] [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: 12/07/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Transcription represents a central aspect of gene expression with RNA polymerase machineries (RNA Pol) driving the synthesis of RNA from DNA template molecules. In eukaryotes, a total of three RNA Pol enzymes generate the plethora of RNA species and RNA Pol II is the one transcribing all protein-coding genes. A high number of cis- and trans-acting factors orchestrates RNA Pol II-mediated transcription by influencing the chromatin recruitment, activation, elongation, and/or termination steps. The levels of DNA accessibility, defining open-euchromatin versus close-heterochromatin, delimits RNA Pol II activity as well as the encounter with other factors acting on chromatin such as the DNA replication or DNA repair machineries. The stage of the cell cycle highly influences RNA Pol II activity with mitosis representing the major challenge. In fact, there is a massive inhibition of transcription during the mitotic entry coupled with chromatin dissociation of most of the components of the transcriptional machinery. Mitosis, as a consequence, highly compromises the transcriptional memory and the perpetuation of cellular identity. Once mitosis ends, transcription levels immediately recover to define the cell fate and to safeguard the proper progression of daughter cells through the cell cycle. In this review, we evaluate our current understanding of the transcriptional repression associated with mitosis with a special focus on the molecular mechanisms involved, on the potential function behind the general repression, and on the transmission of the transcriptional machinery into the daughter cells. We finally discuss the contribution that errors in the inheritance of the transcriptional machinery across mitosis might play in stem cell aging.
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Affiliation(s)
- A. Contreras
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
| | - C. Perea-Resa
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
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49
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Balasubramanian D, Borges Pinto P, Grasso A, Vincent S, Tarayre H, Lajoignie D, Ghavi-Helm Y. Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries. Nucleic Acids Res 2024; 52:1702-1719. [PMID: 38084924 PMCID: PMC10899756 DOI: 10.1093/nar/gkad1183] [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: 04/25/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 02/29/2024] Open
Abstract
Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer-promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer-promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer-promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.
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Affiliation(s)
- Deevitha Balasubramanian
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
- Indian Institute of Science Education and Research (IISER) Tirupati; Tirupati 517507 Andhra Pradesh, India
| | - Pedro Borges Pinto
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Alexia Grasso
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Séverine Vincent
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Hélène Tarayre
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Damien Lajoignie
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
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Zhang Y, Cameron CJF, Blanchette M. Posterior inference of Hi-C contact frequency through sampling. FRONTIERS IN BIOINFORMATICS 2024; 3:1285828. [PMID: 38455089 PMCID: PMC10919286 DOI: 10.3389/fbinf.2023.1285828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/20/2023] [Indexed: 03/09/2024] Open
Abstract
Hi-C is one of the most widely used approaches to study three-dimensional genome conformations. Contacts captured by a Hi-C experiment are represented in a contact frequency matrix. Due to the limited sequencing depth and other factors, Hi-C contact frequency matrices are only approximations of the true interaction frequencies and are further reported without any quantification of uncertainty. Hence, downstream analyses based on Hi-C contact maps (e.g., TAD and loop annotation) are themselves point estimations. Here, we present the Hi-C interaction frequency sampler (HiCSampler) that reliably infers the posterior distribution of the interaction frequency for a given Hi-C contact map by exploiting dependencies between neighboring loci. Posterior predictive checks demonstrate that HiCSampler can infer highly predictive chromosomal interaction frequency. Summary statistics calculated by HiCSampler provide a measurement of the uncertainty for Hi-C experiments, and samples inferred by HiCSampler are ready for use by most downstream analysis tools off the shelf and permit uncertainty measurements in these analyses without modifications.
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Affiliation(s)
- Yanlin Zhang
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Christopher J. F. Cameron
- School of Computer Science, McGill University, Montréal, QC, Canada
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
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