1
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Valades-Cruz CA, Barth R, Abdellah M, Shaban HA. Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D. Nat Protoc 2024:10.1038/s41596-024-01038-3. [PMID: 39198619 DOI: 10.1038/s41596-024-01038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/22/2024] [Indexed: 09/01/2024]
Abstract
To understand the dynamic nature of the genome, the localization and rearrangement of DNA and DNA-binding proteins must be analyzed across the entire nucleus of single living cells. Recently, we developed a computational light microscopy technique, called high-resolution diffusion (Hi-D) mapping, which can accurately detect, classify and map diffusion dynamics and biophysical parameters such as the diffusion constant, the anomalous exponent, drift velocity and model physical diffusion from the data at a high spatial resolution across the genome in living cells. Hi-D combines dense optical flow to detect and track local chromatin and nuclear protein motion genome-wide and Bayesian inference to characterize this local movement at nanoscale resolution. Here we present the Python implementation of Hi-D, with an option for parallelizing the calculations to run on multicore central processing units (CPUs). The functionality of Hi-D is presented to the users via user-friendly documented Python notebooks. Hi-D reduces the analysis time to less than 1 h using a multicore CPU with a single compute node. We also present different applications of Hi-D for live-imaging of DNA, histone H2B and RNA polymerase II sequences acquired with spinning disk confocal and super-resolution structured illumination microscopy.
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Affiliation(s)
- Cesar Augusto Valades-Cruz
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Roman Barth
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Marwan Abdellah
- Ecole polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Haitham A Shaban
- Spectroscopy Department, Institute of Physics Research National Research Centre, Cairo, Egypt.
- Agora Cancer Research Center, Lausanne, Switzerland.
- Precision Oncology Center, Department of Oncology Lausanne University Hospital, Lausanne, Switzerland.
- Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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2
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Lao Z, Kamat KD, Jiang Z, Zhang B. OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 2024; 13:RP93223. [PMID: 39146200 PMCID: PMC11326778 DOI: 10.7554/elife.93223] [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: 08/17/2024] Open
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of 'fixed points' within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Kartik D Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
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3
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Zhang W, Cheng L, Li K, Xie L, Ji J, Lei X, Jiang A, Chen C, Li H, Li P, Sun Q. Evolutional heterochromatin condensation delineates chromocenter formation and retrotransposon silencing in plants. NATURE PLANTS 2024; 10:1215-1230. [PMID: 39014153 DOI: 10.1038/s41477-024-01746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. It is therefore puzzling that the presence of chromocenters is variable across plant species. Here we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter formation in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimaera of ADCP1 and HMGA, which remarkably enables formation of chromocenters. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and silencing retrotransposons.
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Affiliation(s)
- Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lingling Cheng
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Leiming Xie
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinyao Ji
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xue Lei
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Anjie Jiang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Chunlai Chen
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haitao Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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4
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Czapiewski R, Schirmer EC. Enhancers on the edge - how the nuclear envelope controls gene regulatory elements. Curr Opin Genet Dev 2024; 87:102234. [PMID: 39047586 DOI: 10.1016/j.gde.2024.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/20/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
Precise temporal and sequential control of gene expression during development and in response to environmental stimuli requires tight regulation of the physical contact between gene regulatory elements and promoters. Current models describing how the genome folds in 3D space to establish these interactions often ignore the role of the most stable structural nuclear feature - the nuclear envelope. While contributions of 3D folding within/between topologically associated domains (TADs) have been extensively described, mechanical contributions from the nuclear envelope can impact enhancer-promoter interactions both directly and indirectly through influencing intra/inter-TAD interactions. Importantly, these nuclear envelope contributions clearly link this mechanism to development and, when defective, to human disease. Here, we discuss evidence for nuclear envelope regulation of tissue-specific enhancer-promoter pairings, potential mechanisms for this regulation, exciting recent findings that other regulatory elements such as microRNAs and long noncoding RNAs are under nuclear envelope regulation, the possible involvement of condensates, and how disruption of this regulation can lead to disease.
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Affiliation(s)
- Rafal Czapiewski
- Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
| | - Eric C Schirmer
- Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom.
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5
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Qi W, Bai J, Wang R, Zeng X, Zhang L. SATB1, senescence and senescence-related diseases. J Cell Physiol 2024; 239:e31327. [PMID: 38801120 DOI: 10.1002/jcp.31327] [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: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Aging leads to an accumulation of cellular mutations and damage, increasing the risk of senescence, apoptosis, and malignant transformation. Cellular senescence, which is pivotal in aging, acts as both a guard against cellular transformation and as a check against cancer progression. It is marked by stable cell cycle arrest, widespread macromolecular changes, a pro-inflammatory profile, and altered gene expression. However, it remains to be determined whether these differing subsets of senescent cells result from unique intrinsic programs or are influenced by their environmental contexts. Multiple transcription regulators and chromatin modifiers contribute to these alterations. Special AT-rich sequence-binding protein 1 (SATB1) stands out as a crucial regulator in this process, orchestrating gene expression by structuring chromatin into loop domains and anchoring DNA elements. This review provides an overview of cellular senescence and delves into the role of SATB1 in senescence-related diseases. It highlights SATB1's potential in developing antiaging and anticancer strategies, potentially contributing to improved quality of life and addressing aging-related diseases.
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Affiliation(s)
- Wenjing Qi
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun, Jilin, China
| | - Jinping Bai
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
| | - Ruoxi Wang
- Center for Cell Structure and Function, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, Shandong, China
| | - Xianlu Zeng
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun, Jilin, China
| | - Lihui Zhang
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
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6
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Lequieu J. A physical model of euchromatin organization. Proc Natl Acad Sci U S A 2024; 121:e2410751121. [PMID: 39008683 PMCID: PMC11287279 DOI: 10.1073/pnas.2410751121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Affiliation(s)
- Joshua Lequieu
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA19104
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7
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Zhang X, Venkatachalapathy S, Paysan D, Schaerer P, Tripodo C, Uhler C, Shivashankar GV. Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization in DCIS. Nat Commun 2024; 15:6112. [PMID: 39030176 PMCID: PMC11271523 DOI: 10.1038/s41467-024-50285-1] [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: 04/04/2023] [Accepted: 07/05/2024] [Indexed: 07/21/2024] Open
Abstract
Ductal carcinoma in situ (DCIS) is a pre-invasive tumor that can progress to invasive breast cancer, a leading cause of cancer death. We generate a large-scale tissue microarray dataset of chromatin images, from 560 samples from 122 female patients in 3 disease stages and 11 phenotypic categories. Using representation learning on chromatin images alone, without multiplexed staining or high-throughput sequencing, we identify eight morphological cell states and tissue features marking DCIS. All cell states are observed in all disease stages with different proportions, indicating that cell states enriched in invasive cancer exist in small fractions in normal breast tissue. Tissue-level analysis reveals significant changes in the spatial organization of cell states across disease stages, which is predictive of disease stage and phenotypic category. Taken together, we show that chromatin imaging represents a powerful measure of cell state and disease stage of DCIS, providing a simple and effective tumor biomarker.
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Affiliation(s)
- Xinyi Zhang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Saradha Venkatachalapathy
- Department of Health Sciences and Technology, ETH Zurich, Switzerland
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland
| | - Daniel Paysan
- Department of Health Sciences and Technology, ETH Zurich, Switzerland
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland
| | - Paulina Schaerer
- Department of Health Sciences and Technology, ETH Zurich, Switzerland
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland
| | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo, Palermo, Italy
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Caroline Uhler
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, USA.
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, USA.
| | - G V Shivashankar
- Department of Health Sciences and Technology, ETH Zurich, Switzerland.
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen, Switzerland.
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8
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Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M. Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603769. [PMID: 39071404 PMCID: PMC11275793 DOI: 10.1101/2024.07.16.603769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in-silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in-situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.
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Affiliation(s)
- Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Johan H. Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Krishna M. Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655
| | - Francesca Vercellone
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Fontana
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Florinda Di Pierno
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
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9
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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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10
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Liu S, Athreya A, Lao Z, Zhang B. From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization. Annu Rev Biophys 2024; 53:221-245. [PMID: 38346246 PMCID: PMC11369498 DOI: 10.1146/annurev-biophys-030822-032650] [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: 07/18/2024]
Abstract
Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due to its complex, multiscale nature. Significant progress has been made in studying in vitro systems, uncovering the structure of individual nucleosomes and their arrays, and elucidating the role of physicochemical forces in stabilizing these structures. Additionally, remarkable advancements have been achieved in characterizing chromatin organization in vivo, particularly at the whole-chromosome level, revealing important features such as chromatin loops, topologically associating domains, and nuclear compartments. However, bridging the gap between in vitro and in vivo studies remains challenging. The resemblance between in vitro and in vivo chromatin conformations and the relevance of internucleosomal interactions for chromatin folding in vivo are subjects of debate. This article reviews experimental and computational studies conducted at various length scales, highlighting the significance of intrinsic interactions between nucleosomes and their roles in chromatin folding in vivo.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Advait Athreya
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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11
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2024. [PMID: 38944686 DOI: 10.1111/febs.17211] [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: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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12
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Moindrot B, Imaizumi Y, Feil R. Differential 3D genome architecture and imprinted gene expression: cause or consequence? Biochem Soc Trans 2024; 52:973-986. [PMID: 38775198 PMCID: PMC11346452 DOI: 10.1042/bst20230143] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.
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Affiliation(s)
- Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
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13
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Vemuri K, Kumar S, Chen L, Verzi MP. Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4. Cell Rep 2024; 43:114242. [PMID: 38768033 PMCID: PMC11264335 DOI: 10.1016/j.celrep.2024.114242] [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: 11/08/2023] [Revised: 04/03/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
Terminal differentiation requires massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4,000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identify dynamic occupancy of RNA polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II occupancy and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of-function, chromatin immunoprecipitation sequencing (ChIP-seq), and immunoprecipitation (IP) mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II occupancy at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms that drive differentiation gene expression and find that pause-release of Pol II and post-transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in renewing adult tissue.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Sneha Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA; NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI, Piscataway, NJ 08854, USA.
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14
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Li B, Xiong W, Zuo W, Shi Y, Wang T, Chang L, Wu Y, Ma H, Bian Q, Chang ACY. Proximal telomeric decompaction due to telomere shortening drives FOXC1-dependent myocardial senescence. Nucleic Acids Res 2024; 52:6269-6284. [PMID: 38634789 PMCID: PMC11194093 DOI: 10.1093/nar/gkae274] [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: 04/17/2023] [Revised: 02/29/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Telomeres, TTAGGGn DNA repeat sequences located at the ends of eukaryotic chromosomes, play a pivotal role in aging and are targets of DNA damage response. Although we and others have demonstrated presence of short telomeres in genetic cardiomyopathic and heart failure cardiomyocytes, little is known about the role of telomere lengths in cardiomyocyte. Here, we demonstrate that in heart failure patient cardiomyocytes, telomeres are shortened compared to healthy controls. We generated isogenic human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) with short telomeres (sTL-CMs) and normal telomeres (nTL-CMs) as model. Compared to nTL-CMs, short telomeres result in cardiac dysfunction and expression of senescent markers. Using Hi-C and RNASeq, we observe that short telomeres induced TAD insulation decrease near telomeric ends and this correlated with a transcription upregulation in sTL-CMs. FOXC1, a key transcription factor involved in early cardiogenesis, was upregulated in sTL-CMs and its protein levels were negatively correlated with telomere lengths in heart failure patients. Overexpression of FOXC1 induced hiPSC-CM aging, mitochondrial and contractile dysfunction; knockdown of FOXC1 rescued these phenotypes. Overall, the work presented demonstrate that increased chromatin accessibility due to telomere shortening resulted in the induction of FOXC1-dependent expression network responsible for contractile dysfunction and myocardial senescence.
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Affiliation(s)
- Bin Li
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Weiyao Xiong
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Wu Zuo
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yuanyuan Shi
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Teng Wang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Lingling Chang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Yueheng Wu
- Department of Cardiovascular Medicine, Guangdong General Hospital, Guangzhou, Guangdong, China
| | - Heng Ma
- Department of Physiology and Pathophysiology, Fourth Military Medical University, No. 169 Changle West Rd, Xi'an 710032, China
| | - Qian Bian
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - Alex C Y Chang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
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15
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Alcantar MA, English MA, Valeri JA, Collins JJ. A high-throughput synthetic biology approach for studying combinatorial chromatin-based transcriptional regulation. Mol Cell 2024; 84:2382-2396.e9. [PMID: 38906116 DOI: 10.1016/j.molcel.2024.05.025] [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: 06/05/2023] [Revised: 04/11/2024] [Accepted: 05/24/2024] [Indexed: 06/23/2024]
Abstract
The construction of synthetic gene circuits requires the rational combination of multiple regulatory components, but predicting their behavior can be challenging due to poorly understood component interactions and unexpected emergent behaviors. In eukaryotes, chromatin regulators (CRs) are essential regulatory components that orchestrate gene expression. Here, we develop a screening platform to investigate the impact of CR pairs on transcriptional activity in yeast. We construct a combinatorial library consisting of over 1,900 CR pairs and use a high-throughput workflow to characterize the impact of CR co-recruitment on gene expression. We recapitulate known interactions and discover several instances of CR pairs with emergent behaviors. We also demonstrate that supervised machine learning models trained with low-dimensional amino acid embeddings accurately predict the impact of CR co-recruitment on transcriptional activity. This work introduces a scalable platform and machine learning approach that can be used to study how networks of regulatory components impact gene expression.
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Affiliation(s)
- Miguel A Alcantar
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Max A English
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Jacqueline A Valeri
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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16
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Prevo B, Earnshaw WC. DNA packaging by molecular motors: from bacteriophage to human chromosomes. Nat Rev Genet 2024:10.1038/s41576-024-00740-y. [PMID: 38886215 DOI: 10.1038/s41576-024-00740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Dense packaging of genomic DNA is crucial for organismal survival, as DNA length always far exceeds the dimensions of the cells that contain it. Organisms, therefore, use sophisticated machineries to package their genomes. These systems range across kingdoms from a single ultra-powerful rotary motor that spools the DNA into a bacteriophage head, to hundreds of thousands of relatively weak molecular motors that coordinate the compaction of mitotic chromosomes in eukaryotic cells. Recent technological advances, such as DNA proximity-based sequencing approaches, polymer modelling and in vitro reconstitution of DNA loop extrusion, have shed light on the biological mechanisms driving DNA organization in different systems. Here, we discuss DNA packaging in bacteriophage, bacteria and eukaryotic cells, which, despite their extreme variation in size, structure and genomic content, all rely on the action of molecular motors to package their genomes.
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Affiliation(s)
- Bram Prevo
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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17
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Su L, Zhang M, Ji F, Zhao J, Wang Y, Wang W, Zhang S, Ma H, Wang Y, Jiao J. Microglia homeostasis mediated by epigenetic ARID1A regulates neural progenitor cells response and leads to autism-like behaviors. Mol Psychiatry 2024; 29:1595-1609. [PMID: 35858990 DOI: 10.1038/s41380-022-01703-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 01/26/2023]
Abstract
Microglia are resident macrophages of the central nervous system that selectively emerge in embryonic cortical proliferative zones and regulate neurogenesis by altering molecular and phenotypic states. Despite their important roles in inflammatory phagocytosis and neurodegenerative diseases, microglial homeostasis during early brain development has not been fully elucidated. Here, we demonstrate a notable interplay between microglial homeostasis and neural progenitor cell signal transduction during embryonic neurogenesis. ARID1A, an epigenetic subunit of the SWI/SNF chromatin-remodeling complex, disrupts genome-wide H3K9me3 occupancy in microglia and changes the epigenetic chromatin landscape of regulatory elements that influence the switching of microglial states. Perturbation of microglial homeostasis impairs the release of PRG3, which regulates neural progenitor cell self-renewal and differentiation during embryonic development. Furthermore, the loss of microglia-driven PRG3 alters the downstream cascade of the Wnt/β-catenin signaling pathway through its interaction with the neural progenitor receptor LRP6, which leads to misplaced regulation in neuronal development and causes autism-like behaviors at later stages. Thus, during early fetal brain development, microglia progress toward a more homeostatic competent phenotype, which might render neural progenitor cells respond to environmental cross-talk perturbations.
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Affiliation(s)
- Libo Su
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Mengtian Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jinyue Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yuanyuan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wenwen Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Shukui Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- College of Life Sciences, Yantai University, Yantai, 264005, Shandong, China
| | - Hongyan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yanyan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
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18
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Rudnizky S, Murray PJ, Wolfe CH, Ha T. Single-Macromolecule Studies of Eukaryotic Genomic Maintenance. Annu Rev Phys Chem 2024; 75:209-230. [PMID: 38382570 DOI: 10.1146/annurev-physchem-090722-010601] [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] [Indexed: 02/23/2024]
Abstract
Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.
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Affiliation(s)
- Sergei Rudnizky
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter J Murray
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
| | - Clara H Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
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19
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Uckelmann M, Davidovich C. Chromatin compaction by Polycomb group proteins revisited. Curr Opin Struct Biol 2024; 86:102806. [PMID: 38537534 DOI: 10.1016/j.sbi.2024.102806] [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: 11/29/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 05/19/2024]
Abstract
The chromatin compaction activity of Polycomb group proteins has traditionally been considered essential for transcriptional repression. However, there is very little information on how Polycomb group proteins compact chromatin at the molecular level and no causal link between the compactness of chromatin and transcriptional repression. Recently, a more complete picture of Polycomb-dependent chromatin architecture has started to emerge, owing to advanced methods for imaging and chromosome conformation capture. Discoveries into Polycomb-driven phase separation add another layer of complexity. Recent observations generally imply that Polycomb group proteins modulate chromatin structure at multiple scales to reduce its dynamics and segregate it from active domains. Hence, it is reasonable to hypothesise that Polycomb group proteins maintain the energetically favourable state of compacted chromatin, rather than actively compact it.
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Affiliation(s)
- Michael Uckelmann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, 3800, Australia.
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, 3800, Australia; EMBL-Australia, Clayton, Victoria, 3800, Australia.
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20
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Gu Y, Wei K, Wang J. Phase separation and transcriptional regulation in cancer development. J Biomed Res 2024; 38:307-321. [PMID: 39113127 PMCID: PMC11300516 DOI: 10.7555/jbr.37.20230214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 08/10/2024] Open
Abstract
Liquid-liquid phase separation, a novel biochemical phenomenon, has been increasingly studied for its medical applications. It underlies the formation of membrane-less organelles and is involved in many cellular and biological processes. During transcriptional regulation, dynamic condensates are formed through interactions between transcriptional elements, such as transcription factors, coactivators, and mediators. Cancer is a disease characterized by uncontrolled cell proliferation, but the precise mechanisms underlying tumorigenesis often remain to be elucidated. Emerging evidence has linked abnormal transcriptional condensates to several diseases, especially cancer, implying that phase separation plays an important role in tumorigenesis. Condensates formed by phase separation may have an effect on gene transcription in tumors. In the present review, we focus on the correlation between phase separation and transcriptional regulation, as well as how this phenomenon contributes to cancer development.
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Affiliation(s)
- Yan Gu
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Ke Wei
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jun Wang
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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21
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Packard JE, Kumar N, Weitzman MD, Dembowski JA. Identifying Protein Interactions with Viral DNA Genomes during Virus Infection. Viruses 2024; 16:845. [PMID: 38932138 PMCID: PMC11209293 DOI: 10.3390/v16060845] [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: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Viruses exploit the host cell machinery to enable infection and propagation. This review discusses the complex landscape of DNA virus-host interactions, focusing primarily on herpesviruses and adenoviruses, which replicate in the nucleus of infected cells, and vaccinia virus, which replicates in the cytoplasm. We discuss experimental approaches used to discover and validate interactions of host proteins with viral genomes and how these interactions impact processes that occur during infection, including the host DNA damage response and viral genome replication, repair, and transcription. We highlight the current state of knowledge regarding virus-host protein interactions and also outline emerging areas and future directions for research.
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Affiliation(s)
- Jessica E. Packard
- Department of Biological Sciences, School of Science and Engineering, Duquesne University, Pittsburgh, PA 15282, USA
| | - Namrata Kumar
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew D. Weitzman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jill A. Dembowski
- Department of Biological Sciences, School of Science and Engineering, Duquesne University, Pittsburgh, PA 15282, USA
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22
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Tomikawa J. Potential roles of inter-chromosomal interactions in cell fate determination. Front Cell Dev Biol 2024; 12:1397807. [PMID: 38774644 PMCID: PMC11106443 DOI: 10.3389/fcell.2024.1397807] [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: 03/08/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024] Open
Abstract
Mammalian genomic DNA is packed in a small nucleus, and its folding and organization in the nucleus are critical for gene regulation and cell fate determination. In interphase, chromosomes are compartmentalized into certain nuclear spaces and territories that are considered incompatible with each other. The regulation of gene expression is influenced by the epigenetic characteristics of topologically associated domains and A/B compartments within chromosomes (intrachromosomal). Previously, interactions among chromosomes detected via chromosome conformation capture-based methods were considered noise or artificial errors. However, recent studies based on newly developed ligation-independent methods have shown that inter-chromosomal interactions play important roles in gene regulation. This review summarizes the recent understanding of spatial genomic organization in mammalian interphase nuclei and discusses the potential mechanisms that determine cell identity. In addition, this review highlights the potential role of inter-chromosomal interactions in early mouse development.
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Affiliation(s)
- Junko Tomikawa
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
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23
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Shaban HA, Friman ET, Deluz C, Tollenaere A, Katanayeva N, Suter DM. Individual transcription factors modulate both the micromovement of chromatin and its long-range structure. Proc Natl Acad Sci U S A 2024; 121:e2311374121. [PMID: 38648478 PMCID: PMC11067044 DOI: 10.1073/pnas.2311374121] [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: 07/05/2023] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here, we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine high-resolution diffusion mapping and dense flow reconstruction and correlation in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.
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Affiliation(s)
- Haitham A. Shaban
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
- Spectroscopy Department, Institute of Physics Research, National Research Centre, Cairo12622, Egypt
| | - Elias T. Friman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Cédric Deluz
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Armelle Tollenaere
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - David M. Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
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24
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Banerjee A, Zhang S, Bahar I. Genome structural dynamics: insights from Gaussian network analysis of Hi-C data. Brief Funct Genomics 2024:elae014. [PMID: 38654598 DOI: 10.1093/bfgp/elae014] [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: 11/02/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Characterization of the spatiotemporal properties of the chromatin is essential to gaining insights into the physical bases of gene co-expression, transcriptional regulation and epigenetic modifications. The Gaussian network model (GNM) has proven in recent work to serve as a useful tool for modeling chromatin structural dynamics, using as input high-throughput chromosome conformation capture data. We focus here on the exploration of the collective dynamics of chromosomal structures at hierarchical levels of resolution, from single gene loci to topologically associating domains or entire chromosomes. The GNM permits us to identify long-range interactions between gene loci, shedding light on the role of cross-correlations between distal regions of the chromosomes in regulating gene expression. Notably, GNM analysis performed across diverse cell lines highlights the conservation of the global/cooperative movements of the chromatin across different types of cells. Variations driven by localized couplings between genomic loci, on the other hand, underlie cell differentiation, underscoring the significance of the four-dimensional properties of the genome in defining cellular identity. Finally, we demonstrate the close relation between the cell type-dependent mobility profiles of gene loci and their gene expression patterns, providing a clear demonstration of the role of chromosomal 4D features in defining cell-specific differential expression of genes.
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Affiliation(s)
- Anupam Banerjee
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, NY 11794, USA
| | - She Zhang
- OpenEye, Cadence Molecular Sciences, Santa Fe, NM 87508, USA
| | - Ivet Bahar
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, NY 11794, USA
- Department of Biochemistry and Cell Biology, Renaissance School of Medicine, Stony Brook University, NY 11794, USA
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25
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Hu S, Chapski DJ, Gehred ND, Kimball TH, Gromova T, Flores A, Rowat AC, Chen J, Packard RRS, Olszewski E, Davis J, Rau CD, McKinsey TA, Rosa-Garrido M, Vondriska TM. Histone H1.0 couples cellular mechanical behaviors to chromatin structure. NATURE CARDIOVASCULAR RESEARCH 2024; 3:441-459. [PMID: 38765203 PMCID: PMC11101354 DOI: 10.1038/s44161-024-00460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 03/06/2024] [Indexed: 05/21/2024]
Abstract
Tuning of genome structure and function is accomplished by chromatin-binding proteins, which determine the transcriptome and phenotype of the cell. Here we investigate how communication between extracellular stress and chromatin structure may regulate cellular mechanical behaviors. We demonstrate that histone H1.0, which compacts nucleosomes into higher-order chromatin fibers, controls genome organization and cellular stress response. We show that histone H1.0 has privileged expression in fibroblasts across tissue types and that its expression is necessary and sufficient to induce myofibroblast activation. Depletion of histone H1.0 prevents cytokine-induced fibroblast contraction, proliferation and migration via inhibition of a transcriptome comprising extracellular matrix, cytoskeletal and contractile genes, through a process that involves locus-specific H3K27 acetylation. Transient depletion of histone H1.0 in vivo prevents fibrosis in cardiac muscle. These findings identify an unexpected role of linker histones to orchestrate cellular mechanical behaviors, directly coupling force generation, nuclear organization and gene transcription.
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Affiliation(s)
- Shuaishuai Hu
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Douglas J. Chapski
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Natalie D. Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Todd H. Kimball
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Angelina Flores
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Amy C. Rowat
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Junjie Chen
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - René R. Sevag Packard
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Physiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
| | - Emily Olszewski
- Department of Bioengineering, University of Washington, Seattle, WA USA
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA USA
| | - Christoph D. Rau
- Department of Genetics and McAllister Heart Institute, University of North Carolina, Chapel Hill, NC USA
| | - Timothy A. McKinsey
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO USA
| | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL USA
| | - Thomas M. Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
- Department of Physiology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA USA
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26
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Yuan T, Yan H, Bailey MLP, Williams JF, Surovtsev I, King MC, Mochrie SGJ. Effect of loops on the mean-square displacement of Rouse-model chromatin. Phys Rev E 2024; 109:044502. [PMID: 38755928 DOI: 10.1103/physreve.109.044502] [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: 04/24/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.
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Affiliation(s)
- Tianyu Yuan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Hao Yan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Megan C King
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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27
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Lao Z, Kamat K, Jiang Z, Zhang B. OpenNucleome for high resolution nuclear structural and dynamical modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562451. [PMID: 37905090 PMCID: PMC10614770 DOI: 10.1101/2023.10.16.562451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of "fixed points" within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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28
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Bastié N, Chapard C, Cournac A, Nejmi S, Mboumba H, Gadal O, Thierry A, Beckouët F, Koszul R. Sister chromatid cohesion halts DNA loop expansion. Mol Cell 2024; 84:1139-1148.e5. [PMID: 38452765 DOI: 10.1016/j.molcel.2024.02.004] [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: 07/26/2023] [Revised: 12/02/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024]
Abstract
Eukaryotic genomes are folded into DNA loops mediated by structural maintenance of chromosomes (SMC) complexes such as cohesin, condensin, and Smc5/6. This organization regulates different DNA-related processes along the cell cycle, such as transcription, recombination, segregation, and DNA repair. During the G2 stage, SMC-mediated DNA loops coexist with cohesin complexes involved in sister chromatid cohesion (SCC). However, the articulation between the establishment of SCC and the formation of SMC-mediated DNA loops along the chromatin remains unknown. Here, we show that SCC is indeed a barrier to cohesin-mediated DNA loop expansion along G2/M Saccharomyces cerevisiae chromosomes.
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Affiliation(s)
- Nathalie Bastié
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Christophe Chapard
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Axel Cournac
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Sanae Nejmi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France
| | - Henri Mboumba
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Gadal
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Frederic Beckouët
- Molecular, Cellular, and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France.
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29
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Liu E, Lyu H, Liu Y, Fu L, Cheng X, Yin X. Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection. Bioinformatics 2024; 40:btae138. [PMID: 38449288 PMCID: PMC10960928 DOI: 10.1093/bioinformatics/btae138] [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: 07/03/2023] [Revised: 01/10/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
MOTIVATION Topologically associating domains (TADs) are fundamental building blocks of 3D genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity. RESULTS We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data. It takes Hi-C contact matrix as the adjacency matrix for a graph, embeds the graph structures into a low-dimensional space with the help of sparse matrix factorization followed by spectral propagation, and the TAD-like domains can be identified using a kernel-based changepoint detection in the embedding space. The results tell that our scKTLD is superior to the other methods on the sparse contact matrices, including downsampled bulk Hi-C data as well as simulated and experimental single-cell Hi-C data. Besides, we demonstrated the conservation of TAD-like domain boundaries at single-cell level apart from heterogeneity within and across cell types, and found that the boundaries with higher frequency across single cells are more enriched for architectural proteins and chromatin marks, and they preferentially occur at TAD boundaries in bulk cells, especially at those with higher hierarchical levels. AVAILABILITY AND IMPLEMENTATION scKTLD is freely available at https://github.com/lhqxinghun/scKTLD.
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Affiliation(s)
- Erhu Liu
- School of Information and Control Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Hongqiang Lyu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi'an 710049, China
| | - Yuan Liu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi'an 710049, China
| | - Laiyi Fu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi'an 710049, China
| | - Xiaoliang Cheng
- Department of Pharmacy, The First Affiliated Hospital of Xi’an Jiaotong University, Xi'an 710061, China
| | - Xiaoran Yin
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an 710004, China
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30
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Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and deep learning methods for predicting 3D genome organization. ARXIV 2024:arXiv:2403.03231v1. [PMID: 38495565 PMCID: PMC10942493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.
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Affiliation(s)
- Brydon P. G. Wall
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - My Nguyen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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31
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Braunger JM, Cammarata LV, Sornapudi TR, Uhler C, Shivashankar GV. Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging. Aging Cell 2024; 23:e14056. [PMID: 38062919 PMCID: PMC10928569 DOI: 10.1111/acel.14056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Human life expectancy is constantly increasing and aging has become a major risk factor for many diseases, although the underlying gene regulatory mechanisms are still unclear. Using transcriptomic and chromosomal conformation capture (Hi-C) data from human skin fibroblasts from individuals across different age groups, we identified a tight coupling between the changes in co-regulation and co-localization of genes. We obtained transcription factors, cofactors, and chromatin regulators that could drive the cellular aging process by developing a time-course prize-collecting Steiner tree algorithm. In particular, by combining RNA-Seq data from different age groups and protein-protein interaction data we determined the key transcription regulators and gene regulatory changes at different life stage transitions. We then mapped these transcription regulators to the 3D reorganization of chromatin in young and old skin fibroblasts. Collectively, we identified key transcription regulators whose target genes are spatially rearranged and correlate with changes in their expression, thereby providing potential targets for reverting cellular aging.
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Affiliation(s)
- Jana M. Braunger
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Louis V. Cammarata
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Department of StatisticsHarvard UniversityCambridgeMassachusettsUSA
| | | | - Caroline Uhler
- Eric and Wendy Schmidt CenterBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Laboratory for Information and Decision SystemsMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - G. V. Shivashankar
- Division of Biology and ChemistryPaul Scherrer InstituteVilligenSwitzerland
- Department of Health Sciences and TechnologyETH ZurichZurichSwitzerland
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32
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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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33
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Zhou S, Abdihamid O, Tan F, Zhou H, Liu H, Li Z, Xiao S, Li B. KIT mutations and expression: current knowledge and new insights for overcoming IM resistance in GIST. Cell Commun Signal 2024; 22:153. [PMID: 38414063 PMCID: PMC10898159 DOI: 10.1186/s12964-023-01411-x] [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: 07/19/2023] [Accepted: 11/25/2023] [Indexed: 02/29/2024] Open
Abstract
Gastrointestinal stromal tumor (GIST) is the most common sarcoma located in gastrointestinal tract and derived from the interstitial cell of Cajal (ICC) lineage. Both ICC and GIST cells highly rely on KIT signal pathway. Clinically, about 80-90% of treatment-naive GIST patients harbor primary KIT mutations, and special KIT-targeted TKI, imatinib (IM) showing dramatic efficacy but resistance invariably occur, 90% of them was due to the second resistance mutations emerging within the KIT gene. Although there are multiple variants of KIT mutant which did not show complete uniform biologic characteristics, most of them have high KIT expression level. Notably, the high expression level of KIT gene is not correlated to its gene amplification. Recently, accumulating evidences strongly indicated that the gene coding, epigenetic regulation, and pre- or post- protein translation of KIT mutants in GIST were quite different from that of wild type (WT) KIT. In this review, we elucidate the biologic mechanism of KIT variants and update the underlying mechanism of the expression of KIT gene, which are exclusively regulated in GIST, providing a promising yet evidence-based therapeutic landscape and possible target for the conquer of IM resistance. Video Abstract.
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Affiliation(s)
- Shishan Zhou
- Division of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China, Xiangya road 87
| | - Omar Abdihamid
- Garissa Cancer Center, Garissa County Referral Hospital, Kismayu road, Garissa town, P.O BOX, 29-70100, Kenya
| | - Fengbo Tan
- Division of Surgery, Xiangya Hospital, Central South University, China, Hunan, Changsha
| | - Haiyan Zhou
- Division of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Heli Liu
- Division of Surgery, Xiangya Hospital, Central South University, China, Hunan, Changsha
| | - Zhi Li
- Center for Molecular Medicine of Xiangya Hospital, Collaborative Innovation Center for Cancer Medicine, Central South University, Changsha, Hunan, China, 410008
| | - Sheng Xiao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, 410008, MA, USA
| | - Bin Li
- Division of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China, Xiangya road 87#.
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34
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Wang Z, Zhang Z, Luo S, Zhou T, Zhang J. Power-law behavior of transcriptional bursting regulated by enhancer-promoter communication. Genome Res 2024; 34:106-118. [PMID: 38171575 PMCID: PMC10903953 DOI: 10.1101/gr.278631.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Revealing how transcriptional bursting kinetics are genomically encoded is challenging because genome structures are stochastic at the organization level and are suggestively linked to gene transcription. To address this challenge, we develop a generic theoretical framework that integrates chromatin dynamics, enhancer-promoter (E-P) communication, and gene-state switching to study transcriptional bursting. The theory predicts that power law can be a general rule to quantitatively describe bursting modulations by E-P spatial communication. Specifically, burst frequency and burst size are up-regulated by E-P communication strength, following power laws with positive exponents. Analysis of the scaling exponents further reveals that burst frequency is preferentially regulated. Bursting kinetics are down-regulated by E-P genomic distance with negative power-law exponents, and this negative modulation desensitizes at large distances. The mutual information between burst frequency (or burst size) and E-P spatial distance further reveals essential characteristics of the information transfer from E-P communication to transcriptional bursting kinetics. These findings, which are in agreement with experimental observations, not only reveal fundamental principles of E-P communication in transcriptional bursting but also are essential for understanding cellular decision-making.
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Affiliation(s)
- Zihao Wang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
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35
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Hung TC, Kingsley DM, Boettiger AN. Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. Nat Genet 2024; 56:306-314. [PMID: 38238628 DOI: 10.1038/s41588-023-01641-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/06/2023] [Indexed: 02/15/2024]
Abstract
Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.
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Affiliation(s)
- Tzu-Chiao Hung
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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36
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Remini L, Segers M, Palmeri J, Walter JC, Parmeggiani A, Carlon E. Chromatin structure from high resolution microscopy: Scaling laws and microphase separation. Phys Rev E 2024; 109:024408. [PMID: 38491617 DOI: 10.1103/physreve.109.024408] [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: 08/14/2023] [Accepted: 01/11/2024] [Indexed: 03/18/2024]
Abstract
Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50 nm) of the three-dimensional physical location of multiple (up to ∼10^{2}) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr21 obtained from multiplexed fluorescence in situ hybridization (FISH) methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags with the aim being to unravel the chromatin conformational arrangements. We show that for any specific genomic site, there are (at least) two different conformational arrangements of chromatin, implying coexisting distinct topologies which we refer to as phase α and phase β. These two phases show different scaling behaviors: the former is consistent with a crumpled globule, while the latter indicates a confined, but more extended conformation, such as a looped domain. The identification of these distinct phases sheds light on the coexistence of multiple chromatin topologies and provides insights into the effects of cellular context and/or treatments on chromatin structure.
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Affiliation(s)
- Loucif Remini
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Midas Segers
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Enrico Carlon
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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37
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Attar AG, Paturej J, Banigan EJ, Erbas A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.16.571697. [PMID: 38168411 PMCID: PMC10760070 DOI: 10.1101/2023.12.16.571697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Abnormalities in the shapes of mammalian cell nuclei are hallmarks of a variety of diseases, including progeria, muscular dystrophy, and various cancers. Experiments have shown that there is a causal relationship between chromatin organization and nuclear morphology. Decreases in heterochromatin levels, perturbations to heterochromatin organization, and increases in euchromatin levels all lead to misshapen nuclei, which exhibit deformations, such as nuclear blebs and nuclear ruptures. However, the polymer physical mechanisms of how chromatin governs nuclear shape and integrity are poorly understood. To investigate how heterochromatin and euchromatin, which are thought to microphase separate in vivo , govern nuclear morphology, we implemented a composite coarse-grained polymer and elastic shell model. By varying chromatin volume fraction (density), heterochromatin levels and structure, and heterochromatin-lamina interactions, we show how the spatial organization of chromatin polymer phases within the nucleus could perturb nuclear shape in some scenarios. Increasing the volume fraction of chromatin in the cell nucleus stabilizes the nuclear lamina against large fluctuations. However, surprisingly, we find that increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations in our simulations by a "wetting"-like interaction. In contrast, shape fluctuations are largely insensitive to the internal structure of the heterochromatin, such as the presence or absence of chromatin-chromatin crosslinks. Therefore, our simulations suggest that heterochromatin accumulation at the nuclear periphery could perturb nuclear morphology in a nucleus or nuclear region that is sufficiently soft, while stabilization of the nucleus via heterochromatin likely occurs through mechanisms other than chromatin microphase organization.
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38
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Zhang L, Liu L, Li H, He J, Chao H, Yan S, Yin Y, Zhao W, Li M. 3D genome structural variations play important roles in regulating seed oil content of Brassica napus. PLANT COMMUNICATIONS 2024; 5:100666. [PMID: 37496273 PMCID: PMC10811347 DOI: 10.1016/j.xplc.2023.100666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
Dissecting the complex regulatory mechanism of seed oil content (SOC) is one of the main research goals in Brassica napus. Increasing evidence suggests that genome architecture is linked to multiple biological functions. However, the effect of genome architecture on SOC regulation remains unclear. Here, we used high-throughput chromatin conformation capture to characterize differences in the three-dimensional (3D) landscape of genome architecture of seeds from two B. napus lines, N53-2 (with high SOC) and Ken-C8 (with low SOC). Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci (QTLs)/associated genomic regions (AGRs) for SOC. A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural variations in QTLs/AGRs of B. napus. The candidate gene BnaA09g48250D, which showed structural variation in a QTL/AGR on chrA09, was identified by fine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8. Overexpression and knockout of BnaA09g48250D led to significant increases and decreases in SOC, respectively, in the transgenic lines. Taken together, our results reveal the 3D genome architecture of B. napus seeds and the roles of genome structural variations in SOC regulation, enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.
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Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan 430075, China
| | - Huaixin Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Hongbo Chao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shuxiang Yan
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Yontai Yin
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Weiguo Zhao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China.
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39
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Gilbert BR, Luthey-Schulten Z. Replicating Chromosomes in Whole-Cell Models of Bacteria. Methods Mol Biol 2024; 2819:625-653. [PMID: 39028527 DOI: 10.1007/978-1-0716-3930-6_29] [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] [Indexed: 07/20/2024]
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication of genetic material. In a recent study, we presented a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics. This approach was used to investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell cycle. To achieve cell-scale chromosome structures that are realistic, we modeled the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. Additionally, the polymer interacts with ribosomes distributed according to cryo-electron tomograms of Syn3A. The polymer model was further augmented by computational models of loop extrusion by structural maintenance of chromosomes (SMC) protein complexes and topoisomerase action, and the modeling and analysis of multi-fork replication states.
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Affiliation(s)
- Benjamin R Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NSF Science and Technology Center for Quantitative Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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40
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Fok ET, Moorlag SJCFM, Negishi Y, Groh LA, Dos Santos JC, Gräwe C, Monge VV, Craenmehr DDD, van Roosmalen M, da Cunha Jolvino DP, Migliorini LB, Neto AS, Severino P, Vermeulen M, Joosten LAB, Netea MG, Fanucchi S, Mhlanga MM. A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation. Nat Genet 2024; 56:85-99. [PMID: 38092881 DOI: 10.1038/s41588-023-01598-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/26/2023] [Indexed: 12/23/2023]
Abstract
Inflammation is characterized by a biphasic cycle consisting initially of a proinflammatory phase that is subsequently resolved by anti-inflammatory processes. Interleukin-1β (IL-1β) is a master regulator of proinflammation and is encoded within the same topologically associating domain (TAD) as IL-37, which is an anti-inflammatory cytokine that opposes the function of IL-1β. Within this TAD, we identified a long noncoding RNA called AMANZI, which negatively regulates IL-1β expression and trained immunity through the induction of IL37 transcription. We found that the activation of IL37 occurs through the formation of a dynamic long-range chromatin contact that leads to the temporal delay of anti-inflammatory responses. The common variant rs16944 present in AMANZI augments this regulatory circuit, predisposing individuals to enhanced proinflammation or immunosuppression. Our work illuminates a chromatin-mediated biphasic circuit coordinating expression of IL-1β and IL-37, thereby regulating two functionally opposed states of inflammation from within a single TAD.
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Affiliation(s)
- Ezio T Fok
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Lemba Therapeutics, Nijmegen, the Netherlands
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yutaka Negishi
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Laszlo A Groh
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jéssica Cristina Dos Santos
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
| | | | | | | | - David Pablo da Cunha Jolvino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Victoria, Australia
| | - Letícia Busato Migliorini
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Ary Serpa Neto
- Department of Critical Care Medicine, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Musa M Mhlanga
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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41
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Mandal M, Maienschein-Cline M, Hu Y, Mohsin A, Veselits ML, Wright NE, Okoreeh MK, Yoon YM, Veselits J, Georgopoulos K, Clark MR. BRWD1 orchestrates small pre-B cell chromatin topology by converting static to dynamic cohesin. Nat Immunol 2024; 25:129-141. [PMID: 37985858 DOI: 10.1038/s41590-023-01666-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: 02/22/2023] [Accepted: 09/29/2023] [Indexed: 11/22/2023]
Abstract
Lymphocyte development consists of sequential and mutually exclusive cell states of proliferative selection and antigen receptor gene recombination. Transitions between each state require large, coordinated changes in epigenetic landscapes and transcriptional programs. How this occurs remains unclear. Here we demonstrate that in small pre-B cells, the lineage and stage-specific epigenetic reader bromodomain and WD repeat-containing protein 1 (BRWD1) reorders three-dimensional chromatin topology to affect the transition between proliferative and gene recombination molecular programs. BRWD1 regulated the switch between poised and active enhancers interacting with promoters, and coordinated this switch with Igk locus contraction. BRWD1 did so by converting chromatin-bound static to dynamic cohesin competent to mediate long-range looping. ATP-depletion revealed cohesin conversion to be the main energetic mechanism dictating dynamic chromatin looping. Our findings provide a new mechanism of cohesin regulation and reveal how cohesin function can be dictated by lineage contextual mechanisms to facilitate specific cell fate transitions.
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Affiliation(s)
- Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA.
| | | | - Yeguang Hu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Azam Mohsin
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Margaret L Veselits
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Nathaniel E Wright
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Michael K Okoreeh
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Young Me Yoon
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Jacob Veselits
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, USA.
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42
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Saikia S, Postwala H, Athilingam VP, Anandan A, Padma VV, Kalita PP, Chorawala M, Prajapati B. Single Nucleotide Polymorphisms (SNPs) in the Shadows: Uncovering their Function in Non-Coding Region of Esophageal Cancer. Curr Pharm Biotechnol 2024; 25:1915-1938. [PMID: 38310451 DOI: 10.2174/0113892010265004231116092802] [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: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 02/05/2024]
Abstract
Esophageal cancer is a complex disease influenced by genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in non-coding regions of the genome have emerged as crucial contributors to esophageal cancer susceptibility. This review provides a comprehensive overview of the role of SNPs in non-coding regions and their association with esophageal cancer. The accumulation of SNPs in the genome has been implicated in esophageal cancer risk. Various studies have identified specific locations in the genome where SNPs are more likely to occur, suggesting a location-specific response. Chromatin conformational studies have shed light on the localization of SNPs and their impact on gene transcription, posttranscriptional modifications, gene expression regulation, and histone modification. Furthermore, miRNA-related SNPs have been found to play a significant role in esophageal squamous cell carcinoma (ESCC). These SNPs can affect miRNA binding sites, thereby altering target gene regulation and contributing to ESCC development. Additionally, the risk of ESCC has been linked to base excision repair, suggesting that SNPs in this pathway may influence disease susceptibility. Somatic DNA segment alterations and modified expression quantitative trait loci (eQTL) have also been associated with ESCC. These alterations can lead to disrupted gene expression and cellular processes, ultimately contributing to cancer development and progression. Moreover, SNPs have been found to be associated with the long non-coding RNA HOTAIR, which plays a crucial role in ESCC pathogenesis. This review concludes with a discussion of the current and future perspectives in the field of SNPs in non-coding regions and their relevance to esophageal cancer. Understanding the functional implications of these SNPs may lead to the identification of novel therapeutic targets and the development of personalized approaches for esophageal cancer prevention and treatment.
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Affiliation(s)
- Surovi Saikia
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Humzah Postwala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Vishnu Prabhu Athilingam
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Aparna Anandan
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - V Vijaya Padma
- Department of Natural Product Chemistry, Translational Research Laboratory, Bharathiar University, Coimbatore - 641 046, Tamil Nadu, India
| | - Partha P Kalita
- Program of Biotechnology, Assam Down Town University, Panikhaiti, Guwahati 781026, Assam, India
| | - Mehul Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Ahmedabad, India
| | - Bhupendra Prajapati
- Department of Pharmaceutics and Pharmaceutical Technology, Shree. S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva, Gujarat, India
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43
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Zhang J, Wang Y, Guo J, Zhang N, He J, Zhou Z, Wu F. Direct Reprogramming of Mouse Fibroblasts to Osteoblast-like Cells Using Runx2/Dlx5 Factors on Engineered Stiff Hydrogels. ACS APPLIED MATERIALS & INTERFACES 2023; 15:59209-59223. [PMID: 38102996 DOI: 10.1021/acsami.3c14777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Direct reprogramming of somatic cells into functional cells still faces major limitations in terms of efficiency and achieving functional maturity of the reprogramed cells. While different approaches have been developed commonly based on exploiting biochemical signals, introducing appropriate mechanical cues that stimulate the reprogramming process is rarely reported. In this study, collagen-coated polyacrylamide (PAM) hydrogels with stiffness close to that of collagenous bone (40 kPa) were adopted to augment the direct reprogramming process of mouse fibroblasts to osteoblastic-like cells. The results suggested that culturing cells on a hydrogel substrate enhanced the overexpression of osteogenic transcription factors using nonviral vectors and improved the yield of osteoblast-like cells. Particularly, a synergistic effect on achieving osteogenic functionality has been observed for the mechanical cues and overexpression of transcriptional factors, leading to enhanced osteogenic transformation and production of bone mineral matrix. Animal experiments suggested that reprogramed cells generated on matrix hydrogels accelerated bone regeneration and stimulated ectopic osteogenesis. Mechanism analysis suggested the critical involvement of actomyosin contraction and mechanical signal-mediated pathways like the RhoA-ROCK pathway, leading to a synergistic effect on the key transcriptional processes, including chromatin remodeling, nuclear translocation, and epigenetic transition. This study provides insights into the mechanical cue-enhanced direct reprogramming and cell therapy.
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Affiliation(s)
- Junwei Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Yao Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Jing Guo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Nihui Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Jing He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Zongke Zhou
- Orthopedic Research Institute & Department of Orthopedics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Fang Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
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44
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Radzisheuskaya A, Peña‐Rømer I, Lorenzini E, Koche R, Zhan Y, Shliaha PV, Cooper AJ, Fan Z, Shlyueva D, Johansen JV, Hendrickson RC, Helin K. An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions. EMBO J 2023; 42:e114221. [PMID: 37987160 PMCID: PMC10711654 DOI: 10.15252/embj.2023114221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
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Affiliation(s)
- Aliaksandra Radzisheuskaya
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Isabel Peña‐Rømer
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Eugenia Lorenzini
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Richard Koche
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Yingqian Zhan
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Pavel V Shliaha
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Zheng Fan
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Daria Shlyueva
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Jens V Johansen
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
| | - Ronald C Hendrickson
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Kristian Helin
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
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45
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Cammarata LV, Uhler C, Shivashankar GV. Adhesome Receptor Clustering is Accompanied by the Colocalization of the Associated Genes in the Cell Nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570697. [PMID: 38106037 PMCID: PMC10723460 DOI: 10.1101/2023.12.07.570697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Proteins on the cell membrane cluster to respond to extracellular signals; for example, adhesion proteins cluster to enhance extracellular matrix sensing; or T-cell receptors cluster to enhance antigen sensing. Importantly, the maturation of such receptor clusters requires transcriptional control to adapt and reinforce the extracellular signal sensing. However, it has been unclear how such efficient clustering mechanisms are encoded at the level of the genes that code for these receptor proteins. Using the adhesome as an example, we show that genes that code for adhesome receptor proteins are spatially co-localized and co-regulated within the cell nucleus. Towards this, we use Hi-C maps combined with RNA-seq data of adherent cells to map the correspondence between adhesome receptor proteins and their associated genes. Interestingly, we find that the transcription factors that regulate these genes are also co-localized with the adhesome gene loci, thereby potentially facilitating a transcriptional reinforcement of the extracellular matrix sensing machinery. Collectively, our results highlight an important layer of transcriptional control of cellular signal sensing.
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Affiliation(s)
- Louis V. Cammarata
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Caroline Uhler
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - G. V. Shivashankar
- Department of Health Science and Technology, ETH Zurich; Zurich, Switzerland
- Paul Scherrer Institute; Villigen, Switzerland
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46
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Liu S, Zheng P, Wang CY, Jia BB, Zemke NR, Ren B, Zhuang X. Cell-type-specific 3D-genome organization and transcription regulation in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.570024. [PMID: 38105994 PMCID: PMC10723369 DOI: 10.1101/2023.12.04.570024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
3D organization of the genome plays a critical role in regulating gene expression. However, it remains unclear how chromatin organization differs among different cell types in the brain. Here we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the primary motor cortex of the mouse brain. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the physical size of the cell nucleus to the active-inactive chromatin compartmentalization and radial positioning of chromatin loci within the nucleus. These cell-type-dependent variations in nuclear architecture and chromatin organization exhibited strong correlation with both total transcriptional activity of the cell and transcriptional regulation of cell-type-specific marker genes. Moreover, we found that the methylated-DNA-binding protein MeCP2 regulates transcription in a divergent manner, depending on the nuclear radial positions of chromatin loci, through modulating active-inactive chromatin compartmentalization.
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Affiliation(s)
- Shiwei Liu
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Pu Zheng
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Cosmos Yuqi Wang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Bojing Blair Jia
- Bioinformatics and Systems Biology Graduate Program, Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Nathan R. Zemke
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine and Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
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47
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Metzger DCH, Porter I, Mobley B, Sandkam BA, Fong LJM, Anderson AP, Mank JE. Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation. Genome Res 2023; 33:1917-1931. [PMID: 37989601 PMCID: PMC10760456 DOI: 10.1101/gr.278127.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/20/2023] [Indexed: 11/23/2023]
Abstract
Sex chromosome dosage compensation is a model to understand the coordinated evolution of transcription; however, the advanced age of the sex chromosomes in model systems makes it difficult to study how the complex regulatory mechanisms underlying chromosome-wide dosage compensation can evolve. The sex chromosomes of Poecilia picta have undergone recent and rapid divergence, resulting in widespread gene loss on the male Y, coupled with complete X Chromosome dosage compensation, the first case reported in a fish. The recent de novo origin of dosage compensation presents a unique opportunity to understand the genetic and evolutionary basis of coordinated chromosomal gene regulation. By combining a new chromosome-level assembly of P. picta with whole-genome bisulfite sequencing and RNA-seq data, we determine that the YY1 transcription factor (YY1) DNA binding motif is associated with male-specific hypomethylated regions on the X, but not the autosomes. These YY1 motifs are the result of a recent and rapid repetitive element expansion on the P. picta X Chromosome, which is absent in closely related species that lack dosage compensation. Taken together, our results present compelling support that a disruptive wave of repetitive element insertions carrying YY1 motifs resulted in the remodeling of the X Chromosome epigenomic landscape and the rapid de novo origin of a dosage compensation system.
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Affiliation(s)
- David C H Metzger
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada;
| | - Imogen Porter
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Brendan Mobley
- Biology Department, Reed College, Portland, Oregon 97202, USA
| | - Benjamin A Sandkam
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA
| | - Lydia J M Fong
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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48
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Wang Z, Luo S, Zhang Z, Zhou T, Zhang J. 4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction. PLoS Comput Biol 2023; 19:e1011722. [PMID: 38109463 PMCID: PMC10760824 DOI: 10.1371/journal.pcbi.1011722] [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: 04/14/2023] [Revised: 01/02/2024] [Accepted: 11/28/2023] [Indexed: 12/20/2023] Open
Abstract
Recent experimental evidence strongly supports that three-dimensional (3D) long-range enhancer-promoter (E-P) interactions have important influences on gene-expression dynamics, but it is unclear how the interaction information is translated into gene expression over time (4D). To address this question, we developed a general theoretical framework (named as a 4D nucleome equation), which integrates E-P interactions on chromatin and biochemical reactions of gene transcription. With this equation, we first present the distribution of mRNA counts as a function of the E-P genomic distance and then reveal a power-law scaling of the expression level in this distance. Interestingly, we find that long-range E-P interactions can induce bimodal and trimodal mRNA distributions. The 4D nucleome equation also allows for model selection and parameter inference. When this equation is applied to the mouse embryonic stem cell smRNA-FISH data and the E-P genomic-distance data, the predicted E-P contact probability and mRNA distribution are in good agreement with experimental results. Further statistical inference indicates that the E-P interactions prefer to modulate the mRNA level by controlling promoter activation and transcription initiation rates. Our model and results provide quantitative insights into both spatiotemporal gene-expression determinants (i.e., long-range E-P interactions) and cellular fates during development.
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Affiliation(s)
- Zihao Wang
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Mathematics, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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49
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Rahman S, Dong P, Apontes P, Fernando M, Kosoy R, Townsley KG, Girdhar K, Bendl J, Shao Z, Misir R, Tsankova N, Kleopoulos S, Brennand K, Fullard J, Roussos P. Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Res 2023; 51:11142-11161. [PMID: 37811875 PMCID: PMC10639075 DOI: 10.1093/nar/gkad798] [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: 03/03/2023] [Revised: 08/18/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
The human brain is a complex organ comprised of distinct cell types, and the contribution of the 3D genome to lineage specific gene expression remains poorly understood. To decipher cell type specific genome architecture, and characterize fine scale changes in the chromatin interactome across neural development, we compared the 3D genome of the human fetal cortical plate to that of neurons and glia isolated from the adult prefrontal cortex. We found that neurons have weaker genome compartmentalization compared to glia, but stronger TADs, which emerge during fetal development. Furthermore, relative to glia, the neuronal genome shifts more strongly towards repressive compartments. Neurons have differential TAD boundaries that are proximal to active promoters involved in neurodevelopmental processes. CRISPRi on CNTNAP2 in hIPSC-derived neurons reveals that transcriptional inactivation correlates with loss of insulation at the differential boundary. Finally, re-wiring of chromatin loops during neural development is associated with transcriptional and functional changes. Importantly, differential loops in the fetal cortex are associated with autism GWAS loci, suggesting a neuropsychiatric disease mechanism affecting the chromatin interactome. Furthermore, neural development involves gaining enhancer-promoter loops that upregulate genes that control synaptic activity. Altogether, our study provides multi-scale insights on the 3D genome in the human brain.
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Affiliation(s)
- Samir Rahman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pasha Apontes
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Michael B Fernando
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Roman Kosoy
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla G Townsley
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kiran Girdhar
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhiping Shao
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth Misir
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nadia Tsankova
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven P Kleopoulos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
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50
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Vemuri K, Kumar S, Chen L, Verzi MP. Dynamic RNA Polymerase II Recruitment Drives Differentiation of the Intestine under the direction of HNF4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566322. [PMID: 37986803 PMCID: PMC10659318 DOI: 10.1101/2023.11.08.566322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Terminal differentiation requires a massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identified dynamic recruitment of RNA Polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II recruitment and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of- function, ChIP-seq and IP mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II recruitment at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms which drive differentiation gene expression and find pause-release of Pol II and post- transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in a renewing adult tissue.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Sneha Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA
- NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI Piscataway, NJ 08854, USA
- Lead Contact
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