1
|
Lin X, Zhang B. Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 2024; 12:RP90073. [PMID: 38289342 PMCID: PMC10945522 DOI: 10.7554/elife.90073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
Collapse
Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| |
Collapse
|
2
|
Zhou Y, Petrovic J, Zhao J, Zhang W, Bigdeli A, Zhang Z, Berger SL, Pear WS, Faryabi RB. EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. Mol Cell 2022; 82:1003-1020.e15. [PMID: 35182476 PMCID: PMC8897266 DOI: 10.1016/j.molcel.2022.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/05/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022]
Abstract
Chromatin misfolding has been implicated in cancer pathogenesis; yet, its role in therapy resistance remains unclear. Here, we systematically integrated sequencing and imaging data to examine the spatial and linear chromatin structures in targeted therapy-sensitive and -resistant human T cell acute lymphoblastic leukemia (T-ALL). We found widespread alterations in successive layers of chromatin organization including spatial compartments, contact domain boundaries, and enhancer positioning upon the emergence of targeted therapy resistance. The reorganization of genome folding structures closely coincides with the restructuring of chromatin activity and redistribution of architectural proteins. Mechanistically, the derepression and repositioning of the B-lineage-determining transcription factor EBF1 from the heterochromatic nuclear envelope to the euchromatic interior instructs widespread genome refolding and promotes therapy resistance in leukemic T cells. Together, our findings suggest that lineage-determining transcription factors can instruct changes in genome topology as a driving force for epigenetic adaptations in targeted therapy resistance.
Collapse
Affiliation(s)
- Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jelena Petrovic
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jingru Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wu Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ashkan Bigdeli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zhen Zhang
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| |
Collapse
|
3
|
Abstract
High mobility group proteins (HMGs) are the most abundant nuclear proteins next to histones and are robustly expressed across tissues and organs. HMGs can uniquely bend or bind distorted DNA, and are central to such processes as transcription, recombination, and DNA repair. However, their dynamic association with chromatin renders capturing HMGs on chromosomes challenging. Recent work has changed this and now implicates these factors in spatial genome organization. Here, I revisit older and review recent literature to describe how HMGs rewire spatial chromatin interactions to sustain homeostasis or promote cellular aging. I propose a 'rheostat' model to explain how HMG-box proteins (HMGBs), and to some extent HMG A proteins (HMGAs), may control cellular aging and, likely, cancer progression.
Collapse
Affiliation(s)
- Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany.
| |
Collapse
|
4
|
Tan L, Ma W, Wu H, Zheng Y, Xing D, Chen R, Li X, Daley N, Deisseroth K, Xie XS. Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development. Cell 2021; 184:741-758.e17. [PMID: 33484631 DOI: 10.1016/j.cell.2020.12.032] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/14/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
Both transcription and three-dimensional (3D) architecture of the mammalian genome play critical roles in neurodevelopment and its disorders. However, 3D genome structures of single brain cells have not been solved; little is known about the dynamics of single-cell transcriptome and 3D genome after birth. Here, we generated a transcriptome (3,517 cells) and 3D genome (3,646 cells) atlas of the developing mouse cortex and hippocampus by using our high-resolution multiple annealing and looping-based amplification cycles for digital transcriptomics (MALBAC-DT) and diploid chromatin conformation capture (Dip-C) methods and developing multi-omic analysis pipelines. In adults, 3D genome "structure types" delineate all major cell types, with high correlation between chromatin A/B compartments and gene expression. During development, both transcriptome and 3D genome are extensively transformed in the first post-natal month. In neurons, 3D genome is rewired across scales, correlated with gene expression modules, and independent of sensory experience. Finally, we examine allele-specific structure of imprinted genes, revealing local and chromosome (chr)-wide differences. These findings uncover an unknown dimension of neurodevelopment.
Collapse
Affiliation(s)
- Longzhi Tan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Wenping Ma
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Honggui Wu
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Yinghui Zheng
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
| | - Dong Xing
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China
| | - Ritchie Chen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Xiang Li
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nicholas Daley
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Belmont Hill School, Belmont, MA 02478, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - X Sunney Xie
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China.
| |
Collapse
|
5
|
Abstract
Correct 3D genome organization is essential for the proper functioning of the genome. Recent advances in image-based 3D genomics techniques have enabled direct tracing of chromatin folding and multiplexed imaging of nucleome architectures in single cells of several important biological systems. Here, we discuss these advances and the future directions of image-based 3D genomics.
Collapse
Affiliation(s)
- Mengwei Hu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Siyuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA; Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA; Biochemistry, Quantitative Biology, Biophysics, and Structural Biology Program, Yale University, New Haven, CT, USA; MD-PhD Program, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
6
|
Übelmesser N, Papantonis A. Technologies to study spatial genome organization: beyond 3C. Brief Funct Genomics 2020; 18:395-401. [PMID: 31609405 DOI: 10.1093/bfgp/elz019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/27/2019] [Accepted: 07/15/2019] [Indexed: 01/05/2023] Open
Abstract
The way that chromatin is organized in three-dimensional nuclear space is now acknowledged as a factor critical for the major cell processes, like transcription, replication and cell division. Researchers have been armed with new molecular and imaging technologies to study this structure-to-function link of genomes, spearheaded by the introduction of the 'chromosome conformation capture' technology more than a decade ago. However, this technology is not without shortcomings, and novel variants and orthogonal approaches are being developed to overcome these. As a result, the field of nuclear organization is constantly fueled by methods of increasing resolution and/or throughput that strive to eliminate systematic biases and increase precision. In this review, we attempt to highlight the most recent advances in technology that promise to provide novel insights on how chromosomes fold and function.
Collapse
Affiliation(s)
- Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| |
Collapse
|
7
|
Muir KW, Li Y, Weis F, Panne D. The structure of the cohesin ATPase elucidates the mechanism of SMC-kleisin ring opening. Nat Struct Mol Biol 2020; 27:233-239. [PMID: 32066964 PMCID: PMC7100847 DOI: 10.1038/s41594-020-0379-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 01/13/2020] [Indexed: 01/26/2023]
Abstract
Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring-shaped complex that can topologically engage chromatin to regulate chromatin structure. Release from chromatin involves opening of the ring at the Smc3-Scc1 interface in a reaction that is controlled by acetylation and engagement of the Smc ATPase head domains. To understand the underlying molecular mechanisms, we have determined the 3.2-Å resolution cryo-electron microscopy structure of the ATPγS-bound, heterotrimeric cohesin ATPase head module and the 2.1-Å resolution crystal structure of a nucleotide-free Smc1-Scc1 subcomplex from Saccharomyces cerevisiae and Chaetomium thermophilium. We found that ATP-binding and Smc1-Smc3 heterodimerization promote conformational changes within the ATPase that are transmitted to the Smc coiled-coil domains. Remodeling of the coiled-coil domain of Smc3 abrogates the binding surface for Scc1, thus leading to ring opening at the Smc3-Scc1 interface.
Collapse
Affiliation(s)
- Kyle W Muir
- European Molecular Biology Laboratory, Grenoble, France.
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Yan Li
- European Molecular Biology Laboratory, Grenoble, France
| | - Felix Weis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France.
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK.
| |
Collapse
|
8
|
Abstract
Gene expression is orchestrated at the structural level by nucleosome positioning, histone tail acetylation, and linker histone (LH) binding. Here, we integrate available data on nucleosome positioning, nucleosome-free regions (NFRs), acetylation islands, and LH binding sites to "fold" in silico the 55-kb HOXC gene cluster and investigate the role of each feature on the gene's folding. The gene cluster spontaneously forms a dynamic connection hub, characterized by hierarchical loops which accommodate multiple contacts simultaneously and decrease the average distance between promoters by ∼100 nm. Contact probability matrices exhibit "stripes" near promoter regions, a feature associated with transcriptional regulation. Interestingly, while LH proteins alone decrease long-range contacts and acetylation alone increases transient contacts, combined LH and acetylation produce long-range contacts. Thus, our work emphasizes how chromatin architecture is coordinated strongly by epigenetic factors and opens the way for nucleosome resolution models incorporating epigenetic modifications to understand and predict gene activity.
Collapse
|
9
|
Abstract
Polycomb proteins are well-known epigenetic repressors with unexplained roles in chromatin folding. In this issue of Molecular Cell, Kundu et al. (2017) investigate the structures of PRC1-mediated domains in stem cells and probe their changes upon differentiation and in PRC knockouts.
Collapse
Affiliation(s)
- Elena Torlai Triglia
- Epigenetic Regulation and Chromatin Architecture, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Tiago Rito
- Epigenetic Regulation and Chromatin Architecture, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany.
| |
Collapse
|
10
|
Abstract
Eukaryotic DNA is packaged into regularly spaced nucleosomes, resembling beads on a string. Each bead contains ∼147 bp wrapped around a core histone octamer. Linker histone (H1) binds to the linker DNA to drive chromatin folding. Micrococcal nuclease (MNase) digestion studies reveal 2 mono-nucleosomal intermediates: the core particle (∼147 bp) and the chromatosome (∼160 bp; a core particle with additional DNA protected by H1). We have recently developed an improved method for mapping nucleosomes, using exonuclease III to remove residual linker (MNase-Exo-seq). (1) We discovered 2 new intermediate particles corresponding to core particles with ∼7 bp of linker protruding from one side (∼154 bp) or both sides (∼161 bp), which are formed in the absence of H1. We propose that these "proto-chromatosomes" are stabilized by core histone-DNA contacts in the linker, ∼7 bp from the nucleosome boundaries. These contacts may determine the topography of the H1 binding site.
Collapse
Affiliation(s)
- Josefina Ocampo
- a Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Feng Cui
- b Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology , Rochester , NY , USA
| | - Victor B Zhurkin
- c National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
| | - David J Clark
- a Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| |
Collapse
|
11
|
Chen Q, Yang R, Korolev N, Liu CF, Nordenskiöld L. Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail-H2A Acidic Patch Interaction. J Mol Biol 2017; 429:2075-2092. [PMID: 28322915 DOI: 10.1016/j.jmb.2017.03.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 01/15/2023]
Abstract
Chromatin folding and dynamics are critically dependent on nucleosome-nucleosome interactions with important contributions from internucleosome binding of the histone H4 N-terminal tail K16-R23 domain to the surface of the H2A/H2B dimer. The H4 Lys16 plays a pivotal role in this regard. Using in vitro reconstituted 12-mer nucleosome arrays, we have investigated the mechanism of the H4 N-terminal tail in maintaining nucleosome-nucleosome stacking and mediating intra- and inter-array chromatin compaction, with emphasis on the role of K16 and the positive charge region, R17-R23. Analytical ultracentrifugation sedimentation velocity experiments and precipitation assays were employed to analyze effects on chromatin folding and self-association, respectively. Effects on chromatin folding caused by various mutations and modifications at position K16 in the H4 histone were studied. Additionally, using charge-quenching mutations, we characterized the importance of the interaction of the residues within the H4 positive charge region R17-R23 with the H2A acidic patch of the adjacent nucleosome. Furthermore, crosslinking experiments were conducted to establish the proximity of the basic tail region to the acidic patch. Our data indicate that the positive charge and length of the side chain of H4 K16 are important for its access to the adjacent nucleosome in the process of nucleosome-nucleosome stacking and array folding. The location and orientation of the H4 R17-R23 domain on the H2A/H2B dimer surface of the neighboring nucleosome core particle (NCP) in the compacted chromatin fiber were established. The dominance of electrostatic interactions in maintaining intra-array interaction was demonstrated.
Collapse
Affiliation(s)
- Qinming Chen
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Renliang Yang
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Chuan Fa Liu
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore.
| |
Collapse
|
12
|
Abstract
Histone modifications alone or in combination are thought to modulate chromatin structure and function; a concept termed histone code. By combining evidence from several studies, we investigated if the histone code can play a role in higher-order folding of chromatin. Firstly using genomic data, we analyzed associations between histone modifications at the nucleosome level. We could dissect the composition of individual nucleosomes into five predicted clusters of histone modifications. Secondly, by assembling the raw reads of histone modifications at various length scales, we noticed that the histone mark relationships that exist at nucleosome level tend to be maintained at the higher orders of chromatin folding. Recently, a high-resolution imaging study showed that histone marks belonging to three of the five predicted clusters show structurally distinct and anti-correlated chromatin domains at the level of chromosomes. This made us think that the histone code can have a significant impact in the overall compaction of DNA: at the level of nucleosomes, at the level of genes, and finally at the level of chromosomes. As a result, in this article, we put forward a theory where the histone code drives not only the functionality but also the higher-order folding and compaction of chromatin.
Collapse
Affiliation(s)
- Kirti Prakash
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - David Fournier
- Faculty of Biology and Center for Computational Sciences, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| |
Collapse
|
13
|
Chung IM, Ketharnathan S, Kim SH, Thiruvengadam M, Rani MK, Rajakumar G. Making Sense of the Tangle: Insights into Chromatin Folding and Gene Regulation. Genes (Basel) 2016; 7:E71. [PMID: 27669308 DOI: 10.3390/genes7100071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/10/2016] [Accepted: 09/07/2016] [Indexed: 01/03/2023] Open
Abstract
Proximity ligation assays such as circularized chromosome conformation capture and high-throughput chromosome capture assays have shed light on the structural organization of the interphase genome. Functional topologically associating domains (TADs) that constitute the building blocks of genomic organization are disrupted and reconstructed during the cell cycle. Epigenetic memory, as well as the sequence of chromosomes, regulate TAD reconstitution. Sub-TAD domains that are invariant across cell types have been identified, and contacts between these domains, rather than looping, are speculated to drive chromatin folding. Replication domains are established simultaneously with TADs during the cell cycle and the two correlate well in terms of characteristic features, such as lamin association and histone modifications. CCCTC-binding factor (CTCF) and cohesin cooperate across different cell types to regulate genes and genome organization. CTCF elements that demarcate TAD boundaries are commonly disrupted in cancer and promote oncogene activation. Chromatin looping facilitates interactions between distant promoters and enhancers, and the resulting enhanceosome complex promotes gene expression. Deciphering the chromatin tangle requires comprehensive integrative analyses of DNA- and protein-dependent factors that regulate genomic organization.
Collapse
|
14
|
Liang J, Cao Y, Gürsoy G, Naveed H, Terebus A, Zhao J. Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells. Crit Rev Biomed Eng 2015; 43:323-46. [PMID: 27480462 PMCID: PMC4976639 DOI: 10.1615/critrevbiomedeng.2016016559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genome sequences provide the overall genetic blueprint of cells, but cells possessing the same genome can exhibit diverse phenotypes. There is a multitude of mechanisms controlling cellular epigenetic states and that dictate the behavior of cells. Among these, networks of interacting molecules, often under stochastic control, depending on the specific wirings of molecular components and the physiological conditions, can have a different landscape of cellular states. In addition, chromosome folding in three-dimensional space provides another important control mechanism for selective activation and repression of gene expression. Fully differentiated cells with different properties grow, divide, and interact through mechanical forces and communicate through signal transduction, resulting in the formation of complex tissue patterns. Developing quantitative models to study these multi-scale phenomena and to identify opportunities for improving human health requires development of theoretical models, algorithms, and computational tools. Here we review recent progress made in these important directions.
Collapse
Affiliation(s)
- Jie Liang
- Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA
| | - Youfang Cao
- Theoretical Biology and Biophysics (T-6) and Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Gamze Gürsoy
- Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA
| | - Hammad Naveed
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Ave. Chicago, Illinois 60637, USA
| | - Anna Terebus
- Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA
| | - Jieling Zhao
- Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, IL, 60612, USA
| |
Collapse
|
15
|
Abstract
We discuss here a series of testable hypotheses concerning the role of chromosome folding into topologically associating domains (TADs). Several lines of evidence suggest that segmental packaging of chromosomal neighborhoods may underlie features of chromatin that span large domains, such as heterochromatin blocks, association with the nuclear lamina and replication timing. By defining which DNA elements preferentially contact each other, the segmentation of chromosomes into TADs may also underlie many properties of long-range transcriptional regulation. Several observations suggest that TADs can indeed provide a structural basis to regulatory landscapes, by controlling enhancer sharing and allocation. We also discuss how TADs may shape the evolution of chromosomes, by causing maintenance of synteny over large chromosomal segments. Finally we suggest a series of experiments to challenge these ideas and provide concrete examples illustrating how they could be practically applied.
Collapse
|
16
|
Abstract
The genetic information is encoded on double-stranded DNA, a long linear polymer chain. Among the central themes of Nucleus will be the advancement of our understanding of how those chains are folded so that they fit into the cell nucleus, and at the same time their information can be read off efficiently. In fact, a quantitative description of the structure of the folded genome is one of the most challenging problems in structural biology, and poses a much more formidable problem than-for instance-the folding of a protein. There are three main reasons for this: first, the genomic DNA is by orders of magnitude the largest biomolecule in the cell; second, it cannot be defined by a single spatial structure because of its flexibility; and third, even if the 'fold' of the genome were more or less defined in any one cell, variations among individual cells may be very large, for the same reasons of flexibility.
Collapse
Affiliation(s)
- Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|