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Portillo-Ledesma S, Li Z, Schlick T. Genome modeling: From chromatin fibers to genes. Curr Opin Struct Biol 2023; 78:102506. [PMID: 36577295 PMCID: PMC9908845 DOI: 10.1016/j.sbi.2022.102506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 11/06/2022] [Indexed: 12/27/2022]
Abstract
The intricacies of the 3D hierarchical organization of the genome have been approached by many creative modeling studies. The specific model/simulation technique combination defines and restricts the system and phenomena that can be investigated. We present the latest modeling developments and studies of the genome, involving models ranging from nucleosome systems and small polynucleosome arrays to chromatin fibers in the kb-range, chromosomes, and whole genomes, while emphasizing gene folding from first principles. Clever combinations allow the exploration of many interesting phenomena involved in gene regulation, such as nucleosome structure and dynamics, nucleosome-nucleosome stacking, polynucleosome array folding, protein regulation of chromatin architecture, mechanisms of gene folding, loop formation, compartmentalization, and structural transitions at the chromosome and genome levels. Gene-level modeling with full details on nucleosome positions, epigenetic factors, and protein binding, in particular, can in principle be scaled up to model chromosomes and cells to study fundamental biological regulation.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Zilong Li
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, 10012, NY, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200122, China; Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, 10003, NY, USA.
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2
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Davis O. Abnormal Chromatin Folding in the Molecular Pathogenesis of Epilepsy and Autism Spectrum Disorder: a Meta-synthesis with Systematic Searching. Mol Neurobiol 2023; 60:768-779. [PMID: 36367658 PMCID: PMC9849311 DOI: 10.1007/s12035-022-03106-9] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
How DNA is folded and packaged in nucleosomes is an essential regulator of gene expression. Abnormal patterns of chromatin folding are implicated in a wide range of diseases and disorders, including epilepsy and autism spectrum disorder (ASD). These disorders are thought to have a shared pathogenesis involving an imbalance in the number of excitatory-inhibitory neurons formed during neurodevelopment; however, the underlying pathological mechanism behind this imbalance is poorly understood. Studies are increasingly implicating abnormal chromatin folding in neural stem cells as one of the candidate pathological mechanisms, but no review has yet attempted to summarise the knowledge in this field. This meta-synthesis is a systematic search of all the articles on epilepsy, ASD, and chromatin folding. Its two main objectives were to determine to what extent abnormal chromatin folding is implicated in the pathogenesis of epilepsy and ASD, and secondly how abnormal chromatin folding leads to pathological disease processes. This search produced 22 relevant articles, which together strongly implicate abnormal chromatin folding in the pathogenesis of epilepsy and ASD. A range of mutations and chromosomal structural abnormalities lead to this effect, including single nucleotide polymorphisms, copy number variants, translocations and mutations in chromatin modifying. However, knowledge is much more limited into how abnormal chromatin organisation subsequently causes pathological disease processes, not yet showing, for example, whether it leads to abnormal excitation-inhibitory neuron imbalance in human brain organoids.
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Affiliation(s)
- Oliver Davis
- grid.5335.00000000121885934Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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Sengupta K, Denkiewicz M, Chiliński M, Szczepińska T, Mollah AF, Korsak S, D'Souza R, Ruan Y, Plewczynski D. Multi-scale phase separation by explosive percolation with single-chromatin loop resolution. Comput Struct Biotechnol J 2022; 20:3591-3603. [PMID: 35860407 PMCID: PMC9283880 DOI: 10.1016/j.csbj.2022.06.063] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022] Open
Abstract
The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber. This folding leads to the formation of such hierarchical structures as: chromosomal territories, compartments; densely-packed genomic regions known as Topologically Associating Domains (TADs), or Chromatin Contact Domains (CCDs), and loops. We propose models of dynamical human genome folding into hierarchical components in human lymphoblastoid, stem cell, and fibroblast cell lines. Our models are based on explosive percolation theory. The chromosomes are modeled as graphs where CTCF chromatin loops are represented as edges. The folding trajectory is simulated by gradually introducing loops to the graph following various edge addition strategies that are based on topological network properties, chromatin loop frequencies, compartmentalization, or epigenomic features. Finally, we propose the genome folding model - a biophysical pseudo-time process guided by a single scalar order parameter. The parameter is calculated by Linear Discriminant Analysis of chromatin features. We also include dynamics of loop formation by using Loop Extrusion Model (LEM) while adding them to the system. The chromatin phase separation, where fiber folds in 3D space into topological domains and compartments, is observed when the critical number of contacts is reached. We also observe that at least 80% of the loops are needed for chromatin fiber to condense in 3D space, and this is constant through various cell lines. Overall, our in-silico model integrates the high-throughput 3D genome interaction experimental data with the novel theoretical concept of phase separation, which allows us to model event-based time dynamics of chromatin loop formation and folding trajectories.
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Affiliation(s)
- Kaustav Sengupta
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Michał Denkiewicz
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Mateusz Chiliński
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Teresa Szczepińska
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Centre for Advanced Materials and Technologies, Warsaw University of Technology, Warsaw, Poland
| | - Ayatullah Faruk Mollah
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Department of Computer Science and Engineering, Aliah University, Kolkata, West Bengal, India
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Raissa D'Souza
- Department of Computer Science, University of California, Davis, USA
- The Santa Fe Institute, Santa Fe, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, USA
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Department of Computer Science, University of California, Davis, USA
- The Jackson Laboratory for Genomic Medicine, USA
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4
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Srinivasan D, Shisode T, Shrinet J, Fraser P. Chromosome organization through the cell cycle at a glance. J Cell Sci 2022; 135:275498. [PMID: 35608019 DOI: 10.1242/jcs.244004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome organization and the three-dimensional folding of chromosomes are now seen as major contributors to nearly all nuclear functions including gene regulation, replication and repair. Recent studies have shown that in addition to the dramatic metamorphoses in chromosome conformation associated with entry to, and exit from mitosis, chromosomes undergo continual conformational changes throughout interphase with differential dynamics in loop structure, topological domains, compartments and lamina-associated domains. Understanding and accounting for these cell-cycle-dependent conformational changes is essential for the interpretation of data from a growing array of powerful molecular techniques to investigate genome conformation function, and to identify the molecules and mechanisms that drive chromosome conformational changes. In this Cell Science at a Glance article and the accompanying poster, we review Hi-C and microscopy studies describing cell-cycle-dependent conformational changes in chromosome structure.
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Affiliation(s)
- Divyaa Srinivasan
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Tarak Shisode
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
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Abstract
Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation digestion, ligation…) to detect pairs of genomic positions in close proximity. The most common way to represent these data is a matrix, or contact map, which allows visualizing the different chromatin structures (compartments, loops, etc.) that can be associated to other signals such as transcription, protein occupancy, etc. as well as, in some instances, to biological functions.In this chapter we present and discuss the filtering of the events recovered in proximity ligation experiments as well as the application of the balancing normalization procedure on the resulting contact map. We also describe a computational tool for visualizing normalized contact data dubbed Scalogram.The different processes described here are illustrated and supported by the laboratory custom-made scripts pooled into "hicstuff," an open-access python package accessible on github ( https://github.com/koszullab/hicstuff ).
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Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Shogofa Mortaza
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Pierrick Moreau
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Axel Cournac
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France.
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Cheng Y, Liu M, Hu M, Wang S. TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations. Genome Biol 2021; 22:309. [PMID: 34749781 PMCID: PMC8574027 DOI: 10.1186/s13059-021-02523-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains. RESULTS Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. CONCLUSIONS In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.
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Affiliation(s)
- Yubao Cheng
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
| | - Miao Liu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
| | - Mengwei Hu
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT 06510 USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06510 USA
- Molecular Cell Biology, Genetics and Development Program, Yale University, New Haven, CT 06510 USA
- Biochemistry, Quantitative Biology, Biophysics and Structural Biology Program, Yale University, New Haven, CT 06510 USA
- M.D.-Ph.D. Program, Yale University, New Haven, CT 06510 USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT 06510 USA
- Yale Liver Center, Yale University School of Medicine, New Haven, CT 06510 USA
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7
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Golov AK, Golova AV, Gavrilov AA, Razin SV. Sensitivity of cohesin-chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion. Epigenetics Chromatin 2021; 14:36. [PMID: 34321070 PMCID: PMC8320178 DOI: 10.1186/s13072-021-00411-w] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/19/2021] [Indexed: 12/18/2022] Open
Abstract
Cohesin is a key organizer of chromatin folding in eukaryotic cells. The two main activities of this ring-shaped protein complex are the maintenance of sister chromatid cohesion and the establishment of long-range DNA-DNA interactions through the process of loop extrusion. Although the basic principles of both cohesion and loop extrusion have been described, we still do not understand several crucial mechanistic details. One of such unresolved issues is the question of whether a cohesin ring topologically embraces DNA string(s) during loop extrusion. Here, we show that cohesin complexes residing on CTCF-occupied genomic sites in mammalian cells do not interact with DNA topologically. We assessed the stability of cohesin-dependent loops and cohesin association with chromatin in high-ionic-strength conditions in G1-synchronized HeLa cells. We found that increased salt concentration completely displaces cohesin from those genomic regions that correspond to CTCF-defined loop anchors. Unsurprisingly, CTCF-anchored cohesin loops also dissipate in these conditions. Because topologically engaged cohesin is considered to be salt resistant, our data corroborate a non-topological model of loop extrusion. We also propose a model of cohesin activity throughout the interphase, which essentially equates the termination of non-topological loop extrusion with topological loading of cohesin. This theoretical framework enables a parsimonious explanation of various seemingly contradictory experimental findings.
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Affiliation(s)
- Arkadiy K. Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Mental Health Research Center, Moscow, Russia
| | - Anastasia V. Golova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey A. Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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Perez-Rathke A, Sun Q, Wang B, Boeva V, Shao Z, Liang J. CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells. Genome Biol 2020; 21:13. [PMID: 31948478 PMCID: PMC6966897 DOI: 10.1186/s13059-019-1904-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore unsuitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, which reconstructs ensembles of single-cell chromatin structures by deconvolving Hi-C data and identifies significant many-body interactions. For a diverse set of highly active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.
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Affiliation(s)
- Alan Perez-Rathke
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL USA
| | - Qiu Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Boshen Wang
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL USA
| | - Valentina Boeva
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris, 75014 France
- Department of Computer Science, ETH Zurich, Zürich, Switzerland
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Liang
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL USA
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Fischer P, Chen H, Pacho F, Rieder D, Kimmel RA, Meyer D. FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation. BMC Biol 2019; 17:61. [PMID: 31362746 PMCID: PMC6664792 DOI: 10.1186/s12915-019-0683-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022] Open
Abstract
Background FoxH1 is a forkhead transcription factor with conserved key functions in vertebrate mesoderm induction and left-right patterning downstream of the TGF-beta/Nodal signaling pathway. Binding of the forkhead domain (FHD) of FoxH1 to a highly conserved proximal sequence motif was shown to regulate target gene expression. Results We identify the conserved microRNA-430 family (miR-430) as a novel target of FoxH1. miR-430 levels are increased in foxH1 mutants, resulting in a reduced expression of transcripts that are targeted by miR-430 for degradation. To determine the underlying mechanism of miR-430 repression, we performed chromatin immunoprecipitation studies and overexpression experiments with mutant as well as constitutive active and repressive forms of FoxH1. Our studies reveal a molecular interaction of FoxH1 with miR-430 loci independent of the FHD. Furthermore, we show that previously described mutant forms of FoxH1 that disrupt DNA binding or that lack the C-terminal Smad Interaction Domain (SID) dominantly interfere with miR-430 repression, but not with the regulation of previously described FoxH1 targets. Conclusions We were able to identify the distinct roles of protein domains of FoxH1 in the regulation process of miR-430. We provide evidence that the indirect repression of miR-430 loci depends on the connection to a distal repressive chromosome environment via a non-canonical mode. The widespread distribution of such non-canonical binding sites of FoxH1, found not only in our study, argues against a function restricted to regulating miR-430 and for a more global role of FoxH1 in chromatin folding. Electronic supplementary material The online version of this article (10.1186/s12915-019-0683-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Fischer
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Hao Chen
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Frederic Pacho
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Dietmar Rieder
- Division of Bioinformatics, Biocenter, Innsbruck Medical University, Innrain 80, 6020, Innsbruck, Austria
| | - Robin A Kimmel
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Dirk Meyer
- Institute of Molecular Biology/CMBI, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
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Perez-Rathke A, Mali S, Du L, Liang J. Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci. IEEE EMBS Int Conf Biomed Health Inform 2019; 2019. [PMID: 34085045 DOI: 10.1109/bhi.2019.8834565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this study, we focus on the following question: do genomic regions enriched in cancer variant mutations have significantly different chromatin folding patterns? We utilize publicly available Hi-C data to characterize chromatin folding patterns in healthy (GM12878) and cancer (K562) cells based on status of A/B compartmentalization and random vs non-random chromatin physical interactions. We then perform statistical testing to assess if chromatin folding patterns in cancer variant-enriched loci are significantly different from non-enriched loci. Our results indicate that loci with cancer variant status have significantly altered (FDR < 0.05) chromatin folding patterns.
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Affiliation(s)
- Alan Perez-Rathke
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Samira Mali
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Lin Du
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jie Liang
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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11
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Farré P, Heurteau A, Cuvier O, Emberly E. Dense neural networks for predicting chromatin conformation. BMC Bioinformatics 2018; 19:372. [PMID: 30314429 DOI: 10.1186/s12859-018-2286-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 04/30/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022] Open
Abstract
Background DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how the DNA will fold given a distribution of bound factors, here viewed as a type of sequence, is currently an unsolved problem and several heterogeneous polymer models have shown that many features of the measured structure can be reproduced from simulations. However a model that determines the optimal connection between sequence and structure and that can rapidly assess the effects of varying either one is still lacking. Results Here we train a dense neural network to solve for the local folding of chromatin, connecting structure, represented as a contact map, to a sequence of bound chromatin factors. The network includes a convolutional filter that compresses the large number of bound chromatin factors into a single 1D sequence representation that is optimized for predicting structure. We also train a network to solve the inverse problem, namely given only structural information in the form of a contact map, predict the likely sequence of chromatin states that generated it. Conclusions By carrying out sensitivity analysis on both networks, we are able to highlight the importance of chromatin contexts and neighborhoods for regulating long-range contacts, along with critical alterations that affect contact formation. Our analysis shows that the networks have learned physical insights that are informative and intuitive about this complex polymer problem. Electronic supplementary material The online version of this article (10.1186/s12859-018-2286-z) contains supplementary material, which is available to authorized users.
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12
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Kocanova S, Goiffon I, Bystricky K. 3D FISH to analyse gene domain-specific chromatin re-modeling in human cancer cell lines. Methods 2018; 142:3-15. [PMID: 29501423 DOI: 10.1016/j.ymeth.2018.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 09/22/2017] [Revised: 12/19/2017] [Accepted: 02/14/2018] [Indexed: 11/28/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a common technique used to label DNA and/or RNA for detection of a genomic region of interest. However, the technique can be challenging, in particular when applied to single genes in human cancer cells. Here, we provide a step-by-step protocol for analysis of short (35 kb-300 kb) genomic regions in three dimensions (3D). We discuss the experimental design and provide practical considerations for 3D imaging and data analysis to determine chromatin folding. We demonstrate that 3D FISH using BACs (Bacterial Artificial Chromosomes) or fosmids can provide detailed information of the architecture of gene domains. More specifically, we show that mapping of specific chromatin landscapes informs on changes associated with estrogen stimulated gene activity in human breast cancer cell lines.
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Affiliation(s)
- Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
| | - Isabelle Goiffon
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France.
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA, France.
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13
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Abstract
The study of nuclear architecture promises novel insights into genome function and regulation. Hereby, quantitative methods based on chromosome conformation capture (3C) revolutionized the field, as they allow accurate and unbiased characterization of 3D genome organization of genomic regions of interest. The choice of the appropriate 3C derivate is crucial to acquire results suited for a specific research question. Circular 3C (4C) is the method of choice to study the genome-wide 3D architecture of a specific genomic region of interest. Here, I present a robust 4C protocol, established in Arabidopsis thaliana, which can be employed by any experienced molecular biologist and is applicable in various other plant species.
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14
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Abstract
Nuclear organization and higher-order chromosome structure in interphase nuclei are thought to have important effects on fundamental biological processes, including chromosome condensation, replication, and transcription. Until recently, however, nuclear organization could only be analyzed microscopically. The development of chromatin conformation capture (3C)-based techniques now allows a detailed look at chromosomal architecture from the level of individual loci to the entire genome. Here we provide a robust Hi-C protocol, allowing the analysis of nuclear organization in nuclei from different wild-type and mutant plant tissues. This method is quantitative and provides a highly efficient and comprehensive way to study chromatin organization during plant development, in response to different environmental stimuli, and in mutants disrupting a variety of processes, including epigenetic pathways regulating gene expression.
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Abstract
Recent studies have shown that chromosomes in a range of organisms are compartmentalized in different types of chromatin domains. In mammals, chromosomes form compartments that are composed of smaller Topologically Associating Domains (TADs). TADs are thought to represent functional domains of gene regulation but much is still unknown about the mechanisms of their formation and how they exert their regulatory effect on embedded genes. Further, similar domains have been detected in other organisms, including flies, worms, fungi and bacteria. Although in all these cases these domains appear similar as detected by 3C-based methods, their biology appears to be quite distinct with differences in the protein complexes involved in their formation and differences in their internal organization. Here we outline our current understanding of such domains in different organisms and their roles in gene regulation.
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Affiliation(s)
- Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Edith Heard
- Institut Curie, CNRS UMR3215, INSERM U934, 26 Rue d'Ulm, 75248 Paris Cedex 05, France.
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