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Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV, Xiao Y. Cooltools: Enabling high-resolution Hi-C analysis in Python. PLoS Comput Biol 2024; 20:e1012067. [PMID: 38709825 DOI: 10.1371/journal.pcbi.1012067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
Chromosome conformation capture (3C) technologies reveal the incredible complexity of genome organization. Maps of increasing size, depth, and resolution are now used to probe genome architecture across cell states, types, and organisms. Larger datasets add challenges at each step of computational analysis, from storage and memory constraints to researchers' time; however, analysis tools that meet these increased resource demands have not kept pace. Furthermore, existing tools offer limited support for customizing analysis for specific use cases or new biology. Here we introduce cooltools (https://github.com/open2c/cooltools), a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface (CLI) and Python application programming interface (API), which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments. In short, cooltools enables the effective use of the latest and largest genome folding datasets.
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Affiliation(s)
- Nezar Abdennur
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sameer Abraham
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Geoffrey Fudenberg
- Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, California, United States of America
| | - Ilya M Flyamer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Aleksandra A Galitsyna
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Betul A Oksuz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Yao Xiao
- Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, California, United States of America
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2
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Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pucekova N, Abad MA, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. bioRxiv 2024:2024.04.18.590027. [PMID: 38659940 PMCID: PMC11042376 DOI: 10.1101/2024.04.18.590027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During mitosis, interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics and polymer modeling, we determine how the activity and interplay between loop-extruding SMC motors accomplishes this dramatic transition. Our work reveals rules of engagement for SMC complexes that are critical for allowing cells to refold interphase chromatin into mitotic chromosomes. We find that condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. In contrast, condensin bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion while separating the sisters. Studies of mitotic chromosomes formed by cohesin, condensin II and condensin I alone or in combination allow us to develop new models of mitotic chromosome conformation. In these models, loops are consecutive and not overlapping, implying that condensins do not freely pass one another but stall upon encountering each other. The dynamics of Hi-C interactions and chromosome morphology reveal that during prophase loops are extruded in vivo at ~1-3 kb/sec by condensins as they form a disordered discontinuous helical scaffold within individual chromatids.
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3
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Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev S. Bioframe: operations on genomic intervals in Pandas dataframes. Bioinformatics 2024; 40:btae088. [PMID: 38402507 PMCID: PMC10903647 DOI: 10.1093/bioinformatics/btae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/05/2024] [Accepted: 02/22/2024] [Indexed: 02/26/2024] Open
Abstract
MOTIVATION Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants. Operations on genomic intervals provide a language for asking questions about relationships between features. While there are excellent interval arithmetic tools for the command line, they are not smoothly integrated into Python, one of the most popular general-purpose computational and visualization environments. RESULTS Bioframe is a library to enable flexible and performant operations on genomic interval dataframes in Python. Bioframe extends the Python data science stack to use cases for computational genome biology by building directly on top of two of the most commonly-used Python libraries, NumPy and Pandas. The bioframe API enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions, a common scourge for bioinformaticians. Bioframe achieves these goals while maintaining high performance and a rich set of features. AVAILABILITY AND IMPLEMENTATION Bioframe is open-source under MIT license, cross-platform, and can be installed from the Python Package Index. The source code is maintained by Open2C on GitHub at https://github.com/open2c/bioframe.
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Affiliation(s)
| | - Nezar Abdennur
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, United States
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA 01605, United States
| | - Geoffrey Fudenberg
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, United States
| | - Ilya M Flyamer
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Aleksandra A Galitsyna
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Sergey Venev
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA 01605, United States
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4
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Corsi F, Rusch E, Goloborodko A. Loop extrusion rules: the next generation. Curr Opin Genet Dev 2023; 81:102061. [PMID: 37354885 DOI: 10.1016/j.gde.2023.102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 06/26/2023]
Abstract
The interphase genome of vertebrates contains roughly 100 000 dynamic loops formed by cohesins. These loops are thought to play important roles in many functions, but their exact contribution in each case remains hotly disputed. The key challenge in studying these loops is the lack of a single experimental technique that could reliably and comprehensively visualize their locations and dynamics. Yet, we can infer them using theoretical models that integrate complementary experimental observations. Modeling proved instrumental in showing that cohesins form loops via extrusion. The loop extrusion model made numerous successful qualitative and quantitative predictions and inspired many experiments. However, it also demonstrated limited accuracy in predicting contact maps. Recent research suggests that the original model did not fully account for the intricate details of the mechanism of loop extrusion and its complex regulation. Here, we review the progress in visualizing extrusion and characterizing the cohesin cofactors. These discoveries can be summarized as 'rules' of cohesin movement along chromosomes and incorporated into the next generation of models. Such improved models will enable more accurate inferences of positions and dynamics of cohesin loops and generate better predictions for designing experiments.
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Affiliation(s)
- Flavia Corsi
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria. https://twitter.com/@flavia_corsi
| | - Emma Rusch
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria. https://twitter.com/@emma__rush
| | - Anton Goloborodko
- Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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5
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Hill L, Wutz G, Jaritz M, Tagoh H, Calderón L, Peters JM, Goloborodko A, Busslinger M. Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells. Nat Commun 2023; 14:2316. [PMID: 37085514 PMCID: PMC10121685 DOI: 10.1038/s41467-023-37994-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
Extended loop extrusion across the immunoglobulin heavy-chain (Igh) locus facilitates VH-DJH recombination following downregulation of the cohesin-release factor Wapl by Pax5, resulting in global changes in the chromosomal architecture of pro-B cells. Here, we demonstrate that chromatin looping and VK-JK recombination at the Igk locus were insensitive to Wapl upregulation in pre-B cells. Notably, the Wapl protein was expressed at a 2.2-fold higher level in pre-B cells compared with pro-B cells, which resulted in a distinct chromosomal architecture with normal loop sizes in pre-B cells. High-resolution chromosomal contact analysis of the Igk locus identified multiple internal loops, which likely juxtapose VK and JK elements to facilitate VK-JK recombination. The higher Wapl expression in Igμ-transgenic pre-B cells prevented extended loop extrusion at the Igh locus, leading to recombination of only the 6 most 3' proximal VH genes and likely to allelic exclusion of all other VH genes in pre-B cells. These results suggest that pro-B and pre-B cells with their distinct chromosomal architectures use different chromatin folding principles for V gene recombination, thereby enabling allelic exclusion at the Igh locus, when the Igk locus is recombined.
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Affiliation(s)
- Louisa Hill
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Hiromi Tagoh
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Lesly Calderón
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, A-1030, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, A-1030, Vienna, Austria.
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6
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Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV. Pairtools: from sequencing data to chromosome contacts. bioRxiv 2023:2023.02.13.528389. [PMID: 36824968 PMCID: PMC9949071 DOI: 10.1101/2023.02.13.528389] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present pairtools - a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. Pairtools provides both crucial core tools as well as auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarking pairtools against popular 3C+ data pipelines shows advantages of pairtools for high-performance and flexible 3C+ analysis. Finally, pairtools provides protocol-specific tools for multi-way contacts, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makes pairtools a versatile foundation for a broad range of 3C+ pipelines.
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Affiliation(s)
- Open2C
- https://open2c.github.io/
| | - Nezar Abdennur
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, MA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Geoffrey Fudenberg
- Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, CA, USA
| | - Ilya M. Flyamer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Aleksandra A. Galitsyna
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Maxim Imakaev
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
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7
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Mitter M, Gasser C, Takacs Z, Langer CCH, Tang W, Jessberger G, Beales CT, Neuner E, Ameres SL, Peters JM, Goloborodko A, Micura R, Gerlich DW. Conformation of sister chromatids in the replicated human genome. Nature 2020; 586:139-144. [PMID: 32968280 PMCID: PMC7116725 DOI: 10.1038/s41586-020-2744-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
The three-dimensional organization of the genome supports regulated gene expression, recombination, DNA repair, and chromosome segregation during mitosis. Chromosome conformation capture (Hi-C)1,2 analysis has revealed a complex genomic landscape of internal chromosomal structures in vertebrate cells3-7, but the identical sequence of sister chromatids has made it difficult to determine how they topologically interact in replicated chromosomes. Here we describe sister-chromatid-sensitive Hi-C (scsHi-C), which is based on labelling of nascent DNA with 4-thio-thymidine and nucleoside conversion chemistry. Genome-wide conformation maps of human chromosomes reveal that sister-chromatid pairs interact most frequently at the boundaries of topologically associating domains (TADs). Continuous loading of a dynamic cohesin pool separates sister-chromatid pairs inside TADs and is required to focus sister-chromatid contacts at TAD boundaries. We identified a subset of TADs that are overall highly paired and are characterized by facultative heterochromatin and insulated topological domains that form separately within individual sister chromatids. The rich pattern of sister-chromatid topologies and our scsHi-C technology will make it possible to investigate how physical interactions between identical DNA molecules contribute to DNA repair, gene expression, chromosome segregation, and potentially other biological processes.
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Affiliation(s)
- Michael Mitter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
| | - Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innsbruck, Austria
| | - Zsuzsanna Takacs
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Christoph C H Langer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Gregor Jessberger
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Charlie T Beales
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Eva Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innsbruck, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Anton Goloborodko
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, Innsbruck, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
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8
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AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT. Highly structured homolog pairing reflects functional organization of the Drosophila genome. Nat Commun 2019; 10:4485. [PMID: 31582763 PMCID: PMC6776532 DOI: 10.1038/s41467-019-12208-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 12/07/2018] [Accepted: 08/27/2019] [Indexed: 01/14/2023] Open
Abstract
Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing, including the disruption of some interaction peaks.
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Affiliation(s)
- Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Anton Goloborodko
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - Ruth B McCole
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Wren Saylor
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Bryan R Lajoie
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
- Illumina, San Diego, CA, USA
| | - Job Dekker
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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9
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Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat Commun 2019; 10:4486. [PMID: 31582744 PMCID: PMC6776651 DOI: 10.1038/s41467-019-12211-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 01/25/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.
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Affiliation(s)
- Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Anton Goloborodko
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Bryan R Lajoie
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
- Illumina, San Diego, CA, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Maxim Imakaev
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
| | - Ruth B McCole
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - Wren Saylor
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric F Joyce
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
| | - T Niroshini Senaratne
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mohammed A Hannan
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Job Dekker
- Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
| | - C-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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10
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Abstract
Chromosome organization poses a remarkable physical problem with many biological consequences: How can molecular interactions between proteins at the nanometer scale organize micron-long chromatinized DNA molecules, insulating or facilitating interactions between specific genomic elements? The mechanism of active loop extrusion holds great promise for explaining interphase and mitotic chromosome folding, yet remains difficult to assay directly. We discuss predictions from our polymer models of loop extrusion with barrier elements and review recent experimental studies that provide strong support for loop extrusion, focusing on perturbations to CTCF and cohesin assayed via Hi-C in interphase. Finally, we discuss a likely molecular mechanism of loop extrusion by structural maintenance of chromosomes complexes.
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Affiliation(s)
- Geoffrey Fudenberg
- Gladstone Institute of Data Science and Technology, University of California, San Francisco, California 94158
| | - Nezar Abdennur
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.,Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Maxim Imakaev
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Anton Goloborodko
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Leonid A Mirny
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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11
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Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. A pathway for mitotic chromosome formation. Science 2018; 359:eaao6135. [PMID: 29348367 PMCID: PMC5924687 DOI: 10.1126/science.aao6135] [Citation(s) in RCA: 401] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/09/2018] [Indexed: 12/23/2022]
Abstract
Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central "spiral staircase" condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of condensin I or II shows that nested loops form by differential action of the two condensins, whereas condensin II is required for helical winding.
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Affiliation(s)
- Johan H Gibcus
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Kumiko Samejima
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Anton Goloborodko
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Itaru Samejima
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Natalia Naumova
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Johannes Nuebler
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems, and Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Linfeng Xie
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA
| | - James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
- Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature 2017; 551:51-56. [PMID: 29094699 PMCID: PMC5687303 DOI: 10.1038/nature24281] [Citation(s) in RCA: 670] [Impact Index Per Article: 95.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 09/19/2017] [Indexed: 01/01/2023]
Abstract
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.
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Affiliation(s)
- Wibke Schwarzer
- Developmental Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
| | - Nezar Abdennur
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Anton Goloborodko
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Aleksandra Pekowska
- Genome Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Yann Loe-Mie
- Institut Pasteur, (Epi)genomics of Animal Development Unit, Developmental and Stem Cell Biology Department. Institut Pasteur. 75015 Paris, France
- CNRS, UMR3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Nuno A Fonseca
- European Bioinformatics Institute. European Molecular Biology Laboratory. Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Wolfgang Huber
- Genome Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Leonid Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts USA
| | - Francois Spitz
- Developmental Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
- Genome Biology Unit. European Molecular Biology Laboratory. 69117 Heidelberg, Germany
- Institut Pasteur, (Epi)genomics of Animal Development Unit, Developmental and Stem Cell Biology Department. Institut Pasteur. 75015 Paris, France
- CNRS, UMR3738, 25 rue du Dr Roux, 75015 Paris, France
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13
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Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nat Cell Biol 2017; 19:1071-1080. [PMID: 28825700 PMCID: PMC5640152 DOI: 10.1038/ncb3594] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/19/2017] [Indexed: 12/26/2022]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion. Polymer simulations demonstrate that this role can be fully accounted for through cis-looping of chromatin. Second, condensin is generally dispensable for compaction along chromosome arms. Instead, it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes.
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MESH Headings
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Structures
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Computer Simulation
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Mitosis
- Models, Genetic
- Models, Molecular
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Nucleic Acid Conformation
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Structure-Activity Relationship
- Cohesins
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Affiliation(s)
| | - Anton Goloborodko
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jon-Matthew Belton
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Catrina Miles
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Miao Yu
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jonathan Baxter
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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Abstract
During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive ∼100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they progressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process.
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Affiliation(s)
- Anton Goloborodko
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - John F Marko
- Department of Molecular Biosciences and Department of Physics and Astronomy, Northwestern University, Evanston, Illinois
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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15
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Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell 2017; 169:930-944.e22. [PMID: 28525758 PMCID: PMC5538188 DOI: 10.1016/j.cell.2017.05.004] [Citation(s) in RCA: 974] [Impact Index Per Article: 139.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 01/17/2023]
Abstract
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.
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Affiliation(s)
- Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Anton Goloborodko
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Johan H Gibcus
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Alec Uebersohn
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
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16
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P.T., Mykhailova E, Matkovska T, Reshetovska N, Goloborodko A. Anxiety-depressive disorders in children: Neurobiological and neurohormonal aspects. Eur Psychiatry 2017. [DOI: 10.1016/j.eurpsy.2017.01.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
ObjectiveThe need for diagnosis and correct classification of depression among children is dictated by its burdeness with age, high risk of recurrence at further stages of child development and propensity to suicidal behavior.Materials and methodsOne hundred and sixty adolescents with ADD were included in our study. The study design comprised: clinicopsychopathological, somatoneurological, psychological and neurohormonal methods.ResultsClustering symptom of anxiety and depression have shown that for children in early puberty is typical more formation of somatic (35.2%), behavioral (21.6%), phobic (21.6%) variants of depression, less-anxiety (13.5%), asthenia (8.1%). For children in puberty – apathetic (30.1%), anxiety (28.9%), dismorfofobic (27.7%), behavioral (13.3%) variants. The proportion of suicidal behavior of depression increases in proportion to age, mainly due to suicidal thoughts, sayings, auto-aggressive behavior. Analysis of the formation conditions of anxiety and depression in children showed a significant correlation of genetic, biological and socio-environmental components.Symptoms of the minimal brain dysfunction (MBD) at an early ontogeny (prognostic value = +4.8), loaded natal period (PV = +4.2), frequent colds in the medical history (PV = 3.7), signs of cerebro-organic failure (PV = +3.8) and obesity as an endocrine disorder (PV = +2.1), sex and age of the manifestation of the first depressive episode in the early stages ontogenesis in boys aged 7 years (PS = +5.3), in girls aged 9 years (PS = +3.9) have been registered among biological risk factors for the ADD formation. Prognostic significance of neurohormonal parameters as regards the risk for ADD formation in adolescents is based on a decreased serotonin level in patients with depressive anxiety (PV = +2.8) and a reduced melatonin level, irrespective of the variant of clinical depression (PV = +2.4).ConclusionDetermination of neurobiological and neurohormonal risk markers for the development of the ADD makes it possible to carry out psychoprophylactic measures.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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P.T., Mykhailova E, Matkovska T, Reshetovska N, Goloborodko A. A technology for providing therapeutic training of children with the anxiety-depressive disorders, comorbid with obesity. Eur Psychiatry 2017. [DOI: 10.1016/j.eurpsy.2017.01.491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background and aimsThe study considers the problem of the anxiety-depressive disorders (ADD) in children with concomitant obesity in the context of the search for effective methods of their correction.Materials and methodsIncluded 64 children at puberty with the anxiety-depressive disorders, comorbid with obesity. Design comprised: clinicopsychopathological, somatoneurological, psychological monitoring (CDRS-R); the Spielberger, “Me and my illness” and “Man in the Rain” projective drawing tests.ResultsThe symptoms of emotional and vegetative tension, depression registered in all studied children.In the developed model of support, the interventions of primary level are aimed on family and closest encirclement of the child (family psychotherapy, psycho-educational programs for children and their parents). Strategies:– stressful situation in the family (practical, psychological support and education of parents);– for relief of depressive and vegetative-anxious symptoms (using art therapy, cognitive behavioral therapy);– for education of patients in the wider context – quality of life, coping, motivation and modification of inappropriate behaviors (modeling of new cognitions).The technology includes the diagnosis of the psychosomatic core of the disease, areas of neurotic fixation of the child with ADD and obesity, correction of emotional homeostasis and cognitive imbalance by activation of the personality individual resources as a result using cognitive-behavioral and art-dynamic therapy, as well as a “Control of eating behavior” training program, and solving certain situational problems by a child with the disease.ConclusionOur method makes the tactics of psychotherapeutic and psycho-educational intervention at an early stage of the disease.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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18
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Goloborodko A, Imakaev M, Marko JF, Mirny L. Compaction and Segregation of Sister Chromatids by Loop-Extruding Enzymes. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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19
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Sawai CM, Babovic S, Upadhaya S, Knapp DJHF, Lavin Y, Lau CM, Goloborodko A, Feng J, Fujisaki J, Ding L, Mirny LA, Merad M, Eaves CJ, Reizis B. Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals. Immunity 2016; 45:597-609. [PMID: 27590115 DOI: 10.1016/j.immuni.2016.08.007] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/14/2016] [Accepted: 06/15/2016] [Indexed: 12/13/2022]
Abstract
Hematopoietic stem cells (HSCs) sustain long-term reconstitution of hematopoiesis in transplantation recipients, yet their role in the endogenous steady-state hematopoiesis remains unclear. In particular, recent studies suggested that HSCs provide a relatively minor contribution to immune cell development in adults. We directed transgene expression in a fraction of HSCs that maintained reconstituting activity during serial transplantations. Inducible genetic labeling showed that transgene-expressing HSCs gave rise to other phenotypic HSCs, confirming their top position in the differentiation hierarchy. The labeled HSCs rapidly contributed to committed progenitors of all lineages and to mature myeloid cells and lymphocytes, but not to B-1a cells or tissue macrophages. Importantly, labeled HSCs gave rise to more than two-thirds of all myeloid cells and platelets in adult mice, and this contribution could be accelerated by an induced interferon response. Thus, classically defined HSCs maintain immune cell development in the steady state and during systemic cytokine responses.
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Affiliation(s)
- Catherine M Sawai
- Department of Pathology, New York University Langone Medical Center, New York, NY 10016, USA.
| | - Sonja Babovic
- Terry Fox Laboratory, British Columbia Cancer Agency and University of British Columbia, Vancouver, BC V5Z 4E6, Canada
| | - Samik Upadhaya
- Department of Pathology, New York University Langone Medical Center, New York, NY 10016, USA; Graduate Program in Pathobiology and Molecular Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - David J H F Knapp
- Terry Fox Laboratory, British Columbia Cancer Agency and University of British Columbia, Vancouver, BC V5Z 4E6, Canada
| | - Yonit Lavin
- Department of Oncological Science, The Tisch Cancer Institute and The Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Colleen M Lau
- Department of Pathology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Anton Goloborodko
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jue Feng
- Department of Pathology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Joji Fujisaki
- Department of Pediatrics and Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Lei Ding
- Department of Regenerative Medicine and Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Miriam Merad
- Department of Oncological Science, The Tisch Cancer Institute and The Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency and University of British Columbia, Vancouver, BC V5Z 4E6, Canada
| | - Boris Reizis
- Department of Pathology, New York University Langone Medical Center, New York, NY 10016, USA; Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
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20
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Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of Chromosomal Domains by Loop Extrusion. Cell Rep 2016; 15:2038-49. [PMID: 27210764 PMCID: PMC4889513 DOI: 10.1016/j.celrep.2016.04.085] [Citation(s) in RCA: 1124] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/01/2015] [Accepted: 04/20/2016] [Indexed: 12/31/2022] Open
Abstract
Topologically associating domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain unclear. Here, we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. Using polymer simulations, we show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops. Loop extrusion both explains diverse experimental observations-including the preferential orientation of CTCF motifs, enrichments of architectural proteins at TAD boundaries, and boundary deletion experiments-and makes specific predictions for the depletion of CTCF versus cohesin. Finally, loop extrusion has potentially far-ranging consequences for processes such as enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes.
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Affiliation(s)
- Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 01238, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Maxim Imakaev
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Carolyn Lu
- Program for Research in Mathematics, Engineering and Science for High School Students (PRIMES) and Undergraduate Research Opportunities Program (UROP), MIT, Cambridge, MA 02139, USA
| | - Anton Goloborodko
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Nezar Abdennur
- PhD Program in Computational and Systems Biology, MIT, Cambridge, MA 02139, USA
| | - Leonid A Mirny
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 01238, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
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21
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Goloborodko A, Imakaev MV, Marko JF, Mirny L. Compaction and segregation of sister chromatids via active loop extrusion. eLife 2016; 5. [PMID: 27192037 PMCID: PMC4914367 DOI: 10.7554/elife.14864] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [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: 01/31/2016] [Accepted: 05/18/2016] [Indexed: 12/17/2022] Open
Abstract
The mechanism by which chromatids and chromosomes are segregated during mitosis and meiosis is a major puzzle of biology and biophysics. Using polymer simulations of chromosome dynamics, we show that a single mechanism of loop extrusion by condensins can robustly compact, segregate and disentangle chromosomes, arriving at individualized chromatids with morphology observed in vivo. Our model resolves the paradox of topological simplification concomitant with chromosome 'condensation', and explains how enzymes a few nanometers in size are able to control chromosome geometry and topology at micron length scales. We suggest that loop extrusion is a universal mechanism of genome folding that mediates functional interactions during interphase and compacts chromosomes during mitosis. DOI:http://dx.doi.org/10.7554/eLife.14864.001
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Affiliation(s)
- Anton Goloborodko
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Department of Physics and Astronomy, Northwestern University, Evanston, United States
| | - Leonid Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
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Goloborodko A, Belton JM, Fudenberg G, Imakaev M, Dekker J, Mirny L. S cerevisiae genome as a confined equilibrium polymer brush. Epigenetics Chromatin 2013. [PMCID: PMC3620581 DOI: 10.1186/1756-8935-6-s1-p129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Fudenberg G, Belton JM, Goloborodko A, Imakaev M, Dekker J, Mirny L. Polymer models of yeast S. cerevisiae genome organization. Epigenetics Chromatin 2013. [PMCID: PMC3620572 DOI: 10.1186/1756-8935-6-s1-p128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Goloborodko A, Fudenberg G, Belton JM, Imakaev M, Dekker J, Mirny L. Polymer Models of Yeast S. Cerevisiae Genome Organization. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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