1
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Harris HL, Rowley MJ. Mechanistic drivers of chromatin organization into compartments. Curr Opin Genet Dev 2024; 86:102193. [PMID: 38626581 DOI: 10.1016/j.gde.2024.102193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024]
Abstract
The human genome is not just a simple string of DNA, it is a complex and dynamic entity intricately folded within the cell's nucleus. This three-dimensional organization of chromatin, the combination of DNA and proteins in the nucleus, is crucial for many biological processes and has been prominently studied for its intricate relationship to gene expression. Indeed, the transcriptional machinery does not operate in isolation but interacts intimately with the folded chromatin structure. Techniques for chromatin conformation capture, including genome-wide sequencing approaches, have revealed key organizational features of chromatin, such as the formation of loops by CCCTC-binding factor (CTCF) and the division of loci into chromatin compartments. While much of the recent research and reviews have focused on CTCF loops, we discuss several new revelations that have emerged concerning chromatin compartments, with a particular focus on what is known about mechanistic drivers of compartmentalization. These insights challenge the traditional views of chromatin organization and reveal the complexity behind the formation and maintenance of chromatin compartments.
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Affiliation(s)
- Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA.
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2
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Lebreton J, Colin L, Chatre E, Bernard P. RNAP II antagonizes mitotic chromatin folding and chromosome segregation by condensin. Cell Rep 2024; 43:113901. [PMID: 38446663 DOI: 10.1016/j.celrep.2024.113901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/07/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Condensin shapes mitotic chromosomes by folding chromatin into loops, but whether it does so by DNA-loop extrusion remains speculative. Although loop-extruding cohesin is stalled by transcription, the impact of transcription on condensin, which is enriched at highly expressed genes in many species, remains unclear. Using degrons of Rpb1 or the torpedo nuclease Dhp1XRN2 to either deplete or displace RNAPII on chromatin in fission yeast metaphase cells, we show that RNAPII does not load condensin on DNA. Instead, RNAPII retains condensin in cis and hinders its ability to fold mitotic chromatin and to support chromosome segregation, consistent with the stalling of a loop extruder. Transcription termination by Dhp1 limits such a hindrance. Our results shed light on the integrated functioning of condensin, and we argue that a tight control of transcription underlies mitotic chromosome assembly by loop-extruding condensin.
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Affiliation(s)
- Jérémy Lebreton
- ENS de Lyon, University Lyon, 46 allée d'Italie, 69007 Lyon, France
| | - Léonard Colin
- CNRS Laboratory of Biology and Modelling of the Cell, UMR 5239, ENS de Lyon, 46 allée d'Italie, 69007 Lyon, France
| | - Elodie Chatre
- Lymic-Platim, University Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS UAR3444, Inserm US8, SFR Biosciences, 50 Avenue Tony Garnier, 69007 Lyon, France
| | - Pascal Bernard
- ENS de Lyon, University Lyon, 46 allée d'Italie, 69007 Lyon, France; CNRS Laboratory of Biology and Modelling of the Cell, UMR 5239, ENS de Lyon, 46 allée d'Italie, 69007 Lyon, France.
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3
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Puerto M, Shukla M, Bujosa P, Pérez-Roldán J, Torràs-Llort M, Tamirisa S, Carbonell A, Solé C, Puspo JA, Cummings CT, de Nadal E, Posas F, Azorín F, Rowley MJ. The zinc-finger protein Z4 cooperates with condensin II to regulate somatic chromosome pairing and 3D chromatin organization. Nucleic Acids Res 2024:gkae198. [PMID: 38520405 DOI: 10.1093/nar/gkae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/24/2023] [Revised: 02/16/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
Chromosome pairing constitutes an important level of genome organization, yet the mechanisms that regulate pairing in somatic cells and the impact on 3D chromatin organization are still poorly understood. Here, we address these questions in Drosophila, an organism with robust somatic pairing. In Drosophila, pairing preferentially occurs at loci consisting of numerous architectural protein binding sites (APBSs), suggesting a role of architectural proteins (APs) in pairing regulation. Amongst these, the anti-pairing function of the condensin II subunit CAP-H2 is well established. However, the factors that regulate CAP-H2 localization and action at APBSs remain largely unknown. Here, we identify two factors that control CAP-H2 occupancy at APBSs and, therefore, regulate pairing. We show that Z4, interacts with CAP-H2 and is required for its localization at APBSs. We also show that hyperosmotic cellular stress induces fast and reversible unpairing in a Z4/CAP-H2 dependent manner. Moreover, by combining the opposite effects of Z4 depletion and osmostress, we show that pairing correlates with the strength of intrachromosomal 3D interactions, such as active (A) compartment interactions, intragenic gene-loops, and polycomb (Pc)-mediated chromatin loops. Altogether, our results reveal new players in CAP-H2-mediated pairing regulation and the intimate interplay between inter-chromosomal and intra-chromosomal 3D interactions.
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Affiliation(s)
- Marta Puerto
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mamta Shukla
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paula Bujosa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mònica Torràs-Llort
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Srividya Tamirisa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carme Solé
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Joynob Akter Puspo
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Eulàlia de Nadal
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesc Posas
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
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Calvo-Roitberg E, Carroll CL, Venev SV, Kim G, Mick ST, Dekker J, Fiszbein A, Pai AA. mRNA initiation and termination are spatially coordinated. bioRxiv 2024:2024.01.05.574404. [PMID: 38260419 PMCID: PMC10802295 DOI: 10.1101/2024.01.05.574404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The expression of a precise mRNA transcriptome is crucial for establishing cell identity and function, with dozens of alternative isoforms produced for a single gene sequence. The regulation of mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processing mechanisms across a gene. Decisions involved in mRNA initiation and termination underlie the largest extent of mRNA isoform diversity, but little is known about any relationships between decisions at both ends of mRNA molecules. Here, we systematically profile the joint usage of mRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues and species. Using both short and long read RNA-seq data, we observe that mRNAs preferentially using upstream TSSs also tend to use upstream PASs, and congruently, the usage of downstream sites is similarly paired. This observation suggests that mRNA 5' end choice may directly influence mRNA 3' ends. Our results suggest a novel "Positional Initiation-Termination Axis" (PITA), in which the usage of alternative terminal sites are coupled based on the order in which they appear in the genome. PITA isoforms are more likely to encode alternative protein domains and use conserved sites. PITA is strongly associated with the length of genomic features, such that PITA is enriched in longer genes with more area devoted to regions that regulate alternative 5' or 3' ends. Strikingly, we found that PITA genes are more likely than non-PITA genes to have multiple, overlapping chromatin structural domains related to pairing of ordinally coupled start and end sites. In turn, PITA coupling is also associated with fast RNA Polymerase II (RNAPII) trafficking across these long gene regions. Our findings indicate that a combination of spatial and kinetic mechanisms couple transcription initiation and mRNA 3' end decisions based on ordinal position to define the expression mRNA isoforms.
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Affiliation(s)
| | | | - Sergey V. Venev
- Department of Systems Biology, University Massachusetts Chan Medical School, Worcester, MA
| | - GyeungYun Kim
- Department of Biology, Boston University, Boston, MA
| | | | - Job Dekker
- Department of Systems Biology, University Massachusetts Chan Medical School, Worcester, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Ana Fiszbein
- Department of Biology, Boston University, Boston, MA
- Center for Computing & Data Sciences, Boston University, Boston, MA
| | - Athma A. Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA
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5
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Colin L, Reyes C, Berthezene J, Maestroni L, Modolo L, Toselli E, Chanard N, Schaak S, Cuvier O, Gachet Y, Coulon S, Bernard P, Tournier S. Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase. eLife 2023; 12:RP89812. [PMID: 37988290 PMCID: PMC10662949 DOI: 10.7554/elife.89812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here, we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.
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Affiliation(s)
- Léonard Colin
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Celine Reyes
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Julien Berthezene
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Laetitia Maestroni
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Laurent Modolo
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Esther Toselli
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Nicolas Chanard
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Stephane Schaak
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Olivier Cuvier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Yannick Gachet
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Stephane Coulon
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Pascal Bernard
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Sylvie Tournier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
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6
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Poulet A, Kratkiewicz AJ, Li D, van Wolfswinkel JC. Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy. Sci Adv 2023; 9:eadh4887. [PMID: 37801496 PMCID: PMC10558129 DOI: 10.1126/sciadv.adh4887] [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] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/05/2023] [Indexed: 10/08/2023]
Abstract
Many highly regenerative organisms maintain adult pluripotent stem cells throughout their life, but how the long-term maintenance of pluripotency is accomplished is unclear. To decipher the regulatory logic of adult pluripotent stem cells, we analyzed the chromatin organization of stem cell genes in the planarian Schmidtea mediterranea. We identify a special chromatin state of stem cell genes, which is distinct from that of tissue-specific genes and resembles constitutive genes. Where tissue-specific promoters have detectable transcription factor binding sites, the promoters of stem cell-specific genes instead have sequence features that broadly decrease nucleosome binding affinity. This genic organization makes pluripotency-related gene expression the default state in these cells, which is maintained by the activity of chromatin remodelers ISWI and SNF2 in the stem cells.
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Affiliation(s)
- Axel Poulet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Arcadia J. Kratkiewicz
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Danyan Li
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Josien C. van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Yale Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06511, USA
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7
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Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori. bioRxiv 2023:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [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: 09/26/2023]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and different types of domains, including topologically associated domains (TADs). Yet, most of these concepts derive from analyses of organisms with monocentric chromosomes. Here we describe the 3D genome architecture of an organism with holocentric chromosomes, the silkworm Bombyx mori . At the genome-wide scale, B. mori chromosomes form highly separated territories and lack substantial trans contacts. As described in other eukaryotes, B. mori chromosomes segregate into an active A and an inactive B compartment. Remarkably, we also identify a third compartment, Secluded "S", with a unique contact pattern. Compartment S shows strong enrichment of short-range contacts and depletion of long-range contacts. It hosts a unique combination of genetic and epigenetic features, localizes at the periphery of CTs and shows developmental plasticity. Biophysical modeling shows that formation of such secluded domains requires a new mechanism - a high density of extruded loops within them along with low level of extrusion and compartmentalization of A and B. Together with other evidence of loop extrusion in interphase, this suggests SMC-mediated loop extrusion in this insect. Overall, our analyses highlight the evolutionary plasticity of 3D genome organization driven by a new combination of known processes.
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Senapati S, Irshad IU, Sharma AK, Kumar H. Fundamental insights into the correlation between chromosome configuration and transcription. Phys Biol 2023; 20:051002. [PMID: 37467757 DOI: 10.1088/1478-3975/ace8e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.
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Affiliation(s)
- Swayamshree Senapati
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
| | - Inayat Ullah Irshad
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu 181221, India
| | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
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Piemonte KM, Webb BM, Bobbitt JR, Majmudar PR, Cuellar-Vite L, Bryson BL, Latina NC, Seachrist DD, Keri RA. Disruption of CDK7 signaling leads to catastrophic chromosomal instability coupled with a loss of condensin-mediated chromatin compaction. J Biol Chem 2023; 299:104834. [PMID: 37201585 PMCID: PMC10300262 DOI: 10.1016/j.jbc.2023.104834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/20/2023] Open
Abstract
Chromatin organization is highly dynamic and modulates DNA replication, transcription, and chromosome segregation. Condensin is essential for chromosome assembly during mitosis and meiosis, as well as maintenance of chromosome structure during interphase. While it is well established that sustained condensin expression is necessary to ensure chromosome stability, the mechanisms that control its expression are not yet known. Herein, we report that disruption of cyclin-dependent kinase 7 (CDK7), the core catalytic subunit of CDK-activating kinase, leads to reduced transcription of several condensin subunits, including structural maintenance of chromosomes 2 (SMC2). Live and static microscopy revealed that inhibiting CDK7 signaling prolongs mitosis and induces chromatin bridge formation, DNA double-strand breaks, and abnormal nuclear features, all of which are indicative of mitotic catastrophe and chromosome instability. Affirming the importance of condensin regulation by CDK7, genetic suppression of the expression of SMC2, a core subunit of this complex, phenocopies CDK7 inhibition. Moreover, analysis of genome-wide chromatin conformation using Hi-C revealed that sustained activity of CDK7 is necessary to maintain chromatin sublooping, a function that is ascribed to condensin. Notably, the regulation of condensin subunit gene expression is independent of superenhancers. Together, these studies reveal a new role for CDK7 in sustaining chromatin configuration by ensuring the expression of condensin genes, including SMC2.
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Affiliation(s)
- Katrina M Piemonte
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Bryan M Webb
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jessica R Bobbitt
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Parth R Majmudar
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Leslie Cuellar-Vite
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Benjamin L Bryson
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Nicholas C Latina
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ruth A Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of General Medical Sciences-Oncology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
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10
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Solé M, Pascual Á, Anton E, Blanco J, Sarrate Z. The courtship choreography of homologous chromosomes: timing and mechanisms of DSB-independent pairing. Front Cell Dev Biol 2023; 11:1191156. [PMID: 37377734 PMCID: PMC10291267 DOI: 10.3389/fcell.2023.1191156] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Meiosis involves deep changes in the spatial organisation and interactions of chromosomes enabling the two primary functions of this process: increasing genetic diversity and reducing ploidy level. These two functions are ensured by crucial events such as homologous chromosomal pairing, synapsis, recombination and segregation. In most sexually reproducing eukaryotes, homologous chromosome pairing depends on a set of mechanisms, some of them associated with the repair of DNA double-strand breaks (DSBs) induced at the onset of prophase I, and others that operate before DSBs formation. In this article, we will review various strategies utilised by model organisms for DSB-independent pairing. Specifically, we will focus on mechanisms such as chromosome clustering, nuclear and chromosome movements, as well as the involvement of specific proteins, non-coding RNA, and DNA sequences.
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Affiliation(s)
| | | | | | - Joan Blanco
- *Correspondence: Joan Blanco, ; Zaida Sarrate,
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11
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Harris HL, Gu H, Olshansky M, Wang A, Farabella I, Eliaz Y, Kalluchi A, Krishna A, Jacobs M, Cauer G, Pham M, Rao SSP, Dudchenko O, Omer A, Mohajeri K, Kim S, Nichols MH, Davis ES, Gkountaroulis D, Udupa D, Aiden AP, Corces VG, Phanstiel DH, Noble WS, Nir G, Di Pierro M, Seo JS, Talkowski ME, Aiden EL, Rowley MJ. Chromatin alternates between A and B compartments at kilobase scale for subgenic organization. Nat Commun 2023; 14:3303. [PMID: 37280210 PMCID: PMC10244318 DOI: 10.1038/s41467-023-38429-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 02/02/2023] [Accepted: 04/28/2023] [Indexed: 06/08/2023] Open
Abstract
Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.
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Affiliation(s)
- Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Huiya Gu
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Moshe Olshansky
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Ailun Wang
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BISB), 17 08028, Barcelona, Spain
- Integrative Nuclear Architecture Laboratory, Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Yossi Eliaz
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Akshay Krishna
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mozes Jacobs
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Gesine Cauer
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Melanie Pham
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Olga Dudchenko
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina Omer
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Michael H Nichols
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dimos Gkountaroulis
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Devika Udupa
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Aviva Presser Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - William Stafford Noble
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jeong-Sun Seo
- Macrogen Inc, Seoul, Republic of Korea
- Asian Genome Institute, Seoul National University Bundang Hospital, Gyeonggi-do, Republic of Korea
| | - Michael E Talkowski
- Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
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12
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Puerto M, Shukla M, Bujosa P, Perez-Roldan J, Tamirisa S, Solé C, de Nadal E, Posas F, Azorin F, Rowley MJ. Somatic chromosome pairing has a determinant impact on 3D chromatin organization. bioRxiv 2023:2023.03.29.534693. [PMID: 37034722 PMCID: PMC10081234 DOI: 10.1101/2023.03.29.534693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In the nucleus, chromatin is intricately structured into multiple layers of 3D organization important for genome activity. How distinct layers influence each other is not well understood. In particular, the contribution of chromosome pairing to 3D chromatin organization has been largely neglected. Here, we address this question in Drosophila, an organism that shows robust chromosome pairing in interphasic somatic cells. The extent of chromosome pairing depends on the balance between pairing and anti-pairing factors, with the anti-pairing activity of the CAP-H2 condensin II subunit being the best documented. Here, we identify the zinc-finger protein Z4 as a strong anti-pairer that interacts with and mediates the chromatin binding of CAP-H2. We also report that hyperosmotic cellular stress induces fast and reversible chromosome unpairing that depends on Z4/CAP-H2. And, most important, by combining Z4 depletion and osmostress, we show that chromosome pairing reinforces intrachromosomal 3D interactions. On the one hand, pairing facilitates RNAPII occupancy that correlates with enhanced intragenic gene-loop interactions. In addition, acting at a distance, pairing reinforces chromatin-loop interactions mediated by Polycomb (Pc). In contrast, chromosome pairing does not affect which genomic intervals segregate to active (A) and inactive (B) compartments, with only minimal effects on the strength of A-A compartmental interactions. Altogether, our results unveil the intimate interplay between inter-chromosomal and intra-chromosomal 3D interactions, unraveling the interwoven relationship between different layers of chromatin organization and the essential contribution of chromosome pairing.
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13
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Kabirova E, Nurislamov A, Shadskiy A, Smirnov A, Popov A, Salnikov P, Battulin N, Fishman V. Function and Evolution of the Loop Extrusion Machinery in Animals. Int J Mol Sci 2023; 24:ijms24055017. [PMID: 36902449 PMCID: PMC10003631 DOI: 10.3390/ijms24055017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/07/2023] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes of all cellular organisms. Essential functions of these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances in chromatin biology showed that SMC proteins are involved in many other genomic processes, acting as active motors extruding DNA, which leads to the formation of chromatin loops. Some loops formed by SMC proteins are highly cell type and developmental stage specific, such as SMC-mediated DNA loops required for VDJ recombination in B-cell progenitors, or dosage compensation in Caenorhabditis elegans and X-chromosome inactivation in mice. In this review, we focus on the extrusion-based mechanisms that are common for multiple cell types and species. We will first describe an anatomy of SMC complexes and their accessory proteins. Next, we provide biochemical details of the extrusion process. We follow this by the sections describing the role of SMC complexes in gene regulation, DNA repair, and chromatin topology.
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Affiliation(s)
- Evelyn Kabirova
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Nurislamov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Artem Shadskiy
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander Smirnov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Andrey Popov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Salnikov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Artificial Intelligence Research Institute (AIRI), 121108 Moscow, Russia
- Correspondence:
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14
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Liu K, Li HD, Li Y, Wang J, Wang J. A Comparison of Topologically Associating Domain Callers Based on Hi-C Data. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:15-29. [PMID: 35104223 DOI: 10.1109/tcbb.2022.3147805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Topologically associating domains (TADs) are local chromatin interaction domains, which have been shown to play an important role in gene expression regulation. TADs were originally discovered in the investigation of 3D genome organization based on High-throughput Chromosome Conformation Capture (Hi-C) data. Continuous considerable efforts have been dedicated to developing methods for detecting TADs from Hi-C data. Different computational methods for TADs identification vary in their assumptions and criteria in calling TADs. As a consequence, the TADs called by these methods differ in their similarities and biological features they are enriched in. In this work, we performed a systematic comparison of twenty-six TAD callers. We first compared the TADs and gaps between adjacent TADs across different methods, resolutions, and sequencing depths. We then assessed the quality of TADs and TAD boundaries according to three criteria: the decay of contact frequencies over the genomic distance, enrichment and depletion of regulatory elements around TAD boundaries, and reproducibility of TADs and TAD boundaries in replicate samples. Last, due to the lack of a gold standard of TADs, we also evaluated the performance of the methods on synthetic datasets. We discussed the key principles of TAD callers, and pinpointed current situation in the detection of TADs. We provide a concise, comprehensive, and systematic framework for evaluating the performance of TAD callers, and expect our work will provide useful guidance in choosing suitable approaches for the detection and evaluation of TADs.
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15
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Amankwaa B, Schoborg T, Labrador M. Drosophila insulator proteins exhibit in vivo liquid-liquid phase separation properties. Life Sci Alliance 2022; 5:5/12/e202201536. [PMID: 35853678 PMCID: PMC9297610 DOI: 10.26508/lsa.202201536] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022] Open
Abstract
Drosophila insulator proteins and the cohesin subunit Rad21 coalesce in vivo to form liquid-droplet condensates, suggesting that liquid–liquid phase separation mediates their function in 3D genome organization. Mounting evidence implicates liquid–liquid phase separation (LLPS), the condensation of biomolecules into liquid-like droplets in the formation and dissolution of membraneless intracellular organelles (MLOs). Cells use MLOs or condensates for various biological processes, including emergency signaling and spatiotemporal control over steady-state biochemical reactions and heterochromatin formation. Insulator proteins are architectural elements involved in establishing independent domains of transcriptional activity within eukaryotic genomes. In Drosophila, insulator proteins form nuclear foci known as insulator bodies in response to osmotic stress. However, the mechanism through which insulator proteins assemble into bodies is yet to be investigated. Here, we identify signatures of LLPS by insulator bodies, including high disorder tendency in insulator proteins, scaffold–client–dependent assembly, extensive fusion behavior, sphericity, and sensitivity to 1,6-hexanediol. We also show that the cohesin subunit Rad21 is a component of insulator bodies, adding to the known insulator protein constituents and γH2Av. Our data suggest a concerted role of cohesin and insulator proteins in insulator body formation and under physiological conditions. We propose a mechanism whereby these architectural proteins modulate 3D genome organization through LLPS.
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Affiliation(s)
- Bright Amankwaa
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, USA
| | - Todd Schoborg
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, USA
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, USA
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16
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Valton AL, Venev SV, Mair B, Khokhar ES, Tong AHY, Usaj M, Chan K, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. Nat Struct Mol Biol 2022; 29:1239-1251. [PMID: 36482254 PMCID: PMC10228515 DOI: 10.1038/s41594-022-00890-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 12/13/2021] [Accepted: 11/01/2022] [Indexed: 12/13/2022]
Abstract
Cohesin-mediated loop extrusion has been shown to be blocked at specific cis-elements, including CTCF sites, producing patterns of loops and domain boundaries along chromosomes. Here we explore such cis-elements, and their role in gene regulation. We find that transcription termination sites of active genes form cohesin- and RNA polymerase II-dependent domain boundaries that do not accumulate cohesin. At these sites, cohesin is first stalled and then rapidly unloaded. Start sites of transcriptionally active genes form cohesin-bound boundaries, as shown before, but are cohesin-independent. Together with cohesin loading, possibly at enhancers, these sites create a pattern of cohesin traffic that guides enhancer-promoter interactions. Disrupting this traffic pattern, by removing CTCF, renders cells sensitive to knockout of genes involved in transcription initiation, such as the SAGA complexes, and RNA processing such DEAD/H-Box RNA helicases. Without CTCF, these factors are less efficiently recruited to active promoters.
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Affiliation(s)
- Anne-Laure Valton
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Barbara Mair
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Eraj Shafiq Khokhar
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amy H Y Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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17
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Rubin T, Macaisne N, Vallés AM, Guilleman C, Gaugué I, Dal Toe L, Huynh JR. Premeiotic pairing of homologous chromosomes during Drosophila male meiosis. Proc Natl Acad Sci U S A 2022; 119:e2207660119. [PMID: 36375065 PMCID: PMC9704699 DOI: 10.1073/pnas.2207660119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/07/2022] [Indexed: 11/15/2022] Open
Abstract
In the early stages of meiosis, maternal and paternal chromosomes pair with their homologous partner and recombine to ensure exchange of genetic information and proper segregation. These events can vary drastically between species and between males and females of the same species. In Drosophila, in contrast to females, males do not form synaptonemal complexes (SCs), do not recombine, and have no crossing over; yet, males are able to segregate their chromosomes properly. Here, we investigated the early steps of homolog pairing in Drosophila males. We found that homolog centromeres are not paired in germline stem cells (GSCs) and become paired in the mitotic region before meiotic entry, similarly to females. Surprisingly, male germline cells express SC proteins, which localize to centromeres and promote pairing. We further found that the SUN/KASH (LINC) complex and microtubules are required for homolog pairing as in females. Chromosome movements in males, however, are much slower than in females and we demonstrate that this slow dynamic is compensated in males by having longer cell cycles. In agreement, slowing down cell cycles was sufficient to rescue pairing-defective mutants in female meiosis. Our results demonstrate that although meiosis differs significantly between males and females, sex-specific cell cycle kinetics integrate similar molecular mechanisms to achieve proper centromere pairing.
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Affiliation(s)
- Thomas Rubin
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | | | - Ana Maria Vallés
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | - Clara Guilleman
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | - Isabelle Gaugué
- Department of Genetics and Developmental Biology, CNRS UMR 3215, INSERM U934, Institut Curie, 75005 Paris, France
| | - Laurine Dal Toe
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | - Jean-René Huynh
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
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18
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Lohia R, Fox N, Gillis J. A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships. Genome Biol 2022; 23:238. [PMID: 36352464 DOI: 10.1186/s13059-022-02790-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/21/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin contacts are essential for gene-expression regulation; however, obtaining a high-resolution genome-wide chromatin contact map is still prohibitively expensive owing to large genome sizes and the quadratic scale of pairwise data. Chromosome conformation capture (3C)-based methods such as Hi-C have been extensively used to obtain chromatin contacts. However, since the sparsity of these maps increases with an increase in genomic distance between contacts, long-range or trans-chromatin contacts are especially challenging to sample. RESULTS Here, we create a high-density reference genome-wide chromatin contact map using a meta-analytic approach. We integrate 3600 human, 6700 mouse, and 500 fly Hi-C experiments to create species-specific meta-Hi-C chromatin contact maps with 304 billion, 193 billion, and 19 billion contacts in respective species. We validate that meta-Hi-C contact maps are uniquely powered to capture functional chromatin contacts in both cis and trans. We find that while individual dataset Hi-C networks are largely unable to predict any long-range coexpression (median 0.54 AUC), meta-Hi-C networks perform comparably in both cis and trans (0.65 AUC vs 0.64 AUC). Similarly, for long-range expression quantitative trait loci (eQTL), meta-Hi-C contacts outperform all individual Hi-C experiments, providing an improvement over the conventionally used linear genomic distance-based association. Assessing between species, we find patterns of chromatin contact conservation in both cis and trans and strong associations with coexpression even in species for which Hi-C data is lacking. CONCLUSIONS We have generated an integrated chromatin interaction network which complements a large number of methodological and analytic approaches focused on improved specificity or interpretation. This high-depth "super-experiment" is surprisingly powerful in capturing long-range functional relationships of chromatin interactions, which are now able to predict coexpression, eQTLs, and cross-species relationships. The meta-Hi-C networks are available at https://labshare.cshl.edu/shares/gillislab/resource/HiC/ .
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19
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Chen Z, Chen X. A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos. Genes (Basel) 2022; 13:1864. [PMID: 36292750 DOI: 10.3390/genes13101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/17/2022] [Revised: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022] Open
Abstract
The 3D chromatin structure within the nucleus is important for gene expression regulation and correct developmental programs. Recently, the rapid development of low-input chromatin conformation capture technologies has made it possible to study 3D chromatin structures in gametes, zygotes and early embryos in a variety of species, including flies, vertebrates and mammals. There are distinct 3D chromatin structures within the male and female gametes. Following the fertilization of male and female gametes, fertilized eggs undergo drastic epigenetic reprogramming at multi levels, including the 3D chromatin structure, to convert the terminally differentiated gamete state into the totipotent state, which can give rise to an individual. However, to what extent the 3D chromatin structure reorganization is evolutionarily conserved and what the underlying mechanisms are for the tremendous reorganization in early embryos remain elusive. Here, we review the latest findings on the 3D chromatin structure reorganization during embryogenesis, and discuss the convergent and divergent reprogramming patterns and key molecular mechanisms for the 3D chromatin structure reorganization from gametes to embryos in different species. These findings shed light on how the 3D chromatin structure reorganization contribute to embryo development in different species. The findings also indicate the role of the 3D chromatin structure on the acquisition of totipotent developmental potential.
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20
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Terrone S, Valat J, Fontrodona N, Giraud G, Claude JB, Combe E, Lapendry A, Polvèche H, Ameur LB, Duvermy A, Modolo L, Bernard P, Mortreux F, Auboeuf D, Bourgeois C. RNA helicase-dependent gene looping impacts messenger RNA processing. Nucleic Acids Res 2022; 50:9226-9246. [PMID: 36039747 PMCID: PMC9458439 DOI: 10.1093/nar/gkac717] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022] Open
Abstract
DDX5 and DDX17 are DEAD-box RNA helicase paralogs which regulate several aspects of gene expression, especially transcription and splicing, through incompletely understood mechanisms. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed the large impact of these RNA helicases on splicing and revealed a widespread deregulation of 3' end processing. In silico analyses and experiments in cultured cells showed the binding and functional contribution of the genome organizing factor CTCF to chromatin sites at or near a subset of DDX5/DDX17-dependent exons that are characterized by a high GC content and a high density of RNA Polymerase II. We propose the existence of an RNA helicase-dependent relationship between CTCF and the dynamics of transcription across DNA and/or RNA structured regions, that contributes to the processing of internal and terminal exons. Moreover, local DDX5/DDX17-dependent chromatin loops spatially connect RNA helicase-regulated exons with their cognate promoter, and we provide the first direct evidence that de novo gene looping modifies alternative splicing and polyadenylation. Overall our findings uncover the impact of DDX5/DDX17-dependent chromatin folding on pre-messenger RNA processing.
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Affiliation(s)
| | | | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Jean-Baptiste Claude
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Hélène Polvèche
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France,CECS/AFM, I-STEM, 28 rue Henri Desbruères, F-91100, Corbeil-Essonnes, France
| | - Lamya Ben Ameur
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Arnaud Duvermy
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Laurent Modolo
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Pascal Bernard
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Cyril F Bourgeois
- To whom correspondence should be addressed. Tel: +33 47272 8663; Fax: +33 47272 8674;
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21
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Fleck K, Raj R, Erceg J. The 3D genome landscape: Diverse chromosomal interactions and their functional implications. Front Cell Dev Biol 2022; 10:968145. [PMID: 36036013 PMCID: PMC9402908 DOI: 10.3389/fcell.2022.968145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Genome organization includes contacts both within a single chromosome and between distinct chromosomes. Thus, regulatory organization in the nucleus may include interplay of these two types of chromosomal interactions with genome activity. Emerging advances in omics and single-cell imaging technologies have allowed new insights into chromosomal contacts, including those of homologs and sister chromatids, and their significance to genome function. In this review, we highlight recent studies in this field and discuss their impact on understanding the principles of chromosome organization and associated functional implications in diverse cellular processes. Specifically, we describe the contributions of intra-chromosomal, inter-homolog, and inter-sister chromatid contacts to genome organization and gene expression.
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Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Romir Raj
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States
- *Correspondence: Jelena Erceg,
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22
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Osuntoki IG, Harrison A, Dai H, Bao Y, Zabet NR. ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data. Bioinformatics 2022; 38:3523-3531. [PMID: 35678507 PMCID: PMC9272800 DOI: 10.1093/bioinformatics/btac387] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Motivation Several computational and statistical methods have been developed to analyze data generated through the 3C-based methods, especially the Hi-C. Most of the existing methods do not account for dependency in Hi-C data. Results Here, we present ZipHiC, a novel statistical method to explore Hi-C data focusing on the detection of enriched contacts. ZipHiC implements a Bayesian method based on a hidden Markov random field (HMRF) model and the Approximate Bayesian Computation (ABC) to detect interactions in two-dimensional space based on a Hi-C contact frequency matrix. ZipHiC uses data on the sources of biases related to the contact frequency matrix, allows borrowing information from neighbours using the Potts model and improves computation speed using the ABC model. In addition to outperforming existing tools on both simulated and real data, our model also provides insights into different sources of biases that affects Hi-C data. We show that some datasets display higher biases from DNA accessibility or Transposable Elements content. Furthermore, our analysis in Drosophila melanogaster showed that approximately half of the detected significant interactions connect promoters with other parts of the genome indicating a functional biological role. Finally, we found that the micro-C datasets display higher biases from DNA accessibility compared to a similar Hi-C experiment, but this can be corrected by ZipHiC. Availability and implementation The R scripts are available at https://github.com/igosungithub/HMRFHiC.git. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Itunu G Osuntoki
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom.,Statistics, Modelling and Economics Department, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Hongsheng Dai
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Yanchun Bao
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, United Kingdom
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23
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Shukla V, Cetnarowska A, Hyldahl M, Mandrup S. Interplay between regulatory elements and chromatin topology in cellular lineage determination. Trends Genet 2022. [DOI: 10.1016/j.tig.2022.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
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24
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de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:cells11081368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomes are organized in distinct nuclear areas designated as chromosome territories (CT). The structural formation of CT is a consequence of chromatin packaging and organization that ultimately affects cell function. Chromosome positioning can identify structural signatures of genomic organization, especially for diseases where changes in gene expression contribute to a given phenotype. The study of CT in hematological diseases revealed chromosome position as an important factor for specific chromosome translocations. In this review, we highlight the history of CT theory, current knowledge on possible clinical applications of CT analysis, and the impact of CT in the development of hematological neoplasia such as multiple myeloma, leukemia, and lymphomas. Accumulating data on nuclear architecture in cancer allow one to propose the three-dimensional nuclear genomic landscape as a novel cancer biomarker for the future.
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Affiliation(s)
- Matheus Fabiao de Lima
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Brazil;
| | - Lucas E. L. Terceiro
- Department of Pathology, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
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25
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Abstract
BACKGROUND Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over High-throughput Chromosome Conformation Capture (Hi-C) interaction dataset. Substantial degree of efforts have been devoted to develop techniques for inferring TADs from Hi-C interaction dataset. Many TAD-calling methods have been developed which differ in their criteria and assumptions in TAD inference. Correspondingly, TADs inferred via these callers vary in terms of both similarities and biological features they are enriched in. RESULT We have carried out a systematic comparison of 27 TAD-calling methods over mammals. We use Micro-C, a recent high-resolution variant of Hi-C, to compare TADs at a very high resolution, and classify the methods into 3 categories: feature-based methods, Clustering methods, Graph-partitioning methods. We have evaluated TAD boundaries, gaps between adjacent TADs, and quality of TADs across various criteria. We also found particularly CTCF and Cohesin proteins to be effective in formation of TADs with corner dots. We have also assessed the callers performance on simulated datasets since a gold standard for TADs is missing. TAD sizes and numbers change remarkably between TAD callers and dataset resolutions, indicating that TADs are hierarchically-organized domains, instead of disjoint regions. A core subset of feature-based TAD callers regularly perform the best while inferring reproducible domains, which are also enriched for TAD related biological properties. CONCLUSION We have analyzed the fundamental principles of TAD-calling methods, and identified the existing situation in TAD inference across high resolution Micro-C interaction datasets over mammals. We come up with a systematic, comprehensive, and concise framework to evaluate the TAD-calling methods performance across Micro-C datasets. Our research will be useful in selecting appropriate methods for TAD inference and evaluation based on available data, experimental design, and biological question of interest. We also introduce our analysis as a benchmarking tool with publicly available source code.
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Affiliation(s)
- Emre Sefer
- Department of Computer Science, Ozyegin University, Istanbul, Turkey.
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26
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Lukyanchikova V, Nuriddinov M, Belokopytova P, Taskina A, Liang J, Reijnders MJMF, Ruzzante L, Feron R, Waterhouse RM, Wu Y, Mao C, Tu Z, Sharakhov IV, Fishman V. Anopheles mosquitoes reveal new principles of 3D genome organization in insects. Nat Commun 2022; 13:1960. [PMID: 35413948 DOI: 10.1038/s41467-022-29599-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for ~100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin. Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehensively characterize chromatin architecture and its evolutionary dynamics in five Anopheles species.
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27
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Chathoth KT, Mikheeva LA, Crevel G, Wolfe JC, Hunter I, Beckett-Doyle S, Cotterill S, Dai H, Harrison A, Zabet NR. The role of insulators and transcription in 3D chromatin organization of flies. Genome Res 2022; 32:682-698. [PMID: 35354608 PMCID: PMC8997359 DOI: 10.1101/gr.275809.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/17/2022] [Indexed: 11/25/2022]
Abstract
The DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro, and Dref leads to changes in TAD organization and chromatin loops. Their depletion predominantly affects TAD borders located in regions moderately enriched in repressive modifications and depleted in active ones, whereas TAD borders located in euchromatin are resilient to these knockdowns. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these knockdowns and showed that the majority of differentially expressed genes are located within reorganized TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders in Drosophila and a link between TAD reorganization and subsequent changes in gene expression.
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Affiliation(s)
- Keerthi T Chathoth
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Liudmila A Mikheeva
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom.,Department of Mathematical Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Gilles Crevel
- Department Basic Medical Sciences, St. Georges University London, London SW17 0RE, United Kingdom
| | - Jareth C Wolfe
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom.,School of Computer Science and Electronic Engineering, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Ioni Hunter
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Saskia Beckett-Doyle
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Sue Cotterill
- Department Basic Medical Sciences, St. Georges University London, London SW17 0RE, United Kingdom
| | - Hongsheng Dai
- Department of Mathematical Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
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28
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Ilyin AA, Kononkova AD, Golova AV, Shloma VV, Olenkina O, Nenasheva V, Abramov Y, Kotov AA, Maksimov D, Laktionov P, Pindyurin A, Galitsyna A, Ulianov S, Khrameeva E, Gelfand M, Belyakin S, Razin S, Shevelyov Y. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3203-3225. [PMID: 35166842 PMCID: PMC8989536 DOI: 10.1093/nar/gkac109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/06/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters’ detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.
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Affiliation(s)
| | | | | | | | | | - Valentina V Nenasheva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Yuri A Abramov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Daniil A Maksimov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Petr P Laktionov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina E Khrameeva
- Correspondence may also be addressed to Ekaterina Khrameeva. Tel: +7 495 2801481; Fax: +7 495 2801481;
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Stepan N Belyakin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yuri Y Shevelyov
- To whom correspondence should be addressed. Tel: +7 499 1960809; Fax: +7 499 1960221;
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29
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Jost D. Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. Methods Mol Biol 2022; 2301:293-305. [PMID: 34415542 DOI: 10.1007/978-1-0716-1390-0_15] [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: 01/12/2023]
Abstract
Mechanistic modeling in biology allows to investigate, based on first principles, if putative hypotheses are compatible with observations and to drive further experimental works. Along this line, polymer modeling has been instrumental in 3D genomics to better understand the impact of key mechanisms on the spatial genome organization. Here, I describe how polymer-based models can be practically used to study the role of epigenome in chromosome folding. I illustrate this methodology in the context of Drosophila epigenome folding.
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Affiliation(s)
- Daniel Jost
- University of Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.
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30
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Di Giammartino DC, Polyzos A, Apostolou E. Assessing Specific Networks of Chromatin Interactions with HiChIP. Methods Mol Biol 2022; 2532:113-141. [PMID: 35867248 DOI: 10.1007/978-1-0716-2497-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The introduction of chromosome conformation capture (3C)-based technologies coupled with next-generation sequencing have significantly advanced our understanding of how the genetic material is organized within the eukaryotic nucleus. Three-dimensional (3D) genomic organization occurs at hierarchical levels, ranging from chromosome territories and subnuclear compartments to smaller self-associated domains and fine-scale chromatin interactions. The latter can be further categorized into different subtypes, such as structural or regulatory, based either on their presumed functionality and/or the factors that mediate their formation. Various enrichment strategies coupled with 3C-based technologies have been developed to prospectively isolate and quantify chromatin interactions around regions occupied by specific proteins or marks of interest. These approaches not only enable high-resolution characterization of the selected chromatin contacts at a cost-effective manner, but also offer important biological insights into their organizational principles and regulatory function. In this chapter, we will focus on the recently developed HiChIP technology with an emphasis on the discovery of putative active enhancers and promoter interactions in cell types of interest. We will describe the specific steps for designing, performing and analyzing successful HiChIP experiments as well as important limitations and considerations.
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Affiliation(s)
- Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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31
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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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32
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Salari H, Di Stefano M, Jost D. Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin. Genome Res 2021. [PMID: 34963660 DOI: 10.1101/gr.275827.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022]
Abstract
Chromosome organization and dynamics are involved in regulating many fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical heterogeneities may emerge from the same structural mechanisms. We found that the formation of topologically associating domains (TADs) is a key driver of chromatin motion heterogeneity. In particular, we showed that the local degree of compaction of the TAD regulates the transition from a weakly compact, fluid state of chromatin to a more compact, gel state exhibiting anomalous diffusion and coherent motion. Our work provides a comprehensive study of chromosome dynamics and a unified view of chromatin motion enabling interpretation of the wide variety of dynamical behaviors observed experimentally across different biological conditions, suggesting that the "liquid" or "solid" state of chromatin are in fact two sides of the same coin.
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33
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Roca J, Dyson S, Segura J, Valdés A, Martínez-García B. Keeping intracellular DNA untangled: A new role for condensin? Bioessays 2021; 44:e2100187. [PMID: 34761394 DOI: 10.1002/bies.202100187] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/25/2022]
Abstract
The DNA-passage activity of topoisomerase II accidentally produces DNA knots and interlinks within and between chromatin fibers. Fortunately, these unwanted DNA entanglements are actively removed by some mechanism. Here we present an outline on DNA knot formation and discuss recent studies that have investigated how intracellular DNA knots are removed. First, although topoisomerase II is able to minimize DNA entanglements in vitro to below equilibrium values, it is unclear whether such capacity performs equally in vivo in chromatinized DNA. Second, DNA supercoiling could bias topoisomerase II to untangle the DNA. However, experimental evidence indicates that transcriptional supercoiling of intracellular DNA boosts knot formation. Last, cohesin and condensin could tighten DNA entanglements via DNA loop extrusion (LE) and force their dissolution by topoisomerase II. Recent observations indicate that condensin activity promotes the removal of DNA knots during interphase and mitosis. This activity might facilitate the spatial organization and dynamics of chromatin.
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Affiliation(s)
- Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Silvia Dyson
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Antonio Valdés
- Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Belén Martínez-García
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
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34
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Wolfe JC, Mikheeva LA, Hagras H, Zabet NR. An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila. Genome Biol 2021; 22:308. [PMID: 34749786 PMCID: PMC8574042 DOI: 10.1186/s13059-021-02532-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/30/2020] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can predict the locations of enhancers with a high degree of accuracy, the mechanisms underpinning the activity of enhancers are often unclear. RESULTS Using machine learning (ML) and a rule-based explainable artificial intelligence (XAI) model, we demonstrate that we can predict the location of known enhancers in Drosophila with a high degree of accuracy. Most importantly, we use the rules of the XAI model to provide insight into the underlying combinatorial histone modifications code of enhancers. In addition, we identified a large set of putative enhancers that display the same epigenetic signature as enhancers identified experimentally. These putative enhancers are enriched in nascent transcription, divergent transcription and have 3D contacts with promoters of transcribed genes. However, they display only intermediary enrichment of mediator and cohesin complexes compared to previously characterised active enhancers. We also found that 10-15% of the predicted enhancers display similar characteristics to super enhancers observed in other species. CONCLUSIONS Here, we applied an explainable AI model to predict enhancers with high accuracy. Most importantly, we identified that different combinations of epigenetic marks characterise different groups of enhancers. Finally, we discovered a large set of putative enhancers which display similar characteristics with previously characterised active enhancers.
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Affiliation(s)
- Jareth C Wolfe
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Liudmila A Mikheeva
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
- Department of Mathematical Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Hani Hagras
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK.
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK.
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35
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Goel VY, Hansen AS. The macro and micro of chromosome conformation capture. Wiley Interdiscip Rev Dev Biol 2021; 10:e395. [PMID: 32987449 PMCID: PMC8236208 DOI: 10.1002/wdev.395] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
Abstract
The 3D organization of the genome facilitates gene regulation, replication, and repair, making it a key feature of genomic function and one that remains to be properly understood. Over the past two decades, a variety of chromosome conformation capture (3C) methods have delineated genome folding from megabase-scale compartments and topologically associating domains (TADs) down to kilobase-scale enhancer-promoter interactions. Understanding the functional role of each layer of genome organization is a gateway to understanding cell state, development, and disease. Here, we discuss the evolution of 3C-based technologies for mapping 3D genome organization. We focus on genomics methods and provide a historical account of the development from 3C to Hi-C. We also discuss ChIP-based techniques that focus on 3D genome organization mediated by specific proteins, capture-based methods that focus on particular regions or regulatory elements, 3C-orthogonal methods that do not rely on restriction digestion and proximity ligation, and methods for mapping the DNA-RNA and RNA-RNA interactomes. We consider the biological discoveries that have come from these methods, examine the mechanistic contributions of CTCF, cohesin, and loop extrusion to genomic folding, and detail the 3D genome field's current understanding of nuclear architecture. Finally, we give special consideration to Micro-C as an emerging frontier in chromosome conformation capture and discuss recent Micro-C findings uncovering fine-scale chromatin organization in unprecedented detail. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.
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Affiliation(s)
- Viraat Y. Goel
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Anders S. Hansen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Zhang S, Übelmesser N, Josipovic N, Forte G, Slotman JA, Chiang M, Gothe HJ, Gusmao EG, Becker C, Altmüller J, Houtsmuller AB, Roukos V, Wendt KS, Marenduzzo D, Papantonis A. RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis. Sci Adv 2021; 7:eabg8205. [PMID: 34678064 PMCID: PMC8535795 DOI: 10.1126/sciadv.abg8205] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Mammalian chromosomes are three-dimensional entities shaped by converging and opposing forces. Mitotic cell division induces marked chromosome condensation, but following reentry into the G1 phase of the cell cycle, chromosomes reestablish their interphase organization. Here, we tested the role of RNA polymerase II (RNAPII) in this transition using a cell line that allows its auxin-mediated degradation. In situ Hi-C showed that RNAPII is required for both compartment and loop establishment following mitosis. RNAPs often counteract loop extrusion, and in their absence, longer and more prominent loops arose. Evidence from chromatin binding, super-resolution imaging, and in silico modeling allude to these effects being a result of RNAPII-mediated cohesin loading upon G1 reentry. Our findings reconcile the role of RNAPII in gene expression with that in chromatin architecture.
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Affiliation(s)
- Shu Zhang
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Giada Forte
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Johan A. Slotman
- Optical Imaging Centre, Erasmus Medical Center, 3015 GD Rotterdam, Netherlands
| | - Michael Chiang
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | | | - Eduardo Gade Gusmao
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | | | | | - Kerstin S. Wendt
- Department of Cell Biology, Erasmus Medical Center, 3015 GD Rotterdam, Netherlands
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
- Corresponding author.
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37
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Trigiante G, Blanes Ruiz N, Cerase A. Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression. Front Cell Dev Biol 2021; 9:735527. [PMID: 34722514 PMCID: PMC8552494 DOI: 10.3389/fcell.2021.735527] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.
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Affiliation(s)
| | | | - Andrea Cerase
- Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
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38
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Vernizzi L, Lehner CF. Bivalent individualization during chromosome territory formation in Drosophila spermatocytes by controlled condensin II protein activity and additional force generators. PLoS Genet 2021; 17:e1009870. [PMID: 34669718 PMCID: PMC8559962 DOI: 10.1371/journal.pgen.1009870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/03/2021] [Revised: 11/01/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Reduction of genome ploidy from diploid to haploid necessitates stable pairing of homologous chromosomes into bivalents before the start of the first meiotic division. Importantly, this chromosome pairing must avoid interlocking of non-homologous chromosomes. In spermatocytes of Drosophila melanogaster, where homolog pairing does not involve synaptonemal complex formation and crossovers, associations between non-homologous chromosomes are broken up by chromosome territory formation in early spermatocytes. Extensive non-homologous associations arise from the coalescence of the large blocks of pericentromeric heterochromatin into a chromocenter and from centromere clustering. Nevertheless, during territory formation, bivalents are moved apart into spatially separate subnuclear regions. The condensin II subunits, Cap-D3 and Cap-H2, have been implicated, but the remarkable separation of bivalents during interphase might require more than just condensin II. For further characterization of this process, we have applied time-lapse imaging using fluorescent markers of centromeres, telomeres and DNA satellites in pericentromeric heterochromatin. We describe the dynamics of the disruption of centromere clusters and the chromocenter in normal spermatocytes. Mutations in Cap-D3 and Cap-H2 abolish chromocenter disruption, resulting in excessive chromosome missegregation during M I. Chromocenter persistence in the mutants is not mediated by the special system, which conjoins homologs in compensation for the absence of crossovers in Drosophila spermatocytes. However, overexpression of Cap-H2 precluded conjunction between autosomal homologs, resulting in random segregation of univalents. Interestingly, Cap-D3 and Cap-H2 mutant spermatocytes displayed conspicuous stretching of the chromocenter, as well as occasional chromocenter disruption, suggesting that territory formation might involve forces unrelated to condensin II. While the molecular basis of these forces remains to be clarified, they are not destroyed by inhibitors of F actin and microtubules. Our results indicate that condensin II activity promotes chromosome territory formation in co-operation with additional force generators and that careful co-ordination with alternative homolog conjunction is crucial.
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Affiliation(s)
- Luisa Vernizzi
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
| | - Christian F. Lehner
- Department of Molecular Life Science (DMLS), University of Zurich, Zurich, Switzerland
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39
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Kainth AS, Chowdhary S, Pincus D, Gross DS. Primordial super-enhancers: heat shock-induced chromatin organization in yeast. Trends Cell Biol 2021; 31:801-813. [PMID: 34001402 PMCID: PMC8448919 DOI: 10.1016/j.tcb.2021.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 02/26/2021] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 01/29/2023]
Abstract
Specialized mechanisms ensure proper expression of critically important genes such as those specifying cell identity or conferring protection from environmental stress. Investigations of the heat shock response have been critical in elucidating basic concepts of transcriptional control. Recent studies demonstrate that in response to thermal stress, heat shock-responsive genes associate with high levels of transcriptional activators and coactivators and those in yeast intensely interact across and between chromosomes, coalescing into condensates. In mammalian cells, cell identity genes that are regulated by super-enhancers (SEs) are also densely occupied by transcriptional machinery that form phase-separated condensates. We suggest that the stress-remodeled yeast nucleome bears functional and structural resemblance to mammalian SEs, and will reveal fundamental mechanisms of gene control by transcriptional condensates.
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Affiliation(s)
- Amoldeep S Kainth
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Surabhi Chowdhary
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
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40
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Zhang C, Xu Z, Yang S, Sun G, Jia L, Zheng Z, Gu Q, Tao W, Cheng T, Li C, Cheng H. tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis. Cell Rep 2021; 32:108206. [PMID: 32997998 DOI: 10.1016/j.celrep.2020.108206] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/08/2020] [Accepted: 09/08/2020] [Indexed: 01/10/2023] Open
Abstract
Spatiotemporal chromatin reorganization during hematopoietic differentiation has not been comprehensively characterized, mainly because of the large numbers of starting cells required for current chromatin conformation capture approaches. Here, we introduce a low-input tagmentation-based Hi-C (tagHi-C) method to capture the chromatin structures of hundreds of cells. Using tagHi-C, we are able to map the spatiotemporal dynamics of chromatin structure in ten primary hematopoietic stem, progenitor, and differentiated cell populations from mouse bone marrow. Our results reveal that changes in compartment dynamics and the Rabl configuration occur during hematopoietic cell differentiation. We identify gene-body-associating domains (GADs) as general structures for highly expressed genes. Moreover, we extend the body of knowledge regarding genes influenced by genome-wide association study (GWAS) loci through spatial chromatin looping. Our study provides the tagHi-C method for studying the three-dimensional (3D) genome of a small number of cells and maps the comprehensive 3D chromatin landscape of bone marrow hematopoietic cells.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China; Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China; PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing, China
| | - Zihan Xu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China
| | - Shangda Yang
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lumeng Jia
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China
| | - Zhaofeng Zheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Quan Gu
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wei Tao
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China.
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China.
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China.
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41
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Perea-Resa C, Wattendorf L, Marzouk S, Blower MD. Cohesin: behind dynamic genome topology and gene expression reprogramming. Trends Cell Biol 2021; 31:760-773. [PMID: 33766521 PMCID: PMC8364472 DOI: 10.1016/j.tcb.2021.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/18/2021] [Revised: 02/23/2021] [Accepted: 03/04/2021] [Indexed: 01/01/2023]
Abstract
Beyond its originally discovered role tethering replicated sister chromatids, cohesin has emerged as a master regulator of gene expression. Recent advances in chromatin topology resolution and single-cell studies have revealed that cohesin has a pivotal role regulating highly dynamic chromatin interactions linked to transcription control. The dynamic association of cohesin with chromatin and its capacity to perform loop extrusion contribute to the heterogeneity of chromatin contacts. Additionally, different cohesin subcomplexes, with specific properties and regulation, control gene expression across the cell cycle and during developmental cell commitment. Here, we discuss the most recent literature in the field to highlight the role of cohesin in gene expression regulation during transcriptional shifts and its relationship with human diseases.
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Affiliation(s)
- Carlos Perea-Resa
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
| | - Lauren Wattendorf
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Sammer Marzouk
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Michael D Blower
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
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42
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Neguembor MV, Martin L, Castells-García Á, Gómez-García PA, Vicario C, Carnevali D, AlHaj Abed J, Granados A, Sebastian-Perez R, Sottile F, Solon J, Wu CT, Lakadamyali M, Cosma MP. Transcription-mediated supercoiling regulates genome folding and loop formation. Mol Cell 2021; 81:3065-3081.e12. [PMID: 34297911 PMCID: PMC9482096 DOI: 10.1016/j.molcel.2021.06.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 03/27/2021] [Accepted: 06/08/2021] [Indexed: 12/21/2022]
Abstract
The chromatin fiber folds into loops, but the mechanisms controlling loop extrusion are still poorly understood. Using super-resolution microscopy, we visualize that loops in intact nuclei are formed by a scaffold of cohesin complexes from which the DNA protrudes. RNA polymerase II decorates the top of the loops and is physically segregated from cohesin. Augmented looping upon increased loading of cohesin on chromosomes causes disruption of Lamin at the nuclear rim and chromatin blending, a homogeneous distribution of chromatin within the nucleus. Altering supercoiling via either transcription or topoisomerase inhibition counteracts chromatin blending, increases chromatin condensation, disrupts loop formation, and leads to altered cohesin distribution and mobility on chromatin. Overall, negative supercoiling generated by transcription is an important regulator of loop formation in vivo.
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Affiliation(s)
- Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Laura Martin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Álvaro Castells-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Chiara Vicario
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Davide Carnevali
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | | | - Alba Granados
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Ruben Sebastian-Perez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Francesco Sottile
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Jérôme Solon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Instituto Biofisika (CSIC, UPV/EHU), Basque Excellence Research Centre, Barrio Sarriena, 48940, Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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43
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Moretti C, Stévant I, Ghavi-Helm Y. 3D genome organisation in Drosophila. Brief Funct Genomics 2021; 19:92-100. [PMID: 31796947 DOI: 10.1093/bfgp/elz029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/02/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Ever since Thomas Hunt Morgan's discovery of the chromosomal basis of inheritance by using Drosophila melanogaster as a model organism, the fruit fly has remained an essential model system in studies of genome biology, including chromatin organisation. Very much as in vertebrates, in Drosophila, the genome is organised in territories, compartments and topologically associating domains (TADs). However, these domains might be formed through a slightly different mechanism than in vertebrates due to the presence of a large and potentially redundant set of insulator proteins and the minor role of dCTCF in TAD boundary formation. Here, we review the different levels of chromatin organisation in Drosophila and discuss mechanisms and factors that might be involved in TAD formation. The dynamics of TADs and enhancer-promoter interactions in the context of transcription are covered in the light of currently conflicting results. Finally, we illustrate the value of polymer modelling approaches to infer the principles governing the three-dimensional organisation of the Drosophila genome.
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Affiliation(s)
- Charlotte Moretti
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
| | - Isabelle Stévant
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
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44
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Abstract
Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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45
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Child MB, Bateman JR, Jahangiri A, Reimer A, Lammers NC, Sabouni N, Villamarin D, McKenzie-Smith GC, Johnson JE, Jost D, Garcia HG. Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila. eLife 2021; 10:64412. [PMID: 34100718 PMCID: PMC8294847 DOI: 10.7554/elife.64412] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 10/28/2020] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Three-dimensional eukaryotic genome organization provides the structural basis for gene regulation. In Drosophila melanogaster, genome folding is characterized by somatic homolog pairing, where homologous chromosomes are intimately paired from end to end; however, how homologs identify one another and pair has remained mysterious. Recently, this process has been proposed to be driven by specifically interacting 'buttons' encoded along chromosomes. Here, we turned this hypothesis into a quantitative biophysical model to demonstrate that a button-based mechanism can lead to chromosome-wide pairing. We tested our model using live-imaging measurements of chromosomal loci tagged with the MS2 and PP7 nascent RNA labeling systems. We show solid agreement between model predictions and experiments in the pairing dynamics of individual homologous loci. Our results strongly support a button-based mechanism of somatic homolog pairing in Drosophila and provide a theoretical framework for revealing the molecular identity and regulation of buttons.
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Affiliation(s)
- Myron Barber Child
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, United States
| | - Amir Jahangiri
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Armando Reimer
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nica Sabouni
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | | | | | | | - Daniel Jost
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France.,Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratory of Biology and Modeling of the Cell, Lyon, France
| | - Hernan G Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
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46
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Abstract
Three-dimensional (3D) genome organization has emerged as an important layer of gene regulation in development and disease. The functional properties of chromatin folding within individual chromosomes (i.e., intra-chromosomal or in cis) have been studied extensively. On the other hand, interactions across different chromosomes (i.e., inter-chromosomal or in trans) have received less attention, being often regarded as background noise or technical artifacts. This viewpoint has been challenged by emerging evidence of functional relationships between specific trans chromatin interactions and epigenetic control, transcription, and splicing. Therefore, it is an intriguing possibility that the key processes involved in the biogenesis of RNAs may both shape and be in turn influenced by inter-chromosomal genome architecture. Here I present the rationale behind this hypothesis, and discuss a potential experimental framework aimed at its formal testing. I present a specific example in the cardiac myocyte, a well-studied post-mitotic cell whose development and response to stress are associated with marked rearrangements of chromatin topology both in cis and in trans. I argue that RNA polymerase II clusters (i.e., transcription factories) and foci of the cardiac-specific splicing regulator RBM20 (i.e., splicing factories) exemplify the existence of trans-interacting chromatin domains (TIDs) with important roles in cellular homeostasis. Overall, I propose that inter-molecular 3D proximity between co-regulated nucleic acids may be a pervasive functional mechanism in biology.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States
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Kaushal A, Mohana G, Dorier J, Özdemir I, Omer A, Cousin P, Semenova A, Taschner M, Dergai O, Marzetta F, Iseli C, Eliaz Y, Weisz D, Shamim MS, Guex N, Lieberman Aiden E, Gambetta MC. CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions. Nat Commun 2021; 12:1011. [PMID: 33579945 DOI: 10.1038/s41467-021-21366-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 05/18/2020] [Accepted: 01/21/2021] [Indexed: 01/30/2023] Open
Abstract
Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding cohesin by CTCF bound at domain boundaries. While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system. We find that CTCF is required to form a small fraction of all domain boundaries, while critically controlling expression patterns of certain genes and supporting nervous system function. We also find that CTCF recruits the pervasive boundary-associated factor Cp190 to CTCF-occupied boundaries and co-regulates a subset of genes near boundaries together with Cp190. These results highlight a profound difference in CTCF-requirement for genome folding in flies and vertebrates, in which a large fraction of boundaries are CTCF-dependent and suggest that CTCF has played mutable roles in genome architecture and direct gene expression control during metazoan evolution.
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Ulianov SV, Zakharova VV, Galitsyna AA, Kos PI, Polovnikov KE, Flyamer IM, Mikhaleva EA, Khrameeva EE, Germini D, Logacheva MD, Gavrilov AA, Gorsky AS, Nechaev SK, Gelfand MS, Vassetzky YS, Chertovich AV, Shevelyov YY, Razin SV. Order and stochasticity in the folding of individual Drosophila genomes. Nat Commun 2021; 12:41. [PMID: 33397980 DOI: 10.1038/s41467-020-20292-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome. Genomes are partitioned into topologically associating domains (TADs). Here the authors present single-nucleus Hi-C maps in Drosophila at 10 kb resolution, demonstrating the presence of chromatin compartments in individual nuclei, and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which resembles population TAD profiles.
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Dyson S, Segura J, Martínez‐García B, Valdés A, Roca J. Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo. EMBO J 2021; 40:e105393. [PMID: 33155682 PMCID: PMC7780148 DOI: 10.15252/embj.2020105393] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 12/24/2022] Open
Abstract
The juxtaposition of intracellular DNA segments, together with the DNA-passage activity of topoisomerase II, leads to the formation of DNA knots and interlinks, which jeopardize chromatin structure and gene expression. Recent studies in budding yeast have shown that some mechanism minimizes the knotting probability of intracellular DNA. Here, we tested whether this is achieved via the intrinsic capacity of topoisomerase II for simplifying the equilibrium topology of DNA; or whether it is mediated by SMC (structural maintenance of chromosomes) protein complexes like condensin or cohesin, whose capacity to extrude DNA loops could enforce dissolution of DNA knots by topoisomerase II. We show that the low knotting probability of DNA does not depend on the simplification capacity of topoisomerase II nor on the activities of cohesin or Smc5/6 complexes. However, inactivation of condensin increases the occurrence of DNA knots throughout the cell cycle. These results suggest an in vivo role for the DNA loop extrusion activity of condensin and may explain why condensin disruption produces a variety of alterations in interphase chromatin, in addition to persistent sister chromatid interlinks in mitotic chromatin.
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Grants
- BFU2015-67007-P Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- PID2019-109482GB-I00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2016-077806 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2012-061167 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2015-071597 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
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Affiliation(s)
- Sílvia Dyson
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Belén Martínez‐García
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Antonio Valdés
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
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50
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Abstract
There are two kinds of condensins in human cells, known as condensin I and condensin II. The canonical roles of condensins are participated in chromosome dynamics, including chromosome condensation and segregation during cell division. Recently, a novel function of human condensins has been found with increasing evidences that they play important roles in cellular senescence. This paper reviewed the research progress of human condensins involved in different types of cellular senescence, mainly oncogene-induced senescence (OIS) and replicative senescence (RS). The future perspectives of human condensins involved in cellular senescence are also discussed.
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Affiliation(s)
- Hongzhen Wang
- School of Life Sciences, Jilin Normal University, 136000, Siping, People's Republic of China. .,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 130012, Changchun, People's Republic of China.
| | - Xin Liu
- School of Life Sciences, Jilin Normal University, 136000, Siping, People's Republic of China
| | - Guiying Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, 130012, Changchun, People's Republic of China
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