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Schindler M, Osterwalder M, Harabula I, Wittler L, Tzika AC, Dechmann DKN, Vingron M, Visel A, Haas SA, Real FM. Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes. Development 2023; 150:dev201562. [PMID: 37519269 PMCID: PMC10499028 DOI: 10.1242/dev.201562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Changes in gene expression represent an important source of phenotypic innovation. Yet how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing integrative analyses of epigenetic and transcriptional data in mole and mouse, we identified the co-option of SALL1 expression in mole ovotestes formation. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but an evolutionary divergence of enhancer activity. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce kidney-related gene programs, which are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a plausible mechanism for the evolution of traits.
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Affiliation(s)
- Magdalena Schindler
- Gene Regulation & Evolution, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
- Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
- Department of Cardiology, Bern University Hospital, Bern 3010, Switzerland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Izabela Harabula
- Epigenetic Regulation and Chromatin Architecture, Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin 10115, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Athanasia C. Tzika
- Department of Genetics & Evolution, University of Geneva, Geneva 1205, Switzerland
| | - Dina K. N. Dechmann
- Department of Migration, Max Planck Institute for Animal Behavior, Radolfzell 78315, Germany
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Stefan A. Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Francisca M. Real
- Gene Regulation & Evolution, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
- Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
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Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
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Affiliation(s)
- Claire Hoencamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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53
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Deng L, Zhou Q, Zhou J, Zhang Q, Jia Z, Zhu G, Cheng S, Cheng L, Yin C, Yang C, Shen J, Nie J, Zhu JK, Li G, Zhao L. 3D organization of regulatory elements for transcriptional regulation in Arabidopsis. Genome Biol 2023; 24:181. [PMID: 37550699 PMCID: PMC10405511 DOI: 10.1186/s13059-023-03018-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants. RESULTS Here we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression. CONCLUSION The results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.
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Affiliation(s)
- Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangfeng Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lulu Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caijun Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junwei Nie
- Vazyme Biotech Co., Ltd., Nanjing, 210000, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Hehmeyer J, Spitz F, Marlow H. Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies. Curr Opin Genet Dev 2023; 81:102064. [PMID: 37390583 PMCID: PMC10547022 DOI: 10.1016/j.gde.2023.102064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/02/2023]
Abstract
3D genome folding enables the physical storage of chromosomes into the compact volume of a cell's nucleus, allows for the accurate segregation of chromatin to daughter cells, and has been shown to be tightly coupled to the way in which genetic information is converted into transcriptional programs [1-3]. Importantly, this link between chromatin architecture and gene regulation is a selectable feature in which modifications to chromatin organization accompany, or perhaps even drive the establishment of new regulatory strategies with enduring impacts on animal body plan complexity. Here, we discuss the nature of different 3D genome folding systems found across the tree of life, with particular emphasis on metazoans, and the relative influence of these systems on gene regulation. We suggest how the properties of these folding systems have influenced regulatory strategies employed by different lineages and may have catalyzed the partitioning and specialization of genetic programs that enabled multicellularity and organ-grade body plan complexity.
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Affiliation(s)
- Jenks Hehmeyer
- Department of Organismal Biology and Anatomy, The University of Chicago, USA
| | - François Spitz
- Department of Human Genetics, The University of Chicago, USA
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, USA.
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55
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Paturej J, Erbaş A. Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization. Phys Biol 2023; 20:056004. [PMID: 37442118 DOI: 10.1088/1478-3975/ace750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/13/2023] [Indexed: 07/15/2023]
Abstract
Interphase chromosomes are known to organize non-randomly in the micron-sized eukaryotic cell nucleus and occupy certain fraction of nuclear volume, often without mixing. Using extensive coarse-grained simulations, we model such chromosome structures as colloidal particles whose surfaces are grafted by cyclic polymers. This model system is known as Rosetta. The cyclic polymers, with varying polymerization degrees, mimic chromatin loops present in interphase chromosomes, while the rigid core models the chromocenter section of the chromosome. Our simulations show that the colloidal chromosome model provides a well-separated particle distribution without specific attraction between the chain monomers. As the polymerization degree of the grafted cyclic chains decreases while maintaining the total chromosomal length (e.g. the more potent activity of condensin-family proteins), the average chromosomal volume becomes smaller, inter-chromosomal contacts decrease, and chromocenters organize in a quasi-crystalline order reminiscent of a glassy state. This order weakens for polymer chains with a characteristic size on the order of the confinement radius. Notably, linear-polymer grafted particles also provide the same chromocenter organization scheme. However, unlike linear chains, cyclic chains result in less contact between the polymer layers of neighboring chromosome particles, demonstrating the effect of DNA breaks in altering genome-wide contacts. Our simulations show that polymer-grafted colloidal systems could help decipher 3D genome architecture along with the fractal globular and loop-extrusion models.
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Affiliation(s)
| | - Aykut Erbaş
- Institute of Physics, University of Silesia, Katowice, Poland
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, 06800 Ankara, Turkey
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56
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Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. The ENCODE Uniform Analysis Pipelines. RESEARCH SQUARE 2023:rs.3.rs-3111932. [PMID: 37503119 PMCID: PMC10371165 DOI: 10.21203/rs.3.rs-3111932/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
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Affiliation(s)
- Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keenan Graham
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy Dreszer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Whaling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T Lee
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Alyssa Ingersoll
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Daniel S Kim
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Nathan Boley
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Blackburn
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Dimos Gkountaroulis
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Mahdi Sadr
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moshe Olshansky
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yossi Eliaz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dat Nguyen
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan Bochkov
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Saad Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Erez Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Tom Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Hirst
- Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada
| | - W James Kent
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anshul Kundaje
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ali Mortazavi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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57
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Ma B, Wang H, Liu J, Chen L, Xia X, Wei W, Yang Z, Yuan J, Luo Y, He N. The gap-free genome of mulberry elucidates the architecture and evolution of polycentric chromosomes. HORTICULTURE RESEARCH 2023; 10:uhad111. [PMID: 37786730 PMCID: PMC10541557 DOI: 10.1093/hr/uhad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 10/04/2023]
Abstract
Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, Morus notabilis, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that M. notabilis is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.
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Affiliation(s)
- Bi Ma
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Honghong Wang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Jingchun Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Lin Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Xiaoyu Xia
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Wuqi Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Zhen Yang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Jianglian Yuan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Yiwei Luo
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
| | - Ningjia He
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China
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58
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Stok C, Tsaridou S, van den Tempel N, Everts M, Wierenga E, Bakker FJ, Kok Y, Alves IT, Jae LT, Raas MWD, Huis In 't Veld PJ, de Boer HR, Bhattacharya A, Karanika E, Warner H, Chen M, van de Kooij B, Dessapt J, Ter Morsche L, Perepelkina P, Fradet-Turcotte A, Guryev V, Tromer EC, Chan KL, Fehrmann RSN, van Vugt MATM. FIRRM/C1orf112 is synthetic lethal with PICH and mediates RAD51 dynamics. Cell Rep 2023; 42:112668. [PMID: 37347663 DOI: 10.1016/j.celrep.2023.112668] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
Joint DNA molecules are natural byproducts of DNA replication and repair. Persistent joint molecules give rise to ultrafine DNA bridges (UFBs) in mitosis, compromising sister chromatid separation. The DNA translocase PICH (ERCC6L) has a central role in UFB resolution. A genome-wide loss-of-function screen is performed to identify the genetic context of PICH dependency. In addition to genes involved in DNA condensation, centromere stability, and DNA-damage repair, we identify FIGNL1-interacting regulator of recombination and mitosis (FIRRM), formerly known as C1orf112. We find that FIRRM interacts with and stabilizes the AAA+ ATPase FIGNL1. Inactivation of either FIRRM or FIGNL1 results in UFB formation, prolonged accumulation of RAD51 at nuclear foci, and impaired replication fork dynamics and consequently impairs genome maintenance. Combined, our data suggest that inactivation of FIRRM and FIGNL1 dysregulates RAD51 dynamics at replication forks, resulting in persistent DNA lesions and a dependency on PICH to preserve cell viability.
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Affiliation(s)
- Colin Stok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Stavroula Tsaridou
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Nathalie van den Tempel
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Marieke Everts
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Elles Wierenga
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Femke J Bakker
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Yannick Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Inês Teles Alves
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Lucas T Jae
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Maximilian W D Raas
- Oncode Institute, Hubrecht Institute, Royal Academy of Arts and Sciences, Uppsalalaan 8, 3584CT Utrecht, the Netherlands; Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Pim J Huis In 't Veld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - H Rudolf de Boer
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Arkajyoti Bhattacharya
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Eleftheria Karanika
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Harry Warner
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Mengting Chen
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Bert van de Kooij
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Julien Dessapt
- CHU de Québec Research Center-Université Laval (L'Hôtel-Dieu de Québec), Cancer Research Center, Université Laval, Québec, QC GIR 3S3, Canada
| | - Lars Ter Morsche
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Polina Perepelkina
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Amelie Fradet-Turcotte
- CHU de Québec Research Center-Université Laval (L'Hôtel-Dieu de Québec), Cancer Research Center, Université Laval, Québec, QC GIR 3S3, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Kok-Lung Chan
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands.
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59
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Dodero-Rojas E, Mello MF, Brahmachari S, Oliveira Junior AB, Contessoto VG, Onuchic JN. PyMEGABASE: Predicting cell-type-specific structural annotations of chromosomes using the epigenome. J Mol Biol 2023:168180. [PMID: 37302549 DOI: 10.1016/j.jmb.2023.168180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
The folding patterns of interphase genomes in higher eukaryotes, as obtained from DNA-proximity-ligation or Hi-C experiments, are used to classify loci into structural classes called compartments and subcompartments. These structurally annotated (sub)compartments are known to exhibit specific epigenomic characteristics and cell-type-specific variations. To explore the relationship between genome structure and the epigenome, we present PyMEGABASE (PYMB), a maximum-entropy-based neural network model that predicts (sub)compartment annotations of a locus based solely on the local epigenome, such as ChIP-Seq of histone post-translational modifications. PYMB builds upon our previous model while improving robustness, capability to handle diverse inputs and user-friendly implementation. We employed PYMB to predict subcompartments for over a hundred human cell types available in ENCODE, shedding light on the links between subcompartments, cell identity, and epigenomic signals. The fact that PYMB, trained on data for human cells, can accurately predict compartments in mice suggests that the model is learning underlying physicochemical principles transferable across cell types and species. Reliable at higher resolutions (up to 5 kbp), PYMB is used to investigate compartment-specific gene expression. Not only can PYMB generate (sub)compartment information without Hi-C experiments, but its predictions are also interpretable. Analyzing PYMB's trained parameters, we explore the importance of various epigenomic marks in each subcompartment prediction. Furthermore, the predictions of the model can be used as input for OpenMiChroM software, which has been calibrated to generate three-dimensional structures of the genome. Detailed documentation of PYMB is available at https://pymegabase.readthedocs.io, including an installation guide using pip or conda, and Jupyter/Colab notebook tutorials.
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Affiliation(s)
| | - Matheus F Mello
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | | | | | | | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Department of Physics & Astronomy, Rice University, Houston, TX, USA; Department of Chemistry, Rice University, Houston, TX, USA; Department of Biosciences, Rice University, Houston, TX, USA.
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60
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Bürmann F, Löwe J. Structural biology of SMC complexes across the tree of life. Curr Opin Struct Biol 2023; 80:102598. [PMID: 37104976 PMCID: PMC10512200 DOI: 10.1016/j.sbi.2023.102598] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 04/29/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes guard and organize the three-dimensional structure of chromosomal DNA across the tree of life. Many SMC functions can be explained by an inherent motor activity that extrudes large DNA loops while the complexes move along their substrate. Here, we review recent structural insights into the architecture and conservation of these molecular machines, their interaction with DNA, and the conformational changes that are linked to their ATP hydrolysis cycle.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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61
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Bajpai G, Safran S. Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics. PLoS Comput Biol 2023; 19:e1011142. [PMID: 37228178 DOI: 10.1371/journal.pcbi.1011142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Chromosomes are arranged in distinct territories within the nucleus of animal cells. Recent experiments have shown that these territories overlap at their edges, suggesting partial mixing during interphase. Experiments that knock-down of condensin II proteins during interphase indicate increased chromosome mixing, which demonstrates control of the mixing. In this study, we use a generic polymer simulation to quantify the dynamics of chromosome mixing over time. We introduce the chromosome mixing index, which quantifies the mixing of distinct chromosomes in the nucleus. We find that the chromosome mixing index in a small confinement volume (as a model of the nucleus), increases as a power-law of the time, with the scaling exponent varying non-monotonically with self-interaction and volume fraction. By comparing the chromosome mixing index with both monomer subdiffusion due to (non-topological) intermingling of chromosomes as well as even slower reptation, we show that for relatively large volume fractions, the scaling exponent of the chromosome mixing index is related to Rouse dynamics for relatively weak chromosome attractions and to reptation for strong attractions. In addition, we extend our model to more realistically account for the situation of the Drosophila chromosome by including the heterogeneity of the polymers and their lengths to account for microphase separation of euchromatin and heterochromatin and their interactions with the nuclear lamina. We find that the interaction with the lamina further impedes chromosome mixing.
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Affiliation(s)
- Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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62
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Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. Comparing chromatin contact maps at scale: methods and insights. RESEARCH SQUARE 2023:rs.3.rs-2842981. [PMID: 37292728 PMCID: PMC10246266 DOI: 10.21203/rs.3.rs-2842981/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, no gold standard exists for comparing contact maps, and even simple methods often disagree. In this study, we propose novel comparison methods and evaluate them alongside existing approaches using genome-wide Hi-C data and 22,500 in silico predicted contact maps. We also quantify the robustness of methods to common sources of biological and technical variation, such as boundary size and noise. We find that simple difference-based methods such as mean squared error are suitable for initial screening, but biologically informed methods are necessary to identify why maps diverge and propose specific functional hypotheses. We provide a reference guide, codebase, and benchmark for rapidly comparing chromatin contact maps at scale to enable biological insights into the 3D organization of the genome.
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Affiliation(s)
- Laura M. Gunsalus
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Evonne McArthur
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Shuzhen Kuang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Maureen Pittman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - John A. Capra
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
| | - Katherine S. Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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63
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Torres DE, Reckard AT, Klocko AD, Seidl MF. Nuclear genome organization in fungi: from gene folding to Rabl chromosomes. FEMS Microbiol Rev 2023; 47:fuad021. [PMID: 37197899 PMCID: PMC10246852 DOI: 10.1093/femsre/fuad021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the postgenomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is critically important. Here, we discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for this hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration, in which centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Further, fungal genomes are regionally organized into topologically associated domain-like (TAD-like) chromatin structures. We discuss how chromatin organization impacts the proper function of DNA-templated processes across the fungal genome. Nevertheless, this view is limited to a few fungal taxa given the paucity of fungal Hi-C experiments. We advocate for exploring genome organization across diverse fungal lineages to ensure the future understanding of the impact of nuclear organization on fungal genome function.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research,Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands
| | - Andrew T Reckard
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, 234 Centennial Hall, 1420 Austin Bluffs Pkwy, Colorado Springs, CO 80918 USA
| | - Andrew D Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, 234 Centennial Hall, 1420 Austin Bluffs Pkwy, Colorado Springs, CO 80918 USA
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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64
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Ruben BS, Brahmachari S, Contessoto VG, Cheng RR, Oliveira Junior AB, Di Pierro M, Onuchic JN. Structural reorganization and relaxation dynamics of axially stressed chromosomes. Biophys J 2023; 122:1633-1645. [PMID: 36960531 PMCID: PMC10183323 DOI: 10.1016/j.bpj.2023.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/06/2023] [Accepted: 03/17/2023] [Indexed: 03/25/2023] Open
Abstract
Chromosomes endure mechanical stresses throughout the cell cycle; for example, resulting from the pulling of chromosomes by spindle fibers during mitosis or deformation of the nucleus during cell migration. The response to physical stress is closely related to chromosome structure and function. Micromechanical studies of mitotic chromosomes have revealed them to be remarkably extensible objects and informed early models of mitotic chromosome organization. We use a data-driven, coarse-grained polymer modeling approach to explore the relationship between the spatial organization of individual chromosomes and their emergent mechanical properties. In particular, we investigate the mechanical properties of our model chromosomes by axially stretching them. Simulated stretching led to a linear force-extension curve for small strain, with mitotic chromosomes behaving about 10-fold stiffer than interphase chromosomes. Studying their relaxation dynamics, we found that chromosomes are viscoelastic solids with a highly liquid-like, viscous behavior in interphase that becomes solid-like in mitosis. This emergent mechanical stiffness originates from lengthwise compaction, an effective potential capturing the activity of loop-extruding SMC complexes. Chromosomes denature under large strains via unraveling, which is characterized by opening of large-scale folding patterns. By quantifying the effect of mechanical perturbations on the chromosome's structural features, our model provides a nuanced understanding of in vivo mechanics of chromosomes.
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Affiliation(s)
- Benjamin S Ruben
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Biophysics PhD Program, Harvard University, Cambridge, Massachusetts.
| | | | | | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | | | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts; Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston, Texas
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65
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Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Three-dimensional genome rewiring in loci with human accelerated regions. Science 2023; 380:eabm1696. [PMID: 37104607 PMCID: PMC10999243 DOI: 10.1126/science.abm1696] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2023] [Indexed: 04/29/2023]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.
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Affiliation(s)
- Kathleen C Keough
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Tyler Fair
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Hane Ryu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Alex Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics and Bakar Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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66
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Nowicka A, Ferková Ľ, Said M, Kovacik M, Zwyrtková J, Baroux C, Pecinka A. Non-Rabl chromosome organization in endoreduplicated nuclei of barley embryo and endosperm tissues. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2527-2541. [PMID: 36705553 DOI: 10.1093/jxb/erad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/25/2023] [Indexed: 06/06/2023]
Abstract
Rabl organization is a type of interphase chromosome arrangement with centromeres and telomeres clustering at opposite nuclear poles. Here, we analyzed nuclear morphology and chromosome organization in cycling and endoreduplicated nuclei isolated from embryo and endosperm tissues of developing barley seeds. We show that endoreduplicated nuclei have an irregular shape, less sister chromatid cohesion at 5S rDNA loci, and a reduced amount of centromeric histone CENH3. While the chromosomes of the embryo and endosperm nuclei are initially organized in Rabl configuration, the centromeres and telomeres are intermingled within the nuclear space in the endoreduplicated nuclei with an increasing endoreduplication level. Such a loss of chromosome organization suggests that Rabl configuration is introduced and further reinforced by mitotic divisions in barley cell nuclei in a tissue- and seed age-dependent manner.
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Affiliation(s)
- Anna Nowicka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30-239 Krakow, Poland
| | - Ľuboslava Ferková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
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67
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Hitz BC, Jin-Wook L, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. The ENCODE Uniform Analysis Pipelines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535623. [PMID: 37066421 PMCID: PMC10104020 DOI: 10.1101/2023.04.04.535623] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
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Affiliation(s)
- Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lee Jin-Wook
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keenan Graham
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy Dreszer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Whaling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T Lee
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Alyssa Ingersoll
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Daniel S Kim
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Nathan Boley
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Blackburn
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Dimos Gkountaroulis
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Mahdi Sadr
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moshe Olshansky
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yossi Eliaz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dat Nguyen
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan Bochkov
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Saad Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Erez Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Tom Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Hirst
- Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada
| | - W James Kent
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anshul Kundaje
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ali Mortazavi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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68
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Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. Comparing chromatin contact maps at scale: methods and insights. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535480. [PMID: 37066196 PMCID: PMC10104037 DOI: 10.1101/2023.04.04.535480] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Comparing chromatin contact maps is an essential step in quantifying how three-dimensional (3D) genome organization shapes development, evolution, and disease. However, no gold standard exists for comparing contact maps, and even simple methods often disagree. In this study, we propose novel comparison methods and evaluate them alongside existing approaches using genome-wide Hi-C data and 22,500 in silico predicted contact maps. We also quantify the robustness of methods to common sources of biological and technical variation, such as boundary size and noise. We find that simple difference-based methods such as mean squared error are suitable for initial screening, but biologically informed methods are necessary to identify why maps diverge and propose specific functional hypotheses. We provide a reference guide, codebase, and benchmark for rapidly comparing chromatin contact maps at scale to enable biological insights into the 3D organization of the genome.
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Affiliation(s)
- Laura M. Gunsalus
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Evonne McArthur
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Shuzhen Kuang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - Maureen Pittman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
| | - John A. Capra
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
| | - Katherine S. Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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69
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Marlétaz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabaldón T, Nakamura T, Tena JJ, Lupiáñez DG, Rokhsar DS, Gómez-Skarmeta JL. The little skate genome and the evolutionary emergence of wing-like fins. Nature 2023; 616:495-503. [PMID: 37046085 PMCID: PMC10115646 DOI: 10.1038/s41586-023-05868-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/21/2023] [Indexed: 04/14/2023]
Abstract
Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.
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Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
| | - Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Victoria A Sleight
- Department of Zoology, University of Cambridge, Cambridge, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dina Navon
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | - Ali Andrescavage
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Edward Duckett
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Álvaro González-Rajal
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Johan H Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lourdes Gallardo-Fuentes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Ismael Sospedra
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Fabrice Darbellay
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers the State University of New Jersey, Piscataway, NJ, USA.
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain.
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
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70
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Clarence T, Robert NS, Sarigol F, Fu X, Bates PA, Simakov O. Robust 3D modeling reveals spatiosyntenic properties of animal genomes. iScience 2023; 26:106136. [PMID: 36876129 PMCID: PMC9976460 DOI: 10.1016/j.isci.2023.106136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/18/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (synteny). Using versatile chromosomal modeling, we infer three-dimensional topology of genomes from representative clades spanning the earliest animal diversification. We apply a partitioning approach using interaction spheres to compensate for varying quality of topological data. Using comparative genomics approaches, we test whether syntenic signal at gene pair, local, and whole chromosomal scale is reflected in the reconstructed spatial organization. We identify evolutionarily conserved three-dimensional networks at all syntenic scales revealing novel evolutionarily maintained interactors associated with known conserved local gene linkages (such as hox). We thus present evidence for evolutionary constraints that are associated with three-, rather than just two-, dimensional animal genome organization, which we term spatiosynteny. As more accurate topological data become available, together with validation approaches, spatiosynteny may become relevant in understanding the functionality behind the observed conservation of animal chromosomes.
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Affiliation(s)
- Tereza Clarence
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Roussos Lab/Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Corresponding author
| | - Nicolas S.M. Robert
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Fatih Sarigol
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Corresponding author
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- Corresponding author
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71
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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; 24:5017. [PMID: 36902449 PMCID: PMC10003631 DOI: 10.3390/ijms24055017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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
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72
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Sato S, Cunha TJ, de Medeiros BAS, Khost DE, Sackton TB, Giribet G. Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in Epiperipatus broadwayi. Genome Biol Evol 2023; 15:7039704. [PMID: 36790097 PMCID: PMC9985152 DOI: 10.1093/gbe/evad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/13/2023] [Accepted: 01/21/2023] [Indexed: 02/16/2023] Open
Abstract
Genome assemblies are growing at an exponential rate and have proved indispensable for studying evolution but the effort has been biased toward vertebrates and arthropods with a particular focus on insects. Onychophora or velvet worms are an ancient group of cryptic, soil dwelling worms noted for their unique mode of prey capture, biogeographic patterns, and diversity of reproductive strategies. They constitute a poorly understood phylum of exclusively terrestrial animals that is sister group to arthropods. Due to this phylogenetic position, they are crucial in understanding the origin of the largest phylum of animals. Despite their significance, there is a paucity of genomic resources for the phylum with only one highly fragmented and incomplete genome publicly available. Initial attempts at sequencing an onychophoran genome proved difficult due to its large genome size and high repeat content. However, leveraging recent advances in long-read sequencing technology, we present here the first annotated draft genome for the phylum. With a total size of 5.6Gb, the gigantism of the Epiperipatus broadwayi genome arises from having high repeat content, intron size inflation, and extensive gene family expansion. Additionally, we report a previously unknown diversity of onychophoran hemocyanins that suggests the diversification of copper-mediated oxygen carriers occurred independently in Onychophora after its split from Arthropoda, parallel to the independent diversification of hemocyanins in each of the main arthropod lineages.
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Affiliation(s)
- Shoyo Sato
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Tauana J Cunha
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts.,Field Museum of Natural History, Chicago, Illinois
| | - Bruno A S de Medeiros
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts.,Field Museum of Natural History, Chicago, Illinois
| | - Danielle E Khost
- FAS Informatics Group, Harvard University, Cambridge, Massachusetts
| | | | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
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73
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Hotaling S, Desvignes T, Sproul JS, Lins LSF, Kelley JL. Pathways to polar adaptation in fishes revealed by long-read sequencing. Mol Ecol 2023; 32:1381-1397. [PMID: 35561000 DOI: 10.1111/mec.16501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/31/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022]
Abstract
Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long-read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage-specific loss of this cluster. Beyond polar fishes, our results highlight the power of long-read sequencing to understand genome evolution.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John S Sproul
- Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Luana S F Lins
- Australian National Insect Collection, CSIRO, Canberra, Australia
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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74
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Kuraku S, Kaiya H, Tanaka T, Hyodo S. Evolution of Vertebrate Hormones and Their Receptors: Insights from Non-Osteichthyan Genomes. Annu Rev Anim Biosci 2023; 11:163-182. [PMID: 36400012 DOI: 10.1146/annurev-animal-050922-071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Homeostatic control and reproductive functions of humans are regulated at the molecular levels largely by peptide hormones secreted from endocrine and/or neuroendocrine cells in the central nervous system and peripheral organs. Homologs of those hormones and their receptors function similarly in many vertebrate species distantly related to humans, but the evolutionary history of the endocrine system involving those factors has been obscured by the scarcity of genome DNA sequence information of some taxa that potentially contain their orthologs. Focusing on non-osteichthyan vertebrates, namely jawless and cartilaginous fishes, this article illustrates how investigating genome sequence information assists our understanding of the diversification of vertebrate gene repertoires in four broad themes: (a) the presence or absence of genes, (b) multiplication and maintenance of paralogs, (c) differential fates of duplicated paralogs, and (d) the evolutionary timing of gene origins.
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Affiliation(s)
- Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan; .,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Hiroyuki Kaiya
- Grandsoul Research Institute of Immunology, Inc., Uda, Japan
| | - Tomohiro Tanaka
- Department of Gastroenterology and Metabolism, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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75
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de Wit E, Nora EP. New insights into genome folding by loop extrusion from inducible degron technologies. Nat Rev Genet 2023; 24:73-85. [PMID: 36180596 DOI: 10.1038/s41576-022-00530-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2022] [Indexed: 01/24/2023]
Abstract
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically wire distant loci together for gene regulation. These loops are continuously created, extended and positioned by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin, and their regulators, including CTCF, in a highly dynamic process known as loop extrusion. Genetic loss of extrusion factors is lethal, complicating their study. Inducible protein degradation technologies enable the depletion of loop extrusion factors within hours, leading to the rapid reconfiguration of chromatin folding. Here, we review how these technologies have changed our understanding of genome organization, upsetting long-held beliefs on its role in transcription. Finally, we examine recent models that attempt to reconcile observations after chronic versus acute perturbations, and discuss future developments in this rapidly developing field of research.
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Affiliation(s)
- Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Amsterdam, the Netherlands.
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Elphège P Nora
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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76
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Cazet JF, Siebert S, Little HM, Bertemes P, Primack AS, Ladurner P, Achrainer M, Fredriksen MT, Moreland RT, Singh S, Zhang S, Wolfsberg TG, Schnitzler CE, Baxevanis AD, Simakov O, Hobmayer B, Juliano CE. A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome Res 2023; 33:283-298. [PMID: 36639202 PMCID: PMC10069465 DOI: 10.1101/gr.277040.122] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best-characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large kilobase-scale chromatin interaction domains in the Hydra genome that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type-specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica more than 400 million years ago.
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Affiliation(s)
- Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
- Lyell Immunopharma, South San Francisco, California 94080, USA
| | - Hannah Morris Little
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | - Philip Bertemes
- Institute of Zoology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Abby S Primack
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | - Peter Ladurner
- Institute of Zoology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Matthias Achrainer
- Institute of Zoology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Mark T Fredriksen
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - R Travis Moreland
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sumeeta Singh
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Suiyuan Zhang
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tyra G Wolfsberg
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience and Department of Biology, University of Florida, St. Augustine, Florida 32080, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, 1010 Vienna, Austria
| | - Bert Hobmayer
- Institute of Zoology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616, USA;
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77
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Portillo-Ledesma S, Li Z, Schlick T. Genome modeling: From chromatin fibers to genes. Curr Opin Struct Biol 2023; 78:102506. [PMID: 36577295 PMCID: PMC9908845 DOI: 10.1016/j.sbi.2022.102506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 11/06/2022] [Indexed: 12/27/2022]
Abstract
The intricacies of the 3D hierarchical organization of the genome have been approached by many creative modeling studies. The specific model/simulation technique combination defines and restricts the system and phenomena that can be investigated. We present the latest modeling developments and studies of the genome, involving models ranging from nucleosome systems and small polynucleosome arrays to chromatin fibers in the kb-range, chromosomes, and whole genomes, while emphasizing gene folding from first principles. Clever combinations allow the exploration of many interesting phenomena involved in gene regulation, such as nucleosome structure and dynamics, nucleosome-nucleosome stacking, polynucleosome array folding, protein regulation of chromatin architecture, mechanisms of gene folding, loop formation, compartmentalization, and structural transitions at the chromosome and genome levels. Gene-level modeling with full details on nucleosome positions, epigenetic factors, and protein binding, in particular, can in principle be scaled up to model chromosomes and cells to study fundamental biological regulation.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Zilong Li
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, 10003, NY, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, 10012, NY, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200122, China; Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, 10003, NY, USA.
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78
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Consistencies and contradictions in different polymer models of chromatin architecture. Comput Struct Biotechnol J 2023; 21:1084-1091. [PMID: 36789261 PMCID: PMC9900451 DOI: 10.1016/j.csbj.2023.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Genetic information is stored in very long DNA molecules, which are folded to form chromatin, a similarly long polymer fibre that is ultimately organised into chromosomes. The organisation of chromatin is fundamental to many cellular functions, from the expression of the genetic information to cell division. As a long polymer, chromatin is very flexible and may adopt a myriad of shapes. Globally, the polymer physics governing chromatin dynamics is very well understood. But chromatin is not uniform and regions of it, with chemical modifications and bound effectors, form domains and compartments through mechanisms not yet clear. Polymer models have been successfully used to investigate these mechanisms to explain cytological observations and build hypothesis for experimental validation. Many different approaches to conceptualise chromatin in polymer models can be envisioned and each reflects different aspects. Here, we compare recent approaches that aim at reproducing prominent features of interphase chromatin organisation: the compartmentalisation into eu- and heterochromatin compartments, the formation of a nucleolus, chromatin loops and the rosette and Rabl conformations of interphase chromosomes. We highlight commonalities and contradictions that point to a modulation of the mechanisms involved to fine degree. Consolidating models will require the inclusion of yet hidden or neglected parameters.
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79
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Contessoto VG, Dudchenko O, Aiden EL, Wolynes PG, Onuchic JN, Di Pierro M. Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nat Commun 2023; 14:326. [PMID: 36658127 PMCID: PMC9852290 DOI: 10.1038/s41467-023-35909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
We use data-driven physical simulations to study the three-dimensional architecture of the Aedes aegypti genome. Hi-C maps exhibit both a broad diagonal and compartmentalization with telomeres and centromeres clustering together. Physical modeling reveals that these observations correspond to an ensemble of 3D chromosomal structures that are folded over and partially condensed. Clustering of the centromeres and telomeres near the nuclear lamina appears to be a necessary condition for the formation of the observed structures. Further analysis of the mechanical properties of the genome reveals that the chromosomes of Aedes aegypti, by virtue of their atypical structural organization, are highly sensitive to the deformation of the nuclei. This last finding provides a possible physical mechanism linking mechanical cues to gene regulation.
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Affiliation(s)
- Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
- Instituto de Biociências, Letras e Ciências Exatas, UNESP - Univ. Estadual Paulista, Departamento de Física, São José do Rio Preto, SP, Brazil.
| | - Olga Dudchenko
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erez Lieberman Aiden
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Physics & Astronomy, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
- Department of Physics & Astronomy, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Biosciences, Rice University, Houston, TX, USA.
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA, USA.
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA.
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80
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Xia C, Huang L, Huang J, Zhang H, Huang Y, Benhamed M, Wang M, Chen X, Zhang M, Liu T, Chen W. Folding Features and Dynamics of 3D Genome Architecture in Plant Fungal Pathogens. Microbiol Spectr 2022; 10:e0260822. [PMID: 36250889 PMCID: PMC9769607 DOI: 10.1128/spectrum.02608-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/18/2022] [Indexed: 01/07/2023] Open
Abstract
The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi. Using high-throughput sequencing coupled with chromosome conformation capture (Hi-C) data, we generated two chromosome-level assemblies for Puccinia striiformis f. sp. tritici, a fungus causing stripe rust disease on wheat, for studying 3D genome architectures of plant pathogenic fungi. The chromatin organization of the fungus followed a combination of the fractal globule model and the equilibrium globule model. Surprisingly, chromosome compartmentalization was not detected. Dynamics of 3D genome organization during two developmental stages of P. striiformis f. sp. tritici indicated that regulation of gene activities might be independent of the changes of genome organization. In addition, chromatin conformation conservation was found to be independent of genome sequence synteny conservation among different fungi. These results highlighted the distinct folding principles of fungal 3D genomes. Our findings should be an important step toward a holistic understanding of the principles and functions of genome architecture across different eukaryotic kingdoms. IMPORTANCE Previously, our understanding of 3D genome architecture has mainly come from model mammals, insects, and plants. However, the organization and regulatory functions of 3D genomes in fungi are largely unknown. In this study, we comprehensively investigated P. striiformis f. sp. tritici, a plant fungal pathogen, and revealed distinct features of the 3D genome, comparing it with the universal folding feature of 3D genomes in higher eukaryotic organisms. We further suggested that there might be distinct regulatory mechanisms of gene expression that are independent of chromatin organization changes during the developmental stages of this rust fungus. Moreover, we showed that the evolutionary pattern of 3D genomes in this fungus is also different from the cases in mammalian genomes. In addition, the genome assembly pipeline and the generated two chromosome-level genomes will be valuable resources. These results highlighted the unexplored distinct features of 3D genome organization in fungi. Therefore, our study provided complementary knowledge to holistically understand the organization and functions of 3D genomes across different eukaryotes.
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Affiliation(s)
- Chongjing Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Liang Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Jie Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Huang
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Moussa Benhamed
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, Washington, USA
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
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81
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Álvarez-González L, Arias-Sardá C, Montes-Espuña L, Marín-Gual L, Vara C, Lister NC, Cuartero Y, Garcia F, Deakin J, Renfree MB, Robinson TJ, Martí-Renom MA, Waters PD, Farré M, Ruiz-Herrera A. Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals. Cell Rep 2022; 41:111839. [PMID: 36543130 DOI: 10.1016/j.celrep.2022.111839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/01/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
Studying the similarities and differences in genomic interactions between species provides fertile grounds for determining the evolutionary dynamics underpinning genome function and speciation. Here, we describe the principles of 3D genome folding in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (1) identified different patterns of chromosome folding in across vertebrate species (centromere clustering versus chromosomal territories); (2) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of species representative of the major therian phylogroups; (3) detected lineage-specific chromosome rearrangements; and (4) identified the dynamics of the structural properties of genome reshuffling through therian evolution. We present evidence of chromatin configurational changes that result from ancestral inversions and fusions/fissions. We catalog the close interplay between chromatin higher-order organization and therian genome evolution and introduce an interpretative hypothesis that explains how chromatin folding influences evolutionary patterns of genome reshuffling.
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Affiliation(s)
- Lucía Álvarez-González
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | - Laia Montes-Espuña
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Laia Marín-Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Covadonga Vara
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Nicholas C Lister
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Yasmina Cuartero
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Francisca Garcia
- Servei de Cultius Cel.lulars-SCAC, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Janine Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Marilyn B Renfree
- School of Biosciences, The University of Melbourne, Victoria, VIC 3010, Australia
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Marc A Martí-Renom
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
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82
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Regulation of the mitotic chromosome folding machines. Biochem J 2022; 479:2153-2173. [PMID: 36268993 DOI: 10.1042/bcj20210140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022]
Abstract
Over the last several years enormous progress has been made in identifying the molecular machines, including condensins and topoisomerases that fold mitotic chromosomes. The discovery that condensins generate chromatin loops through loop extrusion has revolutionized, and energized, the field of chromosome folding. To understand how these machines fold chromosomes with the appropriate dimensions, while disentangling sister chromatids, it needs to be determined how they are regulated and deployed. Here, we outline the current understanding of how these machines and factors are regulated through cell cycle dependent expression, chromatin localization, activation and inactivation through post-translational modifications, and through associations with each other, with other factors and with the chromatin template itself. There are still many open questions about how condensins and topoisomerases are regulated but given the pace of progress in the chromosome folding field, it seems likely that many of these will be answered in the years ahead.
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83
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Ward JR, Khan A, Torres S, Crawford B, Nock S, Frisbie T, Moran J, Longworth M. Condensin I and condensin II proteins form a LINE-1 dependent super condensin complex and cooperate to repress LINE-1. Nucleic Acids Res 2022; 50:10680-10694. [PMID: 36169232 PMCID: PMC9561375 DOI: 10.1093/nar/gkac802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Condensin I and condensin II are multi-subunit complexes that are known for their individual roles in genome organization and preventing genomic instability. However, interactions between condensin I and condensin II subunits and cooperative roles for condensin I and condensin II, outside of their genome organizing functions, have not been reported. We previously discovered that condensin II cooperates with Gamma Interferon Activated Inhibitor of Translation (GAIT) proteins to associate with Long INterspersed Element-1 (LINE-1 or L1) RNA and repress L1 protein expression and the retrotransposition of engineered L1 retrotransposition in cultured human cells. Here, we report that the L1 3'UTR is required for condensin II and GAIT association with L1 RNA, and deletion of the L1 RNA 3'UTR results in increased L1 protein expression and retrotransposition. Interestingly, like condensin II, we report that condensin I also binds GAIT proteins, associates with the L1 RNA 3'UTR, and represses L1 retrotransposition. We provide evidence that the condensin I protein, NCAPD2, is required for condensin II and GAIT protein association with L1 RNA. Furthermore, condensin I and condensin II subunits interact to form a L1-dependent super condensin complex (SCC) which is located primarily within the cytoplasm of both transformed and primary epithelial cells. These data suggest that increases in L1 expression in epithelial cells promote cytoplasmic condensin protein associations that facilitate a feedback loop in which condensins may cooperate to mediate L1 repression.
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Affiliation(s)
- Jacqueline R Ward
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Afshin Khan
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sabrina Torres
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bert Crawford
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sarah Nock
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Trenton Frisbie
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
- Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Michelle S Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, USA
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84
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Nishimura O, Rozewicki J, Yamaguchi K, Tatsumi K, Ohishi Y, Ohta T, Yagura M, Niwa T, Tanegashima C, Teramura A, Hirase S, Kawaguchi A, Tan M, D'Aniello S, Castro F, Machado A, Koyanagi M, Terakita A, Misawa R, Horie M, Kawasaki J, Asahida T, Yamaguchi A, Murakumo K, Matsumoto R, Irisarri I, Miyamoto N, Toyoda A, Tanaka S, Sakamoto T, Semba Y, Yamauchi S, Yamada K, Nishida K, Kiyatake I, Sato K, Hyodo S, Kadota M, Uno Y, Kuraku S. Squalomix: shark and ray genome analysis consortium and its data sharing platform. F1000Res 2022; 11:1077. [PMID: 36262334 PMCID: PMC9561540 DOI: 10.12688/f1000research.123591.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.
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Affiliation(s)
- Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - John Rozewicki
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Tazro Ohta
- Joint Support-Center for Data Science Research, Database Center for Life Science, Mishima, Shizuoka, 411-8540, Japan
| | - Masaru Yagura
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Taiki Niwa
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Akinori Teramura
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Akane Kawaguchi
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Filipe Castro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal
| | - André Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Ryo Misawa
- Japan Fisheries Research and Education Agency, Hachinohe, Aomori, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Junna Kawasaki
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Takashi Asahida
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Atsuko Yamaguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
| | | | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature-Zoology, Hamburg, 20146, Germany
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sho Tanaka
- School of Marine Science and Technology, Tokai University, Shizuoka, Shizuoka, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi, Japan., Okayama, Japan
| | - Yasuko Semba
- Highly Migratory Resources Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shizuoka, Shizuoka, Japan
| | | | - Kazuyuki Yamada
- Marine Science Museum, Tokai University, Shizuoka, Shizuoka, Japan
| | | | | | - Keiichi Sato
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo,, Kashiwa, Chiba, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan,
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85
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García Fernández F, Almayrac E, Carré Simon À, Batrin R, Khalil Y, Boissac M, Fabre E. Global chromatin mobility induced by a DSB is dictated by chromosomal conformation and defines the HR outcome. eLife 2022; 11:78015. [PMID: 36125964 PMCID: PMC9489209 DOI: 10.7554/elife.78015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/08/2022] [Indexed: 12/16/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) is crucial for genome integrity. A conserved response to DSBs is an increase in chromatin mobility that can be local, at the site of the DSB, or global, at undamaged regions of the genome. Here, we address the function of global chromatin mobility during homologous recombination (HR) of a single, targeted, controlled DSB. We set up a system that tracks HR in vivo over time and show that two types of DSB-induced global chromatin mobility are involved in HR, depending on the position of the DSB. Close to the centromere, a DSB induces global mobility that depends solely on H2A(X) phosphorylation and accelerates repair kinetics, but is not essential. In contrast, the global mobility induced by a DSB away from the centromere becomes essential for HR repair and is triggered by homology search through a mechanism that depends on H2A(X) phosphorylation, checkpoint progression, and Rad51. Our data demonstrate that global mobility is governed by chromosomal conformation and differentially coordinates repair by HR.
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Affiliation(s)
| | - Etienne Almayrac
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Ànnia Carré Simon
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Renaud Batrin
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Yasmine Khalil
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Michel Boissac
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Emmanuelle Fabre
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
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86
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Yoshida MM, Kinoshita K, Aizawa Y, Tane S, Yamashita D, Shintomi K, Hirano T. Molecular dissection of condensin II-mediated chromosome assembly using in vitro assays. eLife 2022; 11:78984. [PMID: 35983835 PMCID: PMC9433093 DOI: 10.7554/elife.78984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/11/2022] [Indexed: 11/18/2022] Open
Abstract
In vertebrates, condensin I and condensin II cooperate to assemble rod-shaped chromosomes during mitosis. Although the mechanism of action and regulation of condensin I have been studied extensively, our corresponding knowledge of condensin II remains very limited. By introducing recombinant condensin II complexes into Xenopus egg extracts, we dissect the roles of its individual subunits in chromosome assembly. We find that one of two HEAT subunits, CAP-D3, plays a crucial role in condensin II-mediated assembly of chromosome axes, whereas the other HEAT subunit, CAP-G2, has a very strong negative impact on this process. The structural maintenance of chromosomes ATPase and the basic amino acid clusters of the kleisin subunit CAP-H2 are essential for this process. Deletion of the C-terminal tail of CAP-D3 increases the ability of condensin II to assemble chromosomes and further exposes a hidden function of CAP-G2 in the lateral compaction of chromosomes. Taken together, our results uncover a multilayered regulatory mechanism unique to condensin II, and provide profound implications for the evolution of condensin II.
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Affiliation(s)
| | | | - Yuuki Aizawa
- Chromosome Dynamics Laboratory, RIKEN, Wako, Japan
| | - Shoji Tane
- Chromosome Dynamics Laboratory, RIKEN, Wako, Japan
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87
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A mechanism regulating centromere distribution in Arabidopsis thaliana. NATURE PLANTS 2022; 8:877-878. [PMID: 35948627 DOI: 10.1038/s41477-022-01204-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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88
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Sakamoto T, Sakamoto Y, Grob S, Slane D, Yamashita T, Ito N, Oko Y, Sugiyama T, Higaki T, Hasezawa S, Tanaka M, Matsui A, Seki M, Suzuki T, Grossniklaus U, Matsunaga S. Two-step regulation of centromere distribution by condensin II and the nuclear envelope proteins. NATURE PLANTS 2022; 8:940-953. [PMID: 35915144 DOI: 10.1038/s41477-022-01200-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
The arrangement of centromeres within the nucleus differs among species and cell types. However, neither the mechanisms determining centromere distribution nor its biological significance are currently well understood. In this study, we demonstrate the importance of centromere distribution for the maintenance of genome integrity through the cytogenic and molecular analysis of mutants defective in centromere distribution. We propose a two-step regulatory mechanism that shapes the non-Rabl-like centromere distribution in Arabidopsis thaliana through condensin II and the linker of the nucleoskeleton and cytoskeleton (LINC) complex. Condensin II is enriched at centromeres and, in cooperation with the LINC complex, induces the scattering of centromeres around the nuclear periphery during late anaphase/telophase. After entering interphase, the positions of the scattered centromeres are then stabilized by nuclear lamina proteins of the CROWDED NUCLEI (CRWN) family. We also found that, despite their strong impact on centromere distribution, condensin II and CRWN proteins have little effect on chromatin organization involved in the control of gene expression, indicating a robustness of chromatin organization regardless of the type of centromere distribution.
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Affiliation(s)
- Takuya Sakamoto
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan.
| | - Yuki Sakamoto
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Department of Biological Sciences, Osaka University, Toyonaka, Japan
| | - Stefan Grob
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Daniel Slane
- Department of Integrated Biosciences, The University of Tokyo, Kashiwa, Japan
| | - Tomoe Yamashita
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Nanami Ito
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Department of Integrated Biosciences, The University of Tokyo, Kashiwa, Japan
| | - Yuka Oko
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Tomoya Sugiyama
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Takumi Higaki
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, Japan
| | - Seiichiro Hasezawa
- Department of Integrated Biosciences, The University of Tokyo, Kashiwa, Japan
- Graduate School of Science and Engineering, Hosei University, Tokyo, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan.
- Department of Integrated Biosciences, The University of Tokyo, Kashiwa, Japan.
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89
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Hofstatter PG, Thangavel G, Lux T, Neumann P, Vondrak T, Novak P, Zhang M, Costa L, Castellani M, Scott A, Toegelová H, Fuchs J, Mata-Sucre Y, Dias Y, Vanzela AL, Huettel B, Almeida CC, Šimková H, Souza G, Pedrosa-Harand A, Macas J, Mayer KF, Houben A, Marques A. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell 2022; 185:3153-3168.e18. [DOI: 10.1016/j.cell.2022.06.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 01/30/2023]
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90
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Contessoto VG, Cheng RR, Onuchic JN. Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling. Curr Opin Struct Biol 2022; 75:102418. [PMID: 35839701 DOI: 10.1016/j.sbi.2022.102418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/04/2022] [Accepted: 06/03/2022] [Indexed: 11/03/2022]
Abstract
In recent years, much effort has been devoted to understanding the three-dimensional (3D) organization of the genome and how genomic structure mediates nuclear function. The development of experimental techniques that combine DNA proximity ligation with high-throughput sequencing, such as Hi-C, have substantially improved our knowledge about chromatin organization. Numerous experimental advancements, not only utilizing DNA proximity ligation but also high-resolution genome imaging (DNA tracing), have required theoretical modeling to determine the structural ensembles consistent with such data. These 3D polymer models of the genome provide an understanding of the physical mechanisms governing genome architecture. Here, we present an overview of the recent advances in modeling the ensemble of 3D chromosomal structures by employing the maximum entropy approach combined with polymer physics. Particularly, we discuss the minimal chromatin model (MiChroM) along with the "maximum entropy genomic annotations from biomarkers associated with structural ensembles" (MEGABASE) model, which have been remarkably successful in the accurate modeling of chromosomes consistent with both Hi-C and DNA-tracing data.
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Affiliation(s)
- Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. https://twitter.com/Vini_Contessoto
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. https://twitter.com/ryanrcheng
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Department of Physics and Astronomy, Rice University, Houston, TX, USA; Department of Chemistry, Rice University, Houston, TX, USA; Department of Biosciences, Rice University, Houston, TX, USA.
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91
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Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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92
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Li CX, Liu L, Zhang T, Luo XM, Feng JX, Zhao S. Three-Dimensional Genome Map of the Filamentous Fungus Penicillium oxalicum. Microbiol Spectr 2022; 10:e0212121. [PMID: 35499317 PMCID: PMC9241887 DOI: 10.1128/spectrum.02121-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 01/14/2023] Open
Abstract
Higher-order spatial organization of the chromatin in the nucleus plays crucial roles in the maintenance of cell functions and the regulation of gene expression. Three-dimensional (3D) genome sequencing has been used to great effect in mammal and plants, but the availability of 3D genomes of filamentous fungi is severely limited. Here, we performed a chromosome-level genome assembly of Penicillium oxalicum through single-molecule real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C), with a scaffold N50 of 4.07 Mb and a contig N50 of 3.81 Mb, and further elucidated the 3D genome architecture of P. oxalicum. High-frequency interchromosomal contacts occurred within the centromeres and telomeres, as well as within individual chromosomes. There were 12,203 cis-interactions and 7,884 trans-interactions detected at a resolution of 1 kb. Moreover, a total of 1,099 topologically associated domains (or globules) were found, ranging in size from 2.0 to 76.0 kb. Interestingly, transcription factor-bound motifs were enriched in the globule boundaries. All the cellulase and xylanase genes were discretely distributed in the 3D model of the P. oxalicum genome as a result of few cis- and trans-interactions. Our results from this study provide a global view of chromatin interactions in the P. oxalicum genome and will act as a resource for studying spatial regulation of gene expression in filamentous fungi. IMPORTANCE The spatial structure of chromatin plays important roles in normal cell functions and the regulation of gene expression. The three-dimensional (3D) architectures of the genomes of many mammals and plants have been elucidated, but corresponding studies on filamentous fungi, which play vital roles as decomposers of organic matter in the soil, are very limited. Penicillium oxalicum is one of the predominant cellulolytic aerobic fungi in subtropical and tropical forest soils and can secrete integrative cellulase and xylanase under integrated regulatory control, degrading plant biomass highly efficiently. In the present study, we employed Hi-C technology to construct the 3D genome model of P. oxalicum strain HP7-1 and to further investigate cellulase and xylanase as well as transcription factor genes in 3D genome. These results provide a resource to achieve a deeper understanding of cell function and the regulation of gene expression in filamentous fungi.
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Affiliation(s)
- Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
- Anhui Key Laboratory of Infection and Immunity, Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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93
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Yoshida Y, Tanaka S. Deciphering the Biological Enigma-Genomic Evolution Underlying Anhydrobiosis in the Phylum Tardigrada and the Chironomid Polypedilum vanderplanki. INSECTS 2022; 13:557. [PMID: 35735894 PMCID: PMC9224920 DOI: 10.3390/insects13060557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023]
Abstract
Anhydrobiosis, an ametabolic dehydrated state triggered by water loss, is observed in several invertebrate lineages. Anhydrobiotes revive when rehydrated, and seem not to suffer the ultimately lethal cell damage that results from severe loss of water in other organisms. Here, we review the biochemical and genomic evidence that has revealed the protectant molecules, repair systems, and maintenance pathways associated with anhydrobiosis. We then introduce two lineages in which anhydrobiosis has evolved independently: Tardigrada, where anhydrobiosis characterizes many species within the phylum, and the genus Polypedilum, where anhydrobiosis occurs in only two species. Finally, we discuss the complexity of the evolution of anhydrobiosis within invertebrates based on current knowledge, and propose perspectives to enhance the understanding of anhydrobiosis.
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Affiliation(s)
- Yuki Yoshida
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Sae Tanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Institute for Advanced Biosciences, Keio University, 341-1 Mizukami, Tsuruoka 997-0052, Japan
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94
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Generation of dynamic three-dimensional genome structure through phase separation of chromatin. Proc Natl Acad Sci U S A 2022; 119:e2109838119. [PMID: 35617433 PMCID: PMC9295772 DOI: 10.1073/pnas.2109838119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Significance DNA functions in living cells are crucially affected by the three-dimensional genome structure and dynamics. We analyze the whole genome of human cells by developing a polymer model of interphase nuclei. The model reveals the essential importance of the unfolding process of chromosomes from the condensed mitotic state for describing the interphase nuclei; through the unfolding process, heterogeneous repulsive interactions among chromatin chains induce phase separation of chromatin, which quantitatively explains the experimentally observed various genomic data. We can use this model structure as a platform to analyze the relationship among genome structure, dynamics, and functions.
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95
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Domb K, Wang N, Hummel G, Liu C. Spatial Features and Functional Implications of Plant 3D Genome Organization. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:173-200. [PMID: 35130445 DOI: 10.1146/annurev-arplant-102720-022810] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The advent of high-throughput sequencing-based methods for chromatin conformation, accessibility, and immunoprecipitation assays has been a turning point in 3D genomics. Altogether, these new tools have been pushing upward the interpretation of pioneer cytogenetic evidence for a higher order in chromatin packing. Here, we review the latest development in our understanding of plant spatial genome structures and different levels of organization and discuss their functional implications. Then, we spotlight the complexity of organellar (i.e., mitochondria and plastids) genomes and discuss their 3D packing into nucleoids. Finally, we propose unaddressed research axes to investigate functional links between chromatin-like dynamics and transcriptional regulation within organellar nucleoids.
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Affiliation(s)
- Katherine Domb
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Nan Wang
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Guillaume Hummel
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany;
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96
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Abstract
Many pathogens or symbionts of animals and plants contain multiple replicons, a configuration called a multipartite genome. Multipartite genomes enable those species to replicate their genomes faster and better adapt to new niches. Despite their prevalence, the mechanisms by which multipartite genomes are stably maintained are poorly understood. Agrobacterium tumefaciens is a plant pathogen that contains four replicons: a circular chromosome (Ch1), a linear chromosome (Ch2), and two large plasmids. Recent work indicates that their replication origins are clustered at the cell poles in a manner that depends on their ParB family centromeric proteins: ParB1 for Ch1 and individual RepB paralogs for Ch2 and the plasmids. However, understanding of these interactions and how they contribute to genome maintenance is limited. By combining genome-wide chromosome conformation capture (Hi-C) assays, chromatin-immunoprecipitation sequencing (ChIP-seq), and live cell fluorescence microscopy, we provide evidence here that centromeric clustering is mediated by interactions between these centromeric proteins. We further show that the disruption of centromere clustering results in the loss of replicons. Our data establish the role of centromeric clustering in multipartite genome stability. IMPORTANCE About 10% of sequenced bacteria have multiple replicons, also known as multipartite genomes. How these multipartite genomes are maintained is still poorly understood. Here, we use Agrobacterium tumefaciens as a model and show that the replication origins of the four replicons are clustered through direct interactions between the centromeric proteins; disruption of origin clustering leads to the loss of replicons. Thus, our study provided evidence that centromeric clustering is important for maintaining multipartite genomes.
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97
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Li D, He M, Tang Q, Tian S, Zhang J, Li Y, Wang D, Jin L, Ning C, Zhu W, Hu S, Long K, Ma J, Liu J, Zhang Z, Li M. Comparative 3D genome architecture in vertebrates. BMC Biol 2022; 20:99. [PMID: 35524220 PMCID: PMC9077971 DOI: 10.1186/s12915-022-01301-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The three-dimensional (3D) architecture of the genome has a highly ordered and hierarchical nature, which influences the regulation of essential nuclear processes at the basis of gene expression, such as gene transcription. While the hierarchical organization of heterochromatin and euchromatin can underlie differences in gene expression that determine evolutionary differences among species, the way 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. RESULTS This analysis shows a correlation between genome size and chromosome length that affects chromosome territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through the evolution of vertebrates. Furthermore, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. CONCLUSIONS Our analysis uncovers organizational features that appear to determine the conservation and transcriptional regulation of functional genes across species. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.
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Affiliation(s)
- Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shilin Tian
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Novogene Bioinformatics Institute, Beijing, 100000, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Danyang Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chunyou Ning
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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98
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Rodriguez S, Ward A, Reckard AT, Shtanko Y, Hull-Crew C, Klocko AD. The genome organization of Neurospora crassa at high resolution uncovers principles of fungal chromosome topology. G3 (BETHESDA, MD.) 2022; 12:jkac053. [PMID: 35244156 PMCID: PMC9073679 DOI: 10.1093/g3journal/jkac053] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/25/2022] [Indexed: 01/17/2023]
Abstract
The eukaryotic genome must be precisely organized for its proper function, as genome topology impacts transcriptional regulation, cell division, replication, and repair, among other essential processes. Disruptions to human genome topology can lead to diseases, including cancer. The advent of chromosome conformation capture with high-throughput sequencing (Hi-C) to assess genome organization has revolutionized the study of nuclear genome topology; Hi-C has elucidated numerous genomic structures, including chromosomal territories, active/silent chromatin compartments, Topologically Associated Domains, and chromatin loops. While low-resolution heatmaps can provide important insights into chromosomal level contacts, high-resolution Hi-C datasets are required to reveal folding principles of individual genes. Of particular interest are high-resolution chromosome conformation datasets of organisms modeling the human genome. Here, we report the genome topology of the fungal model organism Neurospora crassa at a high resolution. Our composite Hi-C dataset, which merges 2 independent datasets generated with restriction enzymes that monitor euchromatin (DpnII) and heterochromatin (MseI), along with our DpnII/MseI double digest dataset, provide exquisite detail for both the conformation of entire chromosomes and the folding of chromatin at the resolution of individual genes. Within constitutive heterochromatin, we observe strong yet stochastic internal contacts, while euchromatin enriched with either activating or repressive histone post-translational modifications associates with constitutive heterochromatic regions, suggesting intercompartment contacts form to regulate transcription. Consistent with this, a strain with compromised heterochromatin experiences numerous changes in gene expression. Our high-resolution Neurospora Hi-C datasets are outstanding resources to the fungal community and provide valuable insights into higher organism genome topology.
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Affiliation(s)
- Sara Rodriguez
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Ashley Ward
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Andrew T Reckard
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Yulia Shtanko
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Clayton Hull-Crew
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
| | - Andrew D Klocko
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA
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99
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Brahmachari S, Contessoto V, Di Pierro M, Onuchic J. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. Nucleic Acids Res 2022; 50:4258-4271. [PMID: 35420130 PMCID: PMC9071446 DOI: 10.1093/nar/gkac231] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023] Open
Abstract
The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.
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Affiliation(s)
| | | | - Michele Di Pierro
- Department of Physics, and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston TX 77005, USA
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100
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Yang F, Pecinka A. Multiple Roles of SMC5/6 Complex during Plant Sexual Reproduction. Int J Mol Sci 2022; 23:ijms23094503. [PMID: 35562893 PMCID: PMC9099584 DOI: 10.3390/ijms23094503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Chromatin-based processes are essential for cellular functions. Structural maintenance of chromosomes (SMCs) are evolutionarily conserved molecular machines that organize chromosomes throughout the cell cycle, mediate chromosome compaction, promote DNA repair, or control sister chromatid attachment. The SMC5/6 complex is known for its pivotal role during the maintenance of genome stability. However, a dozen recent plant studies expanded the repertoire of SMC5/6 complex functions to the entire plant sexual reproductive phase. The SMC5/6 complex is essential in meiosis, where its activity must be precisely regulated to allow for normal meiocyte development. Initially, it is attenuated by the recombinase RAD51 to allow for efficient strand invasion by the meiosis-specific recombinase DMC1. At later stages, it is essential for the normal ratio of interfering and non-interfering crossovers, detoxifying aberrant joint molecules, preventing chromosome fragmentation, and ensuring normal chromosome/sister chromatid segregation. The latter meiotic defects lead to the production of diploid male gametes in Arabidopsis SMC5/6 complex mutants, increased seed abortion, and production of triploid offspring. The SMC5/6 complex is directly involved in controlling normal embryo and endosperm cell divisions, and pioneer studies show that the SMC5/6 complex is also important for seed development and normal plant growth in cereals.
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Affiliation(s)
- Fen Yang
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
- Correspondence:
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