1
|
Solovei I, Mirny L. Spandrels of the cell nucleus. Curr Opin Cell Biol 2024; 90:102421. [PMID: 39180905 DOI: 10.1016/j.ceb.2024.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/18/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
S.J. Gould and R. Lewontin in their famous "Spandrels paper" (1979) argued that many anatomical elements arise in evolution not due to their "current utility" but rather due to other "reasons for origin", such as other developmental processes, physical constraints and mechanical forces. Here, in the same spirit, we argue that a variety of molecular processes, physical constraints, and mechanical forces, alone or together, generate structures that are detectable in the cell nucleus, yet these structures themselves may not carry any specific function, being a mere reflection of processes that produced them.
Collapse
Affiliation(s)
- Irina Solovei
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
2
|
Gil J, Navarrete E, Rosin L, Chowdhury N, Abraham S, Cornilleau G, Lei E, Mozziconacci J, Mirny L, Muller H, Drinnenberg I. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. RESEARCH SQUARE 2024:rs.3.rs-4732646. [PMID: 39149482 PMCID: PMC11326380 DOI: 10.21203/rs.3.rs-4732646/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkmoth, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded "S," with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
Collapse
Affiliation(s)
- J. Gil
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - E. Navarrete
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - L.F. Rosin
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - N. Chowdhury
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - S. Abraham
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - G. Cornilleau
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - E.P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - J. Mozziconacci
- StrInG Lab, Museum National d’Histoire Naturelle, Paris, France
| | - L.A. Mirny
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - H. Muller
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| | - I.A. Drinnenberg
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, 75005 Paris, France
| |
Collapse
|
3
|
Gil J, Rosin LF, Navarrete E, Chowdhury N, Abraham S, Cornilleau G, Lei EP, Mozziconacci J, Mirny LA, Muller H, Drinnenberg IA. Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557757. [PMID: 37745315 PMCID: PMC10515926 DOI: 10.1101/2023.09.14.557757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkworm, Bombyx mori. In contrast to other eukaryotes, B. mori chromosomes form highly separated territories. Similar to other eukaryotes, B. mori chromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded S, with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
Collapse
|
4
|
Nagao K, Mochizuki K. Genome organization: Raison d'être of ancestral linkage groups. Curr Biol 2024; 34:R544-R546. [PMID: 38834029 DOI: 10.1016/j.cub.2024.04.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The genomes of extant organisms contain conserved blocks of regions that can be traced back to ancient ancestors, yet the evolutionary pressures that maintained such genomic segments remain unclear. New research on a curious organism with two different genomes sheds light on why our genomes are organized as they are.
Collapse
Affiliation(s)
- Kohei Nagao
- Institute of Human Genetics (IGH), CNRS and University of Montpellier, Montpellier, France
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS and University of Montpellier, Montpellier, France.
| |
Collapse
|
5
|
Hockens C, Lorenzi H, Wang TT, Lei EP, Rosin LF. Chromosome segregation during spermatogenesis occurs through a unique center-kinetic mechanism in holocentric moth species. PLoS Genet 2024; 20:e1011329. [PMID: 38913752 PMCID: PMC11226059 DOI: 10.1371/journal.pgen.1011329] [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: 10/13/2023] [Revised: 07/05/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Precise regulation of chromosome dynamics in the germline is essential for reproductive success across species. Yet, the mechanisms underlying meiotic chromosomal events such as homolog pairing and chromosome segregation are not fully understood in many species. Here, we employ Oligopaint DNA FISH to investigate mechanisms of meiotic homolog pairing and chromosome segregation in the holocentric pantry moth, Plodia interpunctella, and compare our findings to new and previous studies in the silkworm moth, Bombyx mori, which diverged from P. interpunctella over 100 million years ago. We find that pairing in both Bombyx and Plodia spermatogenesis is initiated at gene-rich chromosome ends. Additionally, both species form rod shaped cruciform-like bivalents at metaphase I. However, unlike the telomere-oriented chromosome segregation mechanism observed in Bombyx, Plodia can orient bivalents in multiple different ways at metaphase I. Surprisingly, in both species we find that kinetochores consistently assemble at non-telomeric loci toward the center of chromosomes regardless of where chromosome centers are located in the bivalent. Additionally, sister kinetochores do not seem to be paired in these species. Instead, four distinct kinetochores are easily observed at metaphase I. Despite this, we find clear end-on microtubule attachments and not lateral microtubule attachments co-orienting these separated kinetochores. These findings challenge the classical view of segregation where paired, poleward-facing kinetochores are required for accurate homolog separation in meiosis I. Our studies here highlight the importance of exploring fundamental processes in non-model systems, as employing novel organisms can lead to the discovery of novel biology.
Collapse
Affiliation(s)
- Clio Hockens
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hernan Lorenzi
- TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tricia T. Wang
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Leah F. Rosin
- Unit on Chromosome Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
6
|
Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [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: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
Collapse
Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
| |
Collapse
|
7
|
Mierke CT. Extracellular Matrix Cues Regulate Mechanosensing and Mechanotransduction of Cancer Cells. Cells 2024; 13:96. [PMID: 38201302 PMCID: PMC10777970 DOI: 10.3390/cells13010096] [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: 11/12/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Extracellular biophysical properties have particular implications for a wide spectrum of cellular behaviors and functions, including growth, motility, differentiation, apoptosis, gene expression, cell-matrix and cell-cell adhesion, and signal transduction including mechanotransduction. Cells not only react to unambiguously mechanical cues from the extracellular matrix (ECM), but can occasionally manipulate the mechanical features of the matrix in parallel with biological characteristics, thus interfering with downstream matrix-based cues in both physiological and pathological processes. Bidirectional interactions between cells and (bio)materials in vitro can alter cell phenotype and mechanotransduction, as well as ECM structure, intentionally or unintentionally. Interactions between cell and matrix mechanics in vivo are of particular importance in a variety of diseases, including primarily cancer. Stiffness values between normal and cancerous tissue can range between 500 Pa (soft) and 48 kPa (stiff), respectively. Even the shear flow can increase from 0.1-1 dyn/cm2 (normal tissue) to 1-10 dyn/cm2 (cancerous tissue). There are currently many new areas of activity in tumor research on various biological length scales, which are highlighted in this review. Moreover, the complexity of interactions between ECM and cancer cells is reduced to common features of different tumors and the characteristics are highlighted to identify the main pathways of interaction. This all contributes to the standardization of mechanotransduction models and approaches, which, ultimately, increases the understanding of the complex interaction. Finally, both the in vitro and in vivo effects of this mechanics-biology pairing have key insights and implications for clinical practice in tumor treatment and, consequently, clinical translation.
Collapse
Affiliation(s)
- Claudia Tanja Mierke
- Biological Physics Division, Peter Debye Institute of Soft Matter Physics, Faculty of Physics and Earth Science, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
| |
Collapse
|
8
|
Chung YC, Tu LC. Interplay of dynamic genome organization and biomolecular condensates. Curr Opin Cell Biol 2023; 85:102252. [PMID: 37806293 DOI: 10.1016/j.ceb.2023.102252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/01/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
After 60 years of chromatin investigation, our understanding of chromatin organization has evolved from static chromatin fibers to dynamic nuclear compartmentalization. Chromatin is embedded in a heterogeneous nucleoplasm in which molecules are grouped into distinct compartments, partitioning nuclear space through phase separation. Human genome organization affects transcription which controls euchromatin formation by excluding inactive chromatin. Chromatin condensates have been described as either liquid-like or solid-like. In this short review, we discuss the dynamic nature of chromatin from the perspective of biomolecular condensates and highlight new live-cell synthetic tools to probe and manipulate chromatin organization and associated condensates.
Collapse
Affiliation(s)
- Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Li-Chun Tu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
9
|
Piemonte KM, Webb BM, Bobbitt JR, Majmudar PR, Cuellar-Vite L, Bryson BL, Latina NC, Seachrist DD, Keri RA. Disruption of CDK7 signaling leads to catastrophic chromosomal instability coupled with a loss of condensin-mediated chromatin compaction. J Biol Chem 2023; 299:104834. [PMID: 37201585 PMCID: PMC10300262 DOI: 10.1016/j.jbc.2023.104834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/20/2023] Open
Abstract
Chromatin organization is highly dynamic and modulates DNA replication, transcription, and chromosome segregation. Condensin is essential for chromosome assembly during mitosis and meiosis, as well as maintenance of chromosome structure during interphase. While it is well established that sustained condensin expression is necessary to ensure chromosome stability, the mechanisms that control its expression are not yet known. Herein, we report that disruption of cyclin-dependent kinase 7 (CDK7), the core catalytic subunit of CDK-activating kinase, leads to reduced transcription of several condensin subunits, including structural maintenance of chromosomes 2 (SMC2). Live and static microscopy revealed that inhibiting CDK7 signaling prolongs mitosis and induces chromatin bridge formation, DNA double-strand breaks, and abnormal nuclear features, all of which are indicative of mitotic catastrophe and chromosome instability. Affirming the importance of condensin regulation by CDK7, genetic suppression of the expression of SMC2, a core subunit of this complex, phenocopies CDK7 inhibition. Moreover, analysis of genome-wide chromatin conformation using Hi-C revealed that sustained activity of CDK7 is necessary to maintain chromatin sublooping, a function that is ascribed to condensin. Notably, the regulation of condensin subunit gene expression is independent of superenhancers. Together, these studies reveal a new role for CDK7 in sustaining chromatin configuration by ensuring the expression of condensin genes, including SMC2.
Collapse
Affiliation(s)
- Katrina M Piemonte
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Bryan M Webb
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jessica R Bobbitt
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Parth R Majmudar
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Leslie Cuellar-Vite
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Benjamin L Bryson
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Nicholas C Latina
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ruth A Keri
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Department of General Medical Sciences-Oncology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
| |
Collapse
|
10
|
Streb P, Kowarz E, Benz T, Reis J, Marschalek R. How chromosomal translocations arise to cause cancer: Gene proximity, trans-splicing, and DNA end joining. iScience 2023; 26:106900. [PMID: 37378346 PMCID: PMC10291325 DOI: 10.1016/j.isci.2023.106900] [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: 11/28/2022] [Revised: 04/01/2023] [Accepted: 05/12/2023] [Indexed: 06/29/2023] Open
Abstract
Chromosomal translocations (CTs) are a genetic hallmark of cancer. They could be identified as recurrent genetic aberrations in hemato-malignancies and solid tumors. More than 40% of all "cancer genes" were identified in recurrent CTs. Most of these CTs result in the production of oncofusion proteins of which many have been studied over the past decades. They influence signaling pathways and/or alter gene expression. However, a precise mechanism for how these CTs arise and occur in a nearly identical fashion in individuals remains to be elucidated. Here, we performed experiments that explain the onset of CTs: (1) proximity of genes able to produce prematurely terminated transcripts, which lead to the production of (2) trans-spliced fusion RNAs, and finally, the induction of (3) DNA double-strand breaks which are subsequently repaired via EJ repair pathways. Under these conditions, balanced chromosomal translocations could be specifically induced. The implications of these findings will be discussed.
Collapse
Affiliation(s)
- Patrick Streb
- Goethe-University, Department Biochemistry, Chemistry & Pharmacy, Institute of Pharmaceutical Biology, Max-von-Laue-Street 9, 60438 Frankfurt am Main, Germany
| | - Eric Kowarz
- Goethe-University, Department Biochemistry, Chemistry & Pharmacy, Institute of Pharmaceutical Biology, Max-von-Laue-Street 9, 60438 Frankfurt am Main, Germany
| | - Tamara Benz
- Goethe-University, Department Biochemistry, Chemistry & Pharmacy, Institute of Pharmaceutical Biology, Max-von-Laue-Street 9, 60438 Frankfurt am Main, Germany
| | - Jennifer Reis
- Goethe-University, Department Biochemistry, Chemistry & Pharmacy, Institute of Pharmaceutical Biology, Max-von-Laue-Street 9, 60438 Frankfurt am Main, Germany
| | - Rolf Marschalek
- Goethe-University, Department Biochemistry, Chemistry & Pharmacy, Institute of Pharmaceutical Biology, Max-von-Laue-Street 9, 60438 Frankfurt am Main, Germany
| |
Collapse
|
11
|
Wang L, Wang X, Liu C, Xu W, Kuang W, Bu Q, Li H, Zhao Y, Jiang L, Chen Y, Qin F, Li S, Wei Q, Liu X, Liu B, Chen Y, Dai Y, Wang H, Tian J, Cao G, Zhao Y, Cen X. Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neurons. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:551-572. [PMID: 37209997 PMCID: PMC10787020 DOI: 10.1016/j.gpb.2023.03.003] [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: 11/06/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/22/2023]
Abstract
The expression of linear DNA sequence is precisely regulated by the three-dimensional (3D) architecture of chromatin. Morphine-induced aberrant gene networks of neurons have been extensively investigated; however, how morphine impacts the 3D genomic architecture of neurons is still unknown. Here, we applied digestion-ligation-only high-throughput chromosome conformation capture (DLO Hi-C) technology to investigate the effects of morphine on the 3D chromatin architecture of primate cortical neurons. After receiving continuous morphine administration for 90 days on rhesus monkeys, we discovered that morphine re-arranged chromosome territories, with a total of 391 segmented compartments being switched. Morphine altered over half of the detected topologically associated domains (TADs), most of which exhibited a variety of shifts, followed by separating and fusing types. Analysis of the looping events at kilobase-scale resolution revealed that morphine increased not only the number but also the length of differential loops. Moreover, all identified differentially expressed genes from the RNA sequencing data were mapped to the specific TAD boundaries or differential loops, and were further validated for changed expression. Collectively, an altered 3D genomic architecture of cortical neurons may regulate the gene networks associated with morphine effects. Our finding provides critical hubs connecting chromosome spatial organization and gene networks associated with the morphine effects in humans.
Collapse
Affiliation(s)
- Liang Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaojie Wang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Chunqi Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wei Xu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China; Shenzhen Key Laboratory of Drug Addiction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weihong Kuang
- Department of Psychiatry, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qian Bu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hongchun Li
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Ying Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Linhong Jiang
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yaxing Chen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Feng Qin
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shu Li
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qinfan Wei
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaocong Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Bin Liu
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yuanyuan Chen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yanping Dai
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Jingwei Tian
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinglan Zhao
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiaobo Cen
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China.
| |
Collapse
|
12
|
Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
Collapse
Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
| |
Collapse
|
13
|
Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
Collapse
Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | |
Collapse
|
14
|
Recurrent Translocations in Topoisomerase Inhibitor-Related Leukemia Are Determined by the Features of DNA Breaks Rather Than by the Proximity of the Translocating Genes. Int J Mol Sci 2022; 23:ijms23179824. [PMID: 36077220 PMCID: PMC9456246 DOI: 10.3390/ijms23179824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 11/25/2022] Open
Abstract
Topoisomerase inhibitors are widely used in cancer chemotherapy. However, one of the potential long-term adverse effects of such therapy is acute leukemia. A key feature of such therapy-induced acute myeloid leukemia (t-AML) is recurrent chromosomal translocations involving AML1 (RUNX1) or MLL (KMT2A) genes. The formation of chromosomal translocation depends on the spatial proximity of translocation partners and the mobility of the DNA ends. It is unclear which of these two factors might be decisive for recurrent t-AML translocations. Here, we used fluorescence in situ hybridization (FISH) and chromosome conformation capture followed by sequencing (4C-seq) to investigate double-strand DNA break formation and the mobility of broken ends upon etoposide treatment, as well as contacts between translocation partner genes. We detected the separation of the parts of the broken AML1 gene, as well as the increased mobility of these separated parts. 4C-seq analysis showed no evident contacts of AML1 and MLL with loci, implicated in recurrent t-AML translocations, either before or after etoposide treatment. We suggest that separation of the break ends and their increased non-targeted mobility—but not spatial predisposition of the rearrangement partners—plays a major role in the formation of these translocations.
Collapse
|
15
|
Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP. NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucleic Acids Res 2022; 50:7906-7924. [PMID: 35819192 PMCID: PMC9371915 DOI: 10.1093/nar/gkac600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 11/14/2022] Open
Abstract
Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three core proteins: CP190, Su(Hw), and Mod(mdg4)67.2. These factors concentrate at nuclear foci termed insulator bodies, and changes in insulator body localization have been observed in mutants defective for insulator function. Here, we identified NURF301/E(bx), a nucleosome remodeling factor, as a novel regulator of gypsy insulator body localization through a high-throughput RNAi imaging screen. NURF301 promotes gypsy-dependent insulator barrier activity and physically interacts with gypsy insulator proteins. Using ChIP-seq, we found that NURF301 co-localizes with insulator proteins genome-wide, and NURF301 promotes chromatin association of Su(Hw) and CP190 at gypsy insulator binding sites. These effects correlate with NURF301-dependent nucleosome repositioning. At the same time, CP190 and Su(Hw) both facilitate recruitment of NURF301 to chromatin. Finally, Oligopaint FISH combined with immunofluorescence revealed that NURF301 promotes 3D contact between insulator bodies and gypsy insulator DNA binding sites, and NURF301 is required for proper nuclear positioning of gypsy binding sites. Our data provide new insights into how a nucleosome remodeling factor and insulator proteins cooperatively contribute to nuclear organization.
Collapse
Affiliation(s)
- Shue Chen
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leah F Rosin
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nellie Moshkovich
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrick J Murphy
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Guoyun Yu
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elissa P Lei
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
16
|
Fleck K, Raj R, Erceg J. The 3D genome landscape: Diverse chromosomal interactions and their functional implications. Front Cell Dev Biol 2022; 10:968145. [PMID: 36036013 PMCID: PMC9402908 DOI: 10.3389/fcell.2022.968145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Genome organization includes contacts both within a single chromosome and between distinct chromosomes. Thus, regulatory organization in the nucleus may include interplay of these two types of chromosomal interactions with genome activity. Emerging advances in omics and single-cell imaging technologies have allowed new insights into chromosomal contacts, including those of homologs and sister chromatids, and their significance to genome function. In this review, we highlight recent studies in this field and discuss their impact on understanding the principles of chromosome organization and associated functional implications in diverse cellular processes. Specifically, we describe the contributions of intra-chromosomal, inter-homolog, and inter-sister chromatid contacts to genome organization and gene expression.
Collapse
Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Romir Raj
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Genome-wide mapping of genomic DNA damage: methods and implications. Cell Mol Life Sci 2021; 78:6745-6762. [PMID: 34463773 PMCID: PMC8558167 DOI: 10.1007/s00018-021-03923-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022]
Abstract
Exposures from the external and internal environments lead to the modification of genomic DNA, which is implicated in the cause of numerous diseases, including cancer, cardiovascular, pulmonary and neurodegenerative diseases, together with ageing. However, the precise mechanism(s) linking the presence of damage, to impact upon cellular function and pathogenesis, is far from clear. Genomic location of specific forms of damage is likely to be highly informative in understanding this process, as the impact of downstream events (e.g. mutation, microsatellite instability, altered methylation and gene expression) on cellular function will be positional—events at key locations will have the greatest impact. However, until recently, methods for assessing DNA damage determined the totality of damage in the genomic location, with no positional information. The technique of “mapping DNA adductomics” describes the molecular approaches that map a variety of forms of DNA damage, to specific locations across the nuclear and mitochondrial genomes. We propose that integrated comparison of this information with other genome-wide data, such as mutational hotspots for specific genotoxins, tumour-specific mutation patterns and chromatin organisation and transcriptional activity in non-cancerous lesions (such as nevi), pre-cancerous conditions (such as polyps) and tumours, will improve our understanding of how environmental toxins lead to cancer. Adopting an analogous approach for non-cancer diseases, including the development of genome-wide assays for other cellular outcomes of DNA damage, will improve our understanding of the role of DNA damage in pathogenesis more generally.
Collapse
|
19
|
Wei J, Tian H, Zhou R, Shao Y, Song F, Gao YQ. Topological Constraints with Optimal Length Promote the Formation of Chromosomal Territories at Weakened Degree of Phase Separation. J Phys Chem B 2021; 125:9092-9101. [PMID: 34351763 DOI: 10.1021/acs.jpcb.1c03523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is generally agreed that the nuclei of eukaryotic cells at interphase are partitioned into disjointed territories, with distinct regions occupied by certain chromosomes. However, the underlying mechanism for such territorialization is still under debate. Here we model chromosomes as coarse-grained block copolymers and to investigate the effect of loop domains (LDs) on the formation of compartments and territories based on dissipative particle dynamics. A critical length of LDs, which depends sensitively on the length of polymeric blocks, is obtained to minimize the degree of phase separation. This also applies to the two-polymer system: The critical length not only maximizes the degree of territorialization but also minimizes the degree of phase separation. Interestingly, by comparing with experimental data, we find the critical length for LDs and the corresponding length of blocks to be respectively very close to the mean length of topologically associating domains (TADs) and chromosomal segments with different densities of CpG islands for human chromosomes. The results indicate that topological constraints with optimal length can contribute to the formation of territories by weakening the degree of phase separation, which likely promotes the chromosomal flexibility in response to genetic regulations.
Collapse
Affiliation(s)
- Jiachen Wei
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China.,Shenzhen Bay Laboratory, 5F, No. 9 Duxue Road, Nanshan District, 518055 Shenzhen, Guangdong, China
| | - Hao Tian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Rui Zhou
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yingfeng Shao
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Qin Gao
- Shenzhen Bay Laboratory, 5F, No. 9 Duxue Road, Nanshan District, 518055 Shenzhen, Guangdong, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| |
Collapse
|
20
|
Rosin LF, Gil J, Drinnenberg IA, Lei EP. Oligopaint DNA FISH reveals telomere-based meiotic pairing dynamics in the silkworm, Bombyx mori. PLoS Genet 2021; 17:e1009700. [PMID: 34319984 PMCID: PMC8351950 DOI: 10.1371/journal.pgen.1009700] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/09/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Accurate chromosome segregation during meiosis is essential for reproductive success. Yet, many fundamental aspects of meiosis remain unclear, including the mechanisms regulating homolog pairing across species. This gap is partially due to our inability to visualize individual chromosomes during meiosis. Here, we employ Oligopaint FISH to investigate homolog pairing and compaction of meiotic chromosomes and resurrect a classical model system, the silkworm Bombyx mori. Our Oligopaint design combines multiplexed barcoding with secondary oligo labeling for high flexibility and low cost. These studies illustrate that Oligopaints are highly specific in whole-mount gonads and on meiotic squashes. We show that meiotic pairing is robust in both males and females and that pairing can occur through numerous partially paired intermediate structures. We also show that pairing in male meiosis occurs asynchronously and seemingly in a transcription-biased manner. Further, we reveal that meiotic bivalent formation in B. mori males is highly similar to bivalent formation in C. elegans, with both of these pathways ultimately resulting in the pairing of chromosome ends with non-paired ends facing the spindle pole. Additionally, microtubule recruitment in both C. elegans and B. mori is likely dependent on kinetochore proteins but independent of the centromere-specifying histone CENP-A. Finally, using super-resolution microscopy in the female germline, we show that homologous chromosomes remain associated at telomere domains in the absence of chiasma and after breakdown and modification to the synaptonemal complex in pachytene. These studies reveal novel insights into mechanisms of meiotic homolog pairing both with or without recombination.
Collapse
Affiliation(s)
- Leah F. Rosin
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jose Gil
- Institut Curie, PSL Research University, CNRS, Paris, France; Sorbonne Université, Institut Curie, CNRS, Paris, France
| | - Ines A. Drinnenberg
- Institut Curie, PSL Research University, CNRS, Paris, France; Sorbonne Université, Institut Curie, CNRS, Paris, France
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
21
|
Child MB, Bateman JR, Jahangiri A, Reimer A, Lammers NC, Sabouni N, Villamarin D, McKenzie-Smith GC, Johnson JE, Jost D, Garcia HG. Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila. eLife 2021; 10:64412. [PMID: 34100718 PMCID: PMC8294847 DOI: 10.7554/elife.64412] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Three-dimensional eukaryotic genome organization provides the structural basis for gene regulation. In Drosophila melanogaster, genome folding is characterized by somatic homolog pairing, where homologous chromosomes are intimately paired from end to end; however, how homologs identify one another and pair has remained mysterious. Recently, this process has been proposed to be driven by specifically interacting 'buttons' encoded along chromosomes. Here, we turned this hypothesis into a quantitative biophysical model to demonstrate that a button-based mechanism can lead to chromosome-wide pairing. We tested our model using live-imaging measurements of chromosomal loci tagged with the MS2 and PP7 nascent RNA labeling systems. We show solid agreement between model predictions and experiments in the pairing dynamics of individual homologous loci. Our results strongly support a button-based mechanism of somatic homolog pairing in Drosophila and provide a theoretical framework for revealing the molecular identity and regulation of buttons.
Collapse
Affiliation(s)
- Myron Barber Child
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, United States
| | - Amir Jahangiri
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Armando Reimer
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nica Sabouni
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | | | | | | | - Daniel Jost
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France.,Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratory of Biology and Modeling of the Cell, Lyon, France
| | - Hernan G Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
22
|
Sajid A, Lalani EN, Chen B, Hashimoto T, Griffin DK, Bhartiya A, Thompson G, Robinson IK, Yusuf M. Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus. Int J Mol Sci 2021; 22:ijms22115987. [PMID: 34206020 PMCID: PMC8198510 DOI: 10.3390/ijms22115987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/18/2022] Open
Abstract
Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.
Collapse
Affiliation(s)
- Atiqa Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - Bo Chen
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
- Key Laboratory of Performance Evolution and Control for Engineering Structures of the Ministry of Education, Tongji University, Shanghai 200092, China
| | - Teruo Hashimoto
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | | | - Archana Bhartiya
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
| | - George Thompson
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | - Ian K. Robinson
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mohammed Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Correspondence:
| |
Collapse
|
23
|
Peterson SC, Samuelson KB, Hanlon SL. Multi-Scale Organization of the Drosophila melanogaster Genome. Genes (Basel) 2021; 12:817. [PMID: 34071789 PMCID: PMC8228293 DOI: 10.3390/genes12060817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
Interphase chromatin, despite its appearance, is a highly organized framework of loops and bends. Chromosomes are folded into topologically associating domains, or TADs, and each chromosome and its homolog occupy a distinct territory within the nucleus. In Drosophila, genome organization is exceptional because homologous chromosome pairing is in both germline and somatic tissues, which promote interhomolog interactions such as transvection that can affect gene expression in trans. In this review, we focus on what is known about genome organization in Drosophila and discuss it from TADs to territory. We start by examining intrachromosomal organization at the sub-chromosome level into TADs, followed by a comprehensive analysis of the known proteins that play a key role in TAD formation and boundary establishment. We then zoom out to examine interhomolog interactions such as pairing and transvection that are abundant in Drosophila but rare in other model systems. Finally, we discuss chromosome territories that form within the nucleus, resulting in a complete picture of the multi-scale organization of the Drosophila genome.
Collapse
Affiliation(s)
| | | | - Stacey L. Hanlon
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (S.C.P.); (K.B.S.)
| |
Collapse
|
24
|
Gaffaroglu M, Majtánová Z, Symonová R, Pelikánová Š, Unal S, Lajbner Z, Ráb P. Present and Future Salmonid Cytogenetics. Genes (Basel) 2020; 11:E1462. [PMID: 33291343 PMCID: PMC7762217 DOI: 10.3390/genes11121462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/04/2023] Open
Abstract
Salmonids are extremely important economically and scientifically; therefore, dynamic developments in their research have occurred and will continue occurring in the future. At the same time, their complex phylogeny and taxonomy are challenging for traditional approaches in research. Here, we first provide discoveries regarding the hitherto completely unknown cytogenetic characteristics of the Anatolian endemic flathead trout, Salmo platycephalus, and summarize the presently known, albeit highly complicated, situation in the genus Salmo. Secondly, by outlining future directions of salmonid cytogenomics, we have produced a prototypical virtual karyotype of Salmo trutta, the closest relative of S. platycephalus. This production is now possible thanks to the high-quality genome assembled to the chromosome level in S. trutta via soft-masking, including a direct labelling of repetitive sequences along the chromosome sequence. Repetitive sequences were crucial for traditional fish cytogenetics and hence should also be utilized in fish cytogenomics. As such virtual karyotypes become increasingly available in the very near future, it is necessary to integrate both present and future approaches to maximize their respective benefits. Finally, we show how the presumably repetitive sequences in salmonids can change the understanding of the overall relationship between genome size and G+C content, creating another outstanding question in salmonid cytogenomics waiting to be resolved.
Collapse
Affiliation(s)
- Muhammet Gaffaroglu
- Department of Molecular Biology and Genetics, Faculty of Science, University of Ahi Evran, Kirsehir 40200, Turkey;
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
| | - Sevgi Unal
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin 74000, Turkey;
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology, Graduate University, Onna, Okinawa 904 0495, Japan;
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
| |
Collapse
|
25
|
Das P, Shen T, McCord RP. Inferring chromosome radial organization from Hi-C data. BMC Bioinformatics 2020; 21:511. [PMID: 33167851 PMCID: PMC7654587 DOI: 10.1186/s12859-020-03841-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations. RESULTS A number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromosome ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells. CONCLUSIONS Our analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demonstrate which stages of the approach can extract meaningful information, and also describe limitations of pairwise contacts alone to predict absolute 3D positions.
Collapse
Affiliation(s)
- Priyojit Das
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Tongye Shen
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| |
Collapse
|
26
|
Matveevsky S, Tretiakov A, Kashintsova A, Bakloushinskaya I, Kolomiets O. Meiotic Nuclear Architecture in Distinct Mole Vole Hybrids with Robertsonian Translocations: Chromosome Chains, Stretched Centromeres, and Distorted Recombination. Int J Mol Sci 2020; 21:E7630. [PMID: 33076404 PMCID: PMC7589776 DOI: 10.3390/ijms21207630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/13/2020] [Indexed: 11/24/2022] Open
Abstract
Genome functioning in hybrids faces inconsistency. This mismatch is manifested clearly in meiosis during chromosome synapsis and recombination. Species with chromosomal variability can be a model for exploring genomic battles with high visibility due to the use of advanced immunocytochemical methods. We studied synaptonemal complexes (SC) and prophase I processes in 44-chromosome intraspecific (Ellobius tancrei × E. tancrei) and interspecific (Ellobius talpinus × E. tancrei) hybrid mole voles heterozygous for 10 Robertsonian translocations. The same pachytene failures were found for both types of hybrids. In the intraspecific hybrid, the chains were visible in the pachytene stage, then 10 closed SC trivalents formed in the late pachytene and diplotene stage. In the interspecific hybrid, as a rule, SC trivalents composed the SC chains and rarely could form closed configurations. Metacentrics involved with SC trivalents had stretched centromeres in interspecific hybrids. Linkage between neighboring SC trivalents was maintained by stretched centromeric regions of acrocentrics. This centromeric plasticity in structure and dynamics of SC trivalents was found for the first time. We assume that stretched centromeres were a marker of altered nuclear architecture in heterozygotes due to differences in the ancestral chromosomal territories of the parental species. Restructuring of the intranuclear organization and meiotic disturbances can contribute to the sterility of interspecific hybrids, and lead to the reproductive isolation of studied species.
Collapse
Affiliation(s)
- Sergey Matveevsky
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Artemii Tretiakov
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Anna Kashintsova
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Irina Bakloushinskaya
- Laboratory of Genome Evolution and Mechanisms of Speciation, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Oxana Kolomiets
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| |
Collapse
|
27
|
Deutsch JL, Heath JL. MLLT10 in benign and malignant hematopoiesis. Exp Hematol 2020; 87:1-12. [PMID: 32569758 DOI: 10.1016/j.exphem.2020.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/01/2023]
Abstract
Non-random chromosomal translocations involving the putative transcription factor Mixed Lineage Leukemia Translocated to 10 (MLLT10, also known as AF10) are commonly observed in both acute myeloid and lymphoid leukemias and are indicative of a poor prognosis. Despite the well-described actions of oncogenic MLLT10 fusion proteins, the role of wild-type MLLT10 in hematopoiesis is not well characterized. The protein structure and several interacting partners have been described and provide indications as to the potential functions of MLLT10. This review examines these aspects of MLLT10, contextualizing its function in benign and malignant hematopoiesis.
Collapse
Affiliation(s)
- Jamie L Deutsch
- Department of Pediatrics, University of Vermont, Burlington, VT
| | - Jessica L Heath
- Department of Pediatrics, University of Vermont, Burlington, VT; Department of Biochemistry, University of Vermont, Burlington, VT 05405; University of Vermont Cancer Center, Burlington, VT.
| |
Collapse
|
28
|
Sember A, Pelikánová Š, de Bello Cioffi M, Šlechtová V, Hatanaka T, Do Doan H, Knytl M, Ráb P. Taxonomic Diversity Not Associated with Gross Karyotype Differentiation: The Case of Bighead Carps, Genus Hypophthalmichthys (Teleostei, Cypriniformes, Xenocyprididae). Genes (Basel) 2020; 11:E479. [PMID: 32354012 PMCID: PMC7291238 DOI: 10.3390/genes11050479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/31/2020] [Accepted: 04/24/2020] [Indexed: 11/30/2022] Open
Abstract
The bighead carps of the genus Hypophthalmichthys (H. molitrix and H. nobilis) are important aquaculture species. They were subjected to extensive multidisciplinary research, but with cytogenetics confined to conventional protocols only. Here, we employed Giemsa-/C-/CMA3- stainings and chromosomal mapping of multigene families and telomeric repeats. Both species shared (i) a diploid chromosome number 2n = 48 and the karyotype structure, (ii) low amount of constitutive heterochromatin, (iii) the absence of interstitial telomeric sites (ITSs), (iv) a single pair of 5S rDNA loci adjacent to one major rDNA cluster, and (v) a single pair of co-localized U1/U2 snDNA tandem repeats. Both species, on the other hand, differed in (i) the presence/absence of remarkable interstitial block of constitutive heterochromatin on the largest acrocentric pair 11 and (ii) the number of major (CMA3-positive) rDNA sites. Additionally, we applied here, for the first time, the conventional cytogenetics in H. harmandi, a species considered extinct in the wild and/or extensively cross-hybridized with H. molitrix. Its 2n and karyotype description match those found in the previous two species, while silver staining showed differences in distribution of major rDNA. The bighead carps thus represent another case of taxonomic diversity not associated with gross karyotype differentiation, where 2n and karyotype structure cannot help in distinguishing between genomes of closely related species. On the other hand, we demonstrated that two cytogenetic characters (distribution of constitutive heterochromatin and major rDNA) may be useful for diagnosis of pure species. The universality of these markers must be further verified by analyzing other pure populations of bighead carps.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Hiep Do Doan
- Research Institute of Aquaculture No. 1, Dinh Bang, Tu Son, Bac Ninh 16000, Vietnam
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 2-128-43 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| |
Collapse
|
29
|
Sember A, de Oliveira EA, Ráb P, Bertollo LAC, de Freitas NL, Viana PF, Yano CF, Hatanaka T, Marinho MMF, de Moraes RLR, Feldberg E, Cioffi MDB. Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective. Genes (Basel) 2020; 11:genes11010091. [PMID: 31941136 PMCID: PMC7017317 DOI: 10.3390/genes11010091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Lebiasinidae is a Neotropical freshwater family widely distributed throughout South and Central America. Due to their often very small body size, Lebiasinidae species are cytogenetically challenging and hence largely underexplored. However, the available but limited karyotype data already suggested a high interspecific variability in the diploid chromosome number (2n), which is pronounced in the speciose genus Nannostomus, a popular taxon in ornamental fish trade due to its remarkable body coloration. Aiming to more deeply examine the karyotype diversification in Nannostomus, we combined conventional cytogenetics (Giemsa-staining and C-banding) with the chromosomal mapping of tandemly repeated 5S and 18S rDNA clusters and with interspecific comparative genomic hybridization (CGH) to investigate genomes of four representative Nannostomus species: N. beckfordi, N. eques, N. marginatus, and N. unifasciatus. Our data showed a remarkable variability in 2n, ranging from 2n = 22 in N. unifasciatus (karyotype composed exclusively of metacentrics/submetacentrics) to 2n = 44 in N. beckfordi (karyotype composed entirely of acrocentrics). On the other hand, patterns of 18S and 5S rDNA distribution in the analyzed karyotypes remained rather conservative, with only two 18S and two to four 5S rDNA sites. In view of the mostly unchanged number of chromosome arms (FN = 44) in all but one species (N. eques; FN = 36), and with respect to the current phylogenetic hypothesis, we propose Robertsonian translocations to be a significant contributor to the karyotype differentiation in (at least herein studied) Nannostomus species. Interspecific comparative genome hybridization (CGH) using whole genomic DNAs mapped against the chromosome background of N. beckfordi found a moderate divergence in the repetitive DNA content among the species’ genomes. Collectively, our data suggest that the karyotype differentiation in Nannostomus has been largely driven by major structural rearrangements, accompanied by only low to moderate dynamics of repetitive DNA at the sub-chromosomal level. Possible mechanisms and factors behind the elevated tolerance to such a rate of karyotype change in Nannostomus are discussed.
Collapse
Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic; (A.S.); (P.R.)
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Secretaria de Estado de Educação de Mato Grosso–SEDUC-MT, Cuiabá 78049-909, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic; (A.S.); (P.R.)
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Natália Lourenço de Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Manoela Maria Ferreira Marinho
- Universidade Federal da Paraíba (UFPB), Departamento de Sistemática e Ecologia (DSE), Laboratório de Sistemática e Morfologia de Peixes, João Pessoa 58051-090, Brazil;
| | - Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, Brazil; (P.F.V.); (E.F.)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905, Brazil; (E.A.d.O.); (L.A.C.B.); (N.L.d.F.); (C.F.Y.); (T.H.); (R.L.R.d.M.)
- Correspondence: ; Tel.: +55-16-3351-8431; Fax: +55-16-3351-8377
| |
Collapse
|
30
|
Advantage of Using Spherical over Cartesian Coordinates in the Chromosome Territories 3D Modeling. LECTURE NOTES IN COMPUTER SCIENCE 2020. [PMCID: PMC7302845 DOI: 10.1007/978-3-030-50417-5_49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper shows results of chromosome territory modeling in two cases: when the implementation of the algorithm was based on Cartesian coordinates and when implementation was made with Spherical coordinates. In the article, the summary of measurements of computational times of simulation of chromatin decondensation process (which led to constitute the chromosome territory) was presented. Initially, when implementation was made with the use of Cartesian Coordinates, simulation takes a lot of time to create a model (mean 746.7[sec] with the median 569.1[sec]) and additionally requires restarts of the algorithm, also often exceeds acceptable (given a priori) time for the computational experiment. Because of that, authors attempted changing the coordinate system to Spherical Coordinates (in a few previous projects it leads to improving the efficiency of implementation). After changing the way that 3D point is represented in 3D space the time required to make a successful model reduced to the mean 25.3[sec] with a median 18.5[s] (alongside with lowering the number of necessary algorithm restarts) which gives a significant difference in the efficiency of model’s creation. Therefore we showed, that a more efficient way for implementation was the usage of spherical coordinates.
Collapse
|