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Conti D, Verza AE, Pesenti ME, Cmentowski V, Vetter IR, Pan D, Musacchio A. Role of protein kinase PLK1 in the epigenetic maintenance of centromeres. Science 2024; 385:1091-1097. [PMID: 39236163 DOI: 10.1126/science.ado5178] [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: 02/23/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024]
Abstract
The centromere, a chromosome locus defined by the histone H3-like protein centromeric protein A (CENP-A), promotes assembly of the kinetochore to bind microtubules during cell division. Centromere maintenance requires CENP-A to be actively replenished by dedicated protein machinery in the early G1 phase of the cell cycle to compensate for its dilution after DNA replication. Cyclin-dependent kinases (CDKs) limit CENP-A deposition to once per cell cycle and function as negative regulators outside of early G1. Antithetically, Polo-like kinase 1 (PLK1) promotes CENP-A deposition in early G1, but the molecular details of this process are still unknown. We reveal here a phosphorylation network that recruits PLK1 to the deposition machinery to control a conformational switch required for licensing the CENP-A deposition reaction. Our findings clarify how PLK1 contributes to the epigenetic maintenance of centromeres.
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Affiliation(s)
- Duccio Conti
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Arianna Esposito Verza
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Marion E Pesenti
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Verena Cmentowski
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Ingrid R Vetter
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Dongqing Pan
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
- Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
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2
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Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605654. [PMID: 39131277 PMCID: PMC11312596 DOI: 10.1101/2024.07.31.605654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.
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Affiliation(s)
- DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prajna Hebbar
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Francesca Antonacci
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Steven J Solar
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitry Antipov
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon D Pickett
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yana Safonova
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Francesco Montinaro
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yanting Luo
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joanna Malukiewicz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Jessica M Storer
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Jiadong Lin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Abigail N Sequeira
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Riley J Mangan
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Genetics Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | | | | | - Anton Bankevich
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Christine R Beck
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Arjun Biddanda
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Borchers
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gerard G Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emry Brannan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Shelise Y Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lucia Carbone
- Department of Medicine, KCVI, Oregon Health Sciences University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Laura Carrel
- PSU Medical School, Penn State University School of Medicine, Hershey, PA, USA
| | - Agnes P Chan
- The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Juyun Crawford
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Eric Engelbrecht
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10021, USA
| | - Gage H Garcia
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Luciana de Gennaro
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - David Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | | | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ishaan Gupta
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Junmin Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Robert S Harris
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Goethe University, Frankfurt, Germany
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marlys L Houck
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Kaivan Kamali
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bryce Kille
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Chul Lee
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Youngho Lee
- Laboratory of bioinformatics and population genetics, Interdisciplinary program in bioinformatics, Seoul National University, Republic of Korea
| | - William Lees
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mark Loftus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Yong Hwee Eddie Loh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Hailey Loucks
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Jian Ma
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China
- Shanghai Jiao Tong University Chongqing Research Institute, Chongqing, China
| | - Juan F I Martinez
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Barbara McGrath
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Britta S Meyer
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Saswat K Mohanty
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Karol Pal
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Francisca R Ringeling
- Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany
| | - Joana L Rocha
- Department of Integrative Biology, University of California, Berkeley, Berkeley, USA
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nicholas J Schork
- The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Cole Shanks
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Linnéa Smeds
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Dongmin R Son
- Department of Ecology, Evolution and Marine Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Alexander P Sweeten
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael G Tassia
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Mihir Trivedi
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Wenjie Wei
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Julie Wertz
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Muyu Yang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Zhang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Zhenmiao Zhang
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - Sarah A Zhao
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yixin Zhu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Iker Rivas-González
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Zachary A Szpiech
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Christian D Huber
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Miriam K Konkel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Stefan Canzar
- Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, Berkeley, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, USA
| | - Erin Molloy
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Departments of Molecular and Cell Biology, UConn Storrs, CT, USA
| | - Sergey Koren
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Adam M Phillippy
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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Santinello B, Sun R, Amjad A, Hoyt SJ, Ouyang L, Courret C, Drennan R, Leo L, Larracuente AM, Core L, O'Neill RJ, Mellone BG. Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.14.574223. [PMID: 38293134 PMCID: PMC10827089 DOI: 10.1101/2024.01.14.574223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Centromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the role of centromeric DNA repeats remains unclear. Retroelements are prevalent at centromeres across taxa and represent a potential mechanism for promoting transcription to aid in CENP-A incorporation or for generating RNA transcripts to maintain centromere integrity. Here, we probe into the transcription and RNA localization of the centromere-enriched retroelement G2/Jockey-3 (hereafter referred to as Jockey-3 ) in Drosophila melanogaster , currently the only in vivo model with assembled centromeres. We find that Jockey-3 is a major component of the centromeric transcriptome and produces RNAs that localize to centromeres in metaphase. Leveraging the polymorphism of Jockey-3 and a de novo centromere system, we show that these RNAs remain associated with their cognate DNA sequences in cis , suggesting they are unlikely to perform a sequence-specific function at all centromeres. We show that Jockey-3 transcription is positively correlated with the presence of CENP-A, and that recent Jockey-3 transposition events have occurred preferentially at CENP-A-containing chromatin. We propose that Jockey-3 contributes to the epigenetic maintenance of centromeres by promoting chromatin transcription, while inserting preferentially within these regions, selfishly ensuring its continued expression and transmission. Given the conservation of retroelements as centromere components through evolution, our findings have broad implications in understanding this association in other species.
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Cao RB, Chen R, Liao KX, Li H, Xu GB, Jiang XL. Karyotype and LTR-RTs analysis provide insights into oak genomic evolution. BMC Genomics 2024; 25:328. [PMID: 38566015 PMCID: PMC10988972 DOI: 10.1186/s12864-024-10177-6] [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: 11/23/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests. RESULTS Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes. CONCLUSION Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.
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Affiliation(s)
- Rui-Bin Cao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ran Chen
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Ke-Xin Liao
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - He Li
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Gang-Biao Xu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Xiao-Long Jiang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China.
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5
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Naish M, Henderson IR. The structure, function, and evolution of plant centromeres. Genome Res 2024; 34:161-178. [PMID: 38485193 PMCID: PMC10984392 DOI: 10.1101/gr.278409.123] [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] [Indexed: 03/22/2024]
Abstract
Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem repeats (satellites), and/or specific families of transposons. The functional region of the centromere is defined by loading of a specific histone 3 variant (CENH3), which nucleates the kinetochore and shows dynamic regulation. In many plants, the centromeres are composed of satellite repeat arrays that are densely DNA methylated and invaded by centrophilic retrotransposons. In some cases, the retrotransposons become the sites of CENH3 loading. We review the structure of plant centromeres, including monocentric, holocentric, and metapolycentric architectures, which vary in the number and distribution of kinetochore attachment sites along chromosomes. We discuss how variation in CENH3 loading can drive genome elimination during early cell divisions of plant embryogenesis. We review how epigenetic state may influence centromere identity and discuss evolutionary models that seek to explain the paradoxically rapid change of centromere sequences observed across species, including the potential roles of recombination. We outline putative modes of selection that could act within the centromeres, as well as the role of repeats in driving cycles of centromere evolution. Although our primary focus is on plant genomes, we draw comparisons with animal and fungal centromeres to derive a eukaryote-wide perspective of centromere structure and function.
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Affiliation(s)
- Matthew Naish
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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6
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Ramos-Alonso L, Chymkowitch P. Maintaining transcriptional homeostasis during cell cycle. Transcription 2024; 15:1-21. [PMID: 37655806 PMCID: PMC11093055 DOI: 10.1080/21541264.2023.2246868] [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: 06/21/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
The preservation of gene expression patterns that define cellular identity throughout the cell division cycle is essential to perpetuate cellular lineages. However, the progression of cells through different phases of the cell cycle severely disrupts chromatin accessibility, epigenetic marks, and the recruitment of transcriptional regulators. Notably, chromatin is transiently disassembled during S-phase and undergoes drastic condensation during mitosis, which is a significant challenge to the preservation of gene expression patterns between cell generations. This article delves into the specific gene expression and chromatin regulatory mechanisms that facilitate the preservation of transcriptional identity during replication and mitosis. Furthermore, we emphasize our recent findings revealing the unconventional role of yeast centromeres and mitotic chromosomes in maintaining transcriptional fidelity beyond mitosis.
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Affiliation(s)
- Lucía Ramos-Alonso
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pierre Chymkowitch
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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7
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Gambogi CW, Pandey N, Dawicki-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere innovations within a mouse species. SCIENCE ADVANCES 2023; 9:eadi5764. [PMID: 37967185 PMCID: PMC10651114 DOI: 10.1126/sciadv.adi5764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying centromere protein-A (CENP-A) nucleosomes at the nexus of a satellite repeat that we identified and termed π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ~6 mega-base pairs of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance promotes accumulation of microtubule-binding components of the kinetochore and a microtubule-destabilizing kinesin of the inner centromere. We propose that the balance of pro- and anti-microtubule binding by the new centromere is what permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nootan Pandey
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennine M. Dawicki-McKenna
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Uma P. Arora
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Mikhail A. Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Piero Lamelza
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael A. Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
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8
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Cappelletti E, Piras FM, Sola L, Santagostino M, Petersen JL, Bellone RR, Finno CJ, Peng S, Kalbfleisch TS, Bailey E, Nergadze SG, Giulotto E. The localization of centromere protein A is conserved among tissues. Commun Biol 2023; 6:963. [PMID: 37735603 PMCID: PMC10514049 DOI: 10.1038/s42003-023-05335-7] [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: 04/18/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A. Although mammalian centromeres are typically associated with satellite DNA, we previously demonstrated that the centromere of horse chromosome 11 (ECA11) is completely devoid of satellite DNA. We also showed that the localization of its CENP-A binding domain is not fixed but slides within an about 500 kb region in different individuals, giving rise to positional alleles. These epialleles are inherited as Mendelian traits but their position can move in one generation. It is still unknown whether centromere sliding occurs during meiosis or during development. Here, we first improve the sequence of the ECA11 centromeric region in the EquCab3.0 assembly. Then, to test whether centromere sliding may occur during development, we map the CENP-A binding domains of ECA11 using ChIP-seq in five tissues of different embryonic origin from the four horses of the equine FAANG (Functional Annotation of ANimal Genomes) consortium. Our results demonstrate that the centromere is localized in the same region in all tissues, suggesting that the position of the centromeric domain is maintained during development.
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Affiliation(s)
| | - Francesca M Piras
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Ted S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - Ernest Bailey
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - Solomon G Nergadze
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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9
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Kuse R, Ishii K. Flexible Attachment and Detachment of Centromeres and Telomeres to and from Chromosomes. Biomolecules 2023; 13:1016. [PMID: 37371596 DOI: 10.3390/biom13061016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Accurate transmission of genomic information across multiple cell divisions and generations, without any losses or errors, is fundamental to all living organisms. To achieve this goal, eukaryotes devised chromosomes. Eukaryotic genomes are represented by multiple linear chromosomes in the nucleus, each carrying a centromere in the middle, a telomere at both ends, and multiple origins of replication along the chromosome arms. Although all three of these DNA elements are indispensable for chromosome function, centromeres and telomeres possess the potential to detach from the original chromosome and attach to new chromosomal positions, as evident from the events of telomere fusion, centromere inactivation, telomere healing, and neocentromere formation. These events seem to occur spontaneously in nature but have not yet been elucidated clearly, because they are relatively infrequent and sometimes detrimental. To address this issue, experimental setups have been developed using model organisms such as yeast. In this article, we review some of the key experiments that provide clues as to the extent to which these paradoxical and elusive features of chromosomally indispensable elements may become valuable in the natural context.
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Affiliation(s)
- Riku Kuse
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
| | - Kojiro Ishii
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
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10
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Müller S, Du K, Guiguen Y, Pichler M, Nakagawa S, Stöck M, Schartl M, Lamatsch DK. Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis. BMC Biol 2023; 21:109. [PMID: 37189152 DOI: 10.1186/s12915-023-01607-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND The Western mosquitofish, Gambusia affinis, is a model for sex chromosome organization and evolution of female heterogamety. We previously identified a G. affinis female-specific marker, orthologous to the aminomethyl transferase (amt) gene of the related platyfish (Xiphophorus maculatus). Here, we have analyzed the structure and differentiation of the G. affinis W-chromosome, using a cytogenomics and bioinformatics approach. RESULTS The long arm of the G. affinis W-chromosome (Wq) is highly enriched in dispersed repetitive sequences, but neither heterochromatic nor epigenetically silenced by hypermethylation. In line with this, Wq sequences are highly transcribed, including an active nucleolus organizing region (NOR). Female-specific SNPs and evolutionary young transposable elements were highly enriched and dispersed along the W-chromosome long arm, suggesting constrained recombination. Wq copy number expanded elements also include female-specific transcribed sequences from the amt locus with homology to TE. Collectively, the G. affinis W-chromosome is actively differentiating by sex-specific copy number expansion of transcribed TE-related elements, but not (yet) by extensive sequence divergence or gene decay. CONCLUSIONS The G. affinis W-chromosome exhibits characteristic genomic properties of an evolutionary young sex chromosome. Strikingly, the observed sex-specific changes in the genomic landscape are confined to the W long arm, which is separated from the rest of the W-chromosome by a neocentromere acquired during sex chromosome evolution and may thus have become functionally insulated. In contrast, W short arm sequences were apparently shielded from repeat-driven differentiation, retained Z-chromosome like genomic features, and may have preserved pseudo-autosomal properties.
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Affiliation(s)
- Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig Maximilians University, Munich, Germany.
| | - Kang Du
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | | | - Maria Pichler
- Universität Innsbruck, Research Department for Limnology, Mondsee, Mondsee, Austria
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Matthias Stöck
- Leibniz-Institute for Freshwater Ecology and Inland Fisheries (IGB), Department of Ecophysiology and Aquaculture, Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashihiroshima, 739-8526, Japan
| | - Manfred Schartl
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
- Developmental Biochemistry, University of Würzburg, BiozentrumWürzburg, Germany
| | - Dunja K Lamatsch
- Universität Innsbruck, Research Department for Limnology, Mondsee, Mondsee, Austria.
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11
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Gambogi CW, Pandey N, Dawicki-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere Innovations Within a Mouse Species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540353. [PMID: 37333154 PMCID: PMC10274901 DOI: 10.1101/2023.05.11.540353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying CENP-A nucleosomes at the nexus of a satellite repeat that we identified and term π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ~6 Mbp of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance drives accumulation of microtubule-binding components of the kinetochore, as well as a microtubule-destabilizing kinesin of the inner centromere. The balance of pro- and anti-microtubule-binding by the new centromere permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
| | - Nootan Pandey
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Jennine M. Dawicki-McKenna
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Uma P. Arora
- The Jackson Laboratory, Bar Harbor, ME 04609
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111
| | - Mikhail A. Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892
| | - Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Piero Lamelza
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892
| | - Michael A. Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME 04609
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104
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12
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van den Berg SJW, Jansen LET. SUMO control of centromere homeostasis. Front Cell Dev Biol 2023; 11:1193192. [PMID: 37181753 PMCID: PMC10172491 DOI: 10.3389/fcell.2023.1193192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
Centromeres are unique chromosomal loci that form the anchorage point for the mitotic spindle during mitosis and meiosis. Their position and function are specified by a unique chromatin domain featuring the histone H3 variant CENP-A. While typically formed on centromeric satellite arrays, CENP-A nucleosomes are maintained and assembled by a strong self-templated feedback mechanism that can propagate centromeres even at non-canonical sites. Central to the epigenetic chromatin-based transmission of centromeres is the stable inheritance of CENP-A nucleosomes. While long-lived at centromeres, CENP-A can turn over rapidly at non-centromeric sites and even erode from centromeres in non-dividing cells. Recently, SUMO modification of the centromere complex has come to the forefront as a mediator of centromere complex stability, including CENP-A chromatin. We review evidence from different models and discuss the emerging view that limited SUMOylation appears to play a constructive role in centromere complex formation, while polySUMOylation drives complex turnover. The deSUMOylase SENP6/Ulp2 and the proteins segregase p97/Cdc48 constitute the dominant opposing forces that balance CENP-A chromatin stability. This balance may be key to ensuring proper kinetochore strength at the centromere while preventing ectopic centromere formation.
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Affiliation(s)
- Sebastiaan J. W. van den Berg
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
| | - Lars E. T. Jansen
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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13
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A Satellite-Free Centromere in Equus przewalskii Chromosome 10. Int J Mol Sci 2023; 24:ijms24044134. [PMID: 36835543 PMCID: PMC9961726 DOI: 10.3390/ijms24044134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. Here, we investigated by FISH the chromosomal distribution of satellite DNA families in Equus przewalskii (EPR), demonstrating a good degree of conservation of the localization of the major horse satellite families 37cen and 2PI with the domestic horse. Moreover, we demonstrated, by ChIP-seq, that 37cen is the satellite bound by CENP-A and that the centromere of EPR10, the ortholog of ECA11, is devoid of satellite sequences. Our results confirm that these two species are closely related and that the event of centromere repositioning which gave rise to EPR10/ECA11 centromeres occurred in the common ancestor, before the separation of the two horse lineages.
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14
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Saayman X, Graham E, Nathan WJ, Nussenzweig A, Esashi F. Centromeres as universal hotspots of DNA breakage, driving RAD51-mediated recombination during quiescence. Mol Cell 2023; 83:523-538.e7. [PMID: 36702125 PMCID: PMC10009740 DOI: 10.1016/j.molcel.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 10/07/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023]
Abstract
Centromeres are essential for chromosome segregation in most animals and plants yet are among the most rapidly evolving genome elements. The mechanisms underlying this paradoxical phenomenon remain enigmatic. Here, we report that human centromeres innately harbor a striking enrichment of DNA breaks within functionally active centromere regions. Establishing a single-cell imaging strategy that enables comparative assessment of DNA breaks at repetitive regions, we show that centromeric DNA breaks are induced not only during active cellular proliferation but also de novo during quiescence. Markedly, centromere DNA breaks in quiescent cells are resolved enzymatically by the evolutionarily conserved RAD51 recombinase, which in turn safeguards the specification of functional centromeres. This study highlights the innate fragility of centromeres, which may have been co-opted over time to reinforce centromere specification while driving rapid evolution. The findings also provide insights into how fragile centromeres are likely to contribute to human disease.
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Affiliation(s)
- Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - William J Nathan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892-4254, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892-4254, USA
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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15
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Centromere Chromatin Dynamics at a Glance. EPIGENOMES 2022; 6:epigenomes6040039. [PMID: 36412794 PMCID: PMC9680212 DOI: 10.3390/epigenomes6040039] [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: 09/11/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The centromere is a specialized DNA locus that ensures the faithful segregation of chromosomes during cell division. It does so by directing the assembly of an essential proteinaceous structure called the kinetochore. The centromere identity is primarily epigenetically defined by a nucleosome containing an H3 variant called CENP-A as well as by the interplay of several factors such as differential chromatin organization driven by CENP-A and H2A.Z, centromere-associated proteins, and post-translational modifications. At the centromere, CENP-A is not just a driving force for kinetochore assembly but also modifies the structural and dynamic properties of the centromeric chromatin, resulting in a distinctive chromatin organization. An additional level of regulation of the centromeric chromatin conformation is provided by post-translational modifications of the histones in the CENP-A nucleosomes. Further, H2A.Z is present in the regions flanking the centromere for heterochromatinization. In this review, we focus on the above-mentioned factors to describe how they contribute to the organization of the centromeric chromatin: CENP-A at the core centromere, post-translational modifications that decorate CENP-A, and the variant H2A.Z.
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16
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Syu YM, Ma JY, Ou TH, Lee CL, Lin HY, Lin SP, Lee CJ, Chen CP. De Novo Mosaic 6p23-p25.3 Tetrasomy Caused by a Small Supernumerary Marker Chromosome Presenting Trisomy Distal 6p Phenotype: A Case Report and Literature Review. Diagnostics (Basel) 2022; 12:2306. [PMID: 36291995 PMCID: PMC9600663 DOI: 10.3390/diagnostics12102306] [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: 09/03/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMCs) derived from the chromosome 6 short arm are rare and their clinical significance remains unknown. No case with sSMC(6) without centromeric DNA has been reported. Partial trisomy and tetrasomy of distal 6p is a rare but clinically distinct syndrome. We report on a de novo mosaic sSMC causing partial tetrasomy for 6p23-p25.3 in a male infant with symptoms of being small for gestational age, microcephaly, facial dysmorphism, congenital eye defects, and multi-system malformation. Conventional cytogenetic analysis revealed a karyotype of 47,XY,+mar [25]/46,XY [22]. Array comparative genomic hybridization (aCGH) revealed mosaic tetrasomy of distal 6p. This is the first case of mosaic tetrasomy 6p23-p25.3 caused by an inverted duplicated neocentric sSMC with characteristic features of trisomy distal 6p. Comparison of phenotypes in cases with trisomy and tetrasomy of 6p23-p25.3 could facilitate a genotype-phenotype correlation and identification of candidate genes contributing to their presentation. The presentation of anterior segment dysgenesis and anomaly of the renal system suggest triplosensitivity of the FOXC1 gene. In patients with microcephaly growth retardation, and malformation of the cardiac and renal systems, presentation of anterior segment dysgenesis might be indicative of chromosome 6p duplication, and aCGH evaluation should be performed for associated syndromic disease.
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Affiliation(s)
- Yu-Min Syu
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
| | - Juine-Yih Ma
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
| | - Tzu-Hsuen Ou
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
| | - Chung-Lin Lee
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan
| | - Hsiang-Yu Lin
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Medical Research, Division of Genetics and Metabolism, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Childhood Care and Education, MacKay Junior College of Medicine, Nursing and Management, Taipei 11260, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Shuan-Pei Lin
- Division of Genetics and Metabolism, Department of Pediatrics, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Medical Research, Division of Genetics and Metabolism, MacKay Memorial Hospital, Taipei 10449, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei 11219, Taiwan
| | - Chia-Jung Lee
- Department of Pediatrics, Far Eastern Memorial Hospital, New Taipei City 22021, Taiwan
| | - Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei 10449, Taiwan
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
- Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei 11230, Taiwan
- Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11230, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41346, Taiwan
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17
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Abstract
In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.
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Affiliation(s)
- Vineet Bafna
- Department of Computer Science and Engineering and Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA;
| | - Paul S Mischel
- Department of Pathology and ChEM-H, Stanford University School of Medicine, Stanford, California, USA;
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18
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Palazzo A, Piccolo I, Minervini CF, Purgato S, Capozzi O, D'Addabbo P, Cumbo C, Albano F, Rocchi M, Catacchio CR. Genome characterization and CRISPR-Cas9 editing of a human neocentromere. Chromosoma 2022; 131:239-251. [PMID: 35978051 DOI: 10.1007/s00412-022-00779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022]
Abstract
The maintenance of genome integrity is ensured by proper chromosome inheritance during mitotic and meiotic cell divisions. The chromosomal counterpart responsible for chromosome segregation to daughter cells is the centromere, at which the spindle apparatus attaches through the kinetochore. Although all mammalian centromeres are primarily composed of megabase-long repetitive sequences, satellite-free human neocentromeres have been described. Neocentromeres and evolutionary new centromeres have revolutionized traditional knowledge about centromeres. Over the past 20 years, insights have been gained into their organization, but in spite of these advancements, the mechanisms underlying their formation and evolution are still unclear. Today, through modern and increasingly accessible genome editing and long-read sequencing techniques, research in this area is undergoing a sudden acceleration. In this article, we describe the primary sequence of a previously described human chromosome 3 neocentromere and observe its possible evolution and repair results after a chromosome breakage induced through CRISPR-Cas9 technologies. Our data represent an exciting advancement in the field of centromere/neocentromere evolution and chromosome stability.
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Affiliation(s)
- Antonio Palazzo
- Department of Biology, University of Bari Aldo Moro, Bari, Italy.
| | - Ilaria Piccolo
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Crescenzio Francesco Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Purgato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Oronzo Capozzi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Pietro D'Addabbo
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Mariano Rocchi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
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19
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Kumon T, Lampson MA. Evolution of eukaryotic centromeres by drive and suppression of selfish genetic elements. Semin Cell Dev Biol 2022; 128:51-60. [PMID: 35346579 PMCID: PMC9232976 DOI: 10.1016/j.semcdb.2022.03.026] [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: 01/11/2022] [Revised: 03/20/2022] [Accepted: 03/20/2022] [Indexed: 10/18/2022]
Abstract
Despite the universal requirement for faithful chromosome segregation, eukaryotic centromeres are rapidly evolving. It is hypothesized that rapid centromere evolution represents an evolutionary arms race between selfish genetic elements that drive, or propagate at the expense of organismal fitness, and mechanisms that suppress fitness costs. Selfish centromere DNA achieves preferential inheritance in female meiosis by recruiting more effector proteins that alter spindle microtubule interaction dynamics. Parallel pathways for effector recruitment are adaptively evolved to suppress functional differences between centromeres. Opportunities to drive are not limited to female meiosis, and selfish transposons, plasmids and B chromosomes also benefit by maximizing their inheritance. Rapid evolution of selfish genetic elements can diversify suppressor mechanisms in different species that may cause hybrid incompatibility.
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Affiliation(s)
- Tomohiro Kumon
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Xue C, Liu G, Sun S, Liu X, Guo R, Cheng Z, Yu H, Gu M, Liu K, Zhou Y, Zhang T, Gong Z. De novo centromere formation in pericentromeric region of rice chromosome 8. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:859-871. [PMID: 35678753 DOI: 10.1111/tpj.15862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Neocentromeres develop when kinetochores assemble de novo at DNA loci that are not previously associated with CenH3 nucleosomes, and can rescue rearranged chromosomes that have lost a functional centromere. The molecular mechanisms associated with neocentromere formation in plants have been elusive. Here, we developed a Xian (indica) rice line with poor growth performance in the field due to approximately 272 kb deletion that spans centromeric DNA sequences, including the centromeric satellite repeat CentO, in the centromere of chromosome 8 (Cen8). The CENH3-binding domains were expanded downstream of the original CentO position in Cen8, which revealed a de novo centromere formation in rice. The neocentromere formation avoids chromosomal regions containing functional genes. Meanwhile, canonical histone H3 was replaced by CENH3 in the regions with low CENH3 levels, and the CenH3 nucleosomes in these regions became more periodic. In addition, we identified active genes in the deleted centromeric region, which are essential for chloroplast growth and development. In summary, our results provide valuable insights into neocentromere formation and show that functional genes exist in the centromeric regions of plant chromosomes.
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Affiliation(s)
- Chao Xue
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Shang Sun
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoyu Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Rui Guo
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhukuan Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hengxiu Yu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Kai Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yong Zhou
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
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21
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Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian fusion and centromere repositioning contributed to the formation of satellite-free centromeres during the evolution of zebras. Mol Biol Evol 2022; 39:6650076. [PMID: 35881460 PMCID: PMC9356731 DOI: 10.1093/molbev/msac162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated to highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and E. asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras E. burchelli (15 of 22) and E. grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine satellite-free centromeres are shared between the two species in agreement with their recent separation. We assembled all centromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a satellite-free centromere was seeded on an inversion breakpoint. At eleven chromosomes, whose primary constrictions seemed to be associated to satellite repeats by cytogenetic analysis, satellite-free neocentromeres were instead located near the ancestral inactivated satellite-based centromeres, therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.
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Affiliation(s)
- Eleonora Cappelletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesca M Piras
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Wasma A Abdelgadir
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Raimondi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesco Lescai
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Solomon G Nergadze
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
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22
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Dharmadhikari AV, Pereira EM, Andrews CC., Macera M, Harkavy N, Wapner R, Jobanputra V, Levy B, Ganapathi M, Liao J. Case Report: Prenatal Identification of a De Novo Mosaic Neocentric Marker Resulting in 13q31.1→qter Tetrasomy in a Mildly Affected Girl. Front Genet 2022; 13:906077. [PMID: 35928455 PMCID: PMC9343796 DOI: 10.3389/fgene.2022.906077] [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: 03/28/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Partial tetrasomy of distal 13q has a reported association with a variable phenotype including microphthalmia, ear abnormalities, hypotelorism, facial dysmorphisms, urogenital defects, pigmentation and skin defects, and severe learning difficulties. A wide range of mosaicism has been reported, which may, to some extent, account for the variable spectrum of observed phenotypes. We report here a pregnancy conceived using intrauterine insemination in a 32-year-old female with a history of infertility. Non-invasive prenatal screening (NIPS) was performed in the first trimester which reported an increased risk for trisomy 13. Follow-up cytogenetic workup using chorionic villus sampling (CVS) and amniotic fluid samples showed a mosaic karyotype with a small supernumerary marker chromosome (sSMC). Chromosomal microarray analysis (CMA) identified a mosaic 31.34 Mb terminal gain on chr13q31.1q34 showing the likely origin of the sSMC to distal chromosome 13q. Follow-up metaphase FISH testing suggested an inverted duplication rearrangement involving 13q31q34 in the marker chromosome and the presence of a neocentromere. At 21 months of age, the proband has a history of gross motor delay, hypotonia, left microphthalmia, strabismus, congenital anomaly of the right optic nerve, hemangiomas, and a tethered spinal cord. Postnatal chromosome analyses in buccal, peripheral blood, and spinal cord ligament tissues were consistent with the previous amniocentesis and CVS findings, and the degree of mosaicism varied from 25 to 80%. It is often challenging to pinpoint the chromosomal identity of sSMCs using banding cytogenetics. A combination of low-pass genome sequencing of cell-free DNA, chromosomal microarray, and FISH enabled the identification of the precise chromosomal rearrangement in this patient. This study adds to the growing list of clinically identified neocentric marker chromosomes and is the first described instance of partial tetrasomy 13q31q34 identified in a mosaic state prenatally. Since NIPS is now being routinely performed along with invasive testing for advanced maternal age, an increased prenatal detection rate for mosaic sSMCs in otherwise normal pregnancies is expected. Future studies investigating how neocentromeres mediate gene expression changes could help identify potential epigenetic targets as treatment options to rescue or reverse the phenotypes seen in patients with congenital neocentromeres.
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Affiliation(s)
- Avinash V. Dharmadhikari
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Elaine M. Pereira
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Carli C . Andrews
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Michael Macera
- Clinical Cytogenetics Laboratory, New York Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Nina Harkavy
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Vaidehi Jobanputra
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Jun Liao
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- *Correspondence: Jun Liao,
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23
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Sundararajan K, Straight AF. Centromere Identity and the Regulation of Chromosome Segregation. Front Cell Dev Biol 2022; 10:914249. [PMID: 35721504 PMCID: PMC9203049 DOI: 10.3389/fcell.2022.914249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Eukaryotes segregate their chromosomes during mitosis and meiosis by attaching chromosomes to the microtubules of the spindle so that they can be distributed into daughter cells. The complexity of centromeres ranges from the point centromeres of yeast that attach to a single microtubule to the more complex regional centromeres found in many metazoans or holocentric centromeres of some nematodes, arthropods and plants, that bind to dozens of microtubules per kinetochore. In vertebrates, the centromere is defined by a centromere specific histone variant termed Centromere Protein A (CENP-A) that replaces histone H3 in a subset of centromeric nucleosomes. These CENP-A nucleosomes are distributed on long stretches of highly repetitive DNA and interspersed with histone H3 containing nucleosomes. The mechanisms by which cells control the number and position of CENP-A nucleosomes is unknown but likely important for the organization of centromeric chromatin in mitosis so that the kinetochore is properly oriented for microtubule capture. CENP-A chromatin is epigenetically determined thus cells must correct errors in CENP-A organization to prevent centromere dysfunction and chromosome loss. Recent improvements in sequencing complex centromeres have paved the way for defining the organization of CENP-A nucleosomes in centromeres. Here we discuss the importance and challenges in understanding CENP-A organization and highlight new discoveries and advances enabled by recent improvements in the human genome assembly.
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24
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Renaud-Pageot C, Quivy JP, Lochhead M, Almouzni G. CENP-A Regulation and Cancer. Front Cell Dev Biol 2022; 10:907120. [PMID: 35721491 PMCID: PMC9201071 DOI: 10.3389/fcell.2022.907120] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
In mammals, CENP-A, a histone H3 variant found in the centromeric chromatin, is critical for faithful chromosome segregation and genome integrity maintenance through cell divisions. Specifically, it has dual functions, enabling to define epigenetically the centromere position and providing the foundation for building up the kinetochore. Regulation of its dynamics of synthesis and deposition ensures to propagate proper centromeres on each chromosome across mitosis and meiosis. However, CENP-A overexpression is a feature identified in many cancers. Importantly, high levels of CENP-A lead to its mislocalization outside the centromere. Recent studies in mammals have begun to uncover how CENP-A overexpression can affect genome integrity, reprogram cell fate and impact 3D nuclear organization in cancer. Here, we summarize the mechanisms that orchestrate CENP-A regulation. Then we review how, beyond its centromeric function, CENP-A overexpression is linked to cancer state in mammalian cells, with a focus on the perturbations that ensue at the level of chromatin organization. Finally, we review the clinical interest for CENP-A in cancer treatment.
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25
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Molecular Dynamics and Evolution of Centromeres in the Genus Equus. Int J Mol Sci 2022; 23:ijms23084183. [PMID: 35457002 PMCID: PMC9024551 DOI: 10.3390/ijms23084183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
The centromere is the chromosomal locus essential for proper chromosome segregation. While the centromeric function is well conserved and epigenetically specified, centromeric DNA sequences are typically composed of satellite DNA and represent the most rapidly evolving sequences in eukaryotic genomes. The presence of satellite sequences at centromeres hampered the comprehensive molecular analysis of these enigmatic loci. The discovery of functional centromeres completely devoid of satellite repetitions and fixed in some animal and plant species represented a turning point in centromere biology, definitively proving the epigenetic nature of the centromere. The first satellite-free centromere, fixed in a vertebrate species, was discovered in the horse. Later, an extraordinary number of satellite-free neocentromeres had been discovered in other species of the genus Equus, which remains the only mammalian genus with numerous satellite-free centromeres described thus far. These neocentromeres arose recently during evolution and are caught in a stage of incomplete maturation. Their presence made the equids a unique model for investigating, at molecular level, the minimal requirements for centromere seeding and evolution. This model system provided new insights on how centromeres are established and transmitted to the progeny and on the role of satellite DNA in different aspects of centromere biology.
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26
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Wilcock DM, McMurtry V, Coleman JF, Kim JT, Khalili P, Deftereos G, Albertson D, Gulbahce EH, Liu T, Sirohi D. Histopathological Correlation of Chromosome 12 Polysomy by Fluorescence in Situ Hybridization in Adipocytic Neoplasms. Int J Surg Pathol 2022; 30:734-742. [PMID: 35261272 DOI: 10.1177/10668969221085289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Background: Identification of MDM2 amplification by fluorescence in situ hybridization is an important diagnostic tool for evaluation of adipocytic neoplasms. Rarely, neoplasms can show increased copies of MDM2 and CEP12 probes (polysomy) without amplification (MDM2/CEP12 ratio <2.0). While noted in the literature, this finding has not been the focus of any study to date. Methods: Consecutive cases were retrospectively screened for increased copies of MDM2 and CEP12 and were classified as: high polysomy (ratio<2.0, CEP12≥10.0), low polysomy (ratio<2.0, but >0.5, CEP12≥4.0 but <9.9), and CEP12 amplification (ratio≤0.5, CEP12 > 4.0). H&E slides were classified by a pathologist into diagnostic categories based on morphology without knowledge of MDM2 amplification result. Correlations between chromosome 12 polysomy and histological features in the same region of the tumor were investigated. Results: There were 19 (0.7%) high polysomy, 52 (2.0%) low polysomy and 3 (0.1%) CEP12 amplification cases identified in the 2541 cases screened. While low polysomy was seen across benign and malignant adipocytic tumors and other sarcomas, high level polysomy was primarily seen in liposarcomas, both atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDLPS) and dedifferentiated liposarcoma (DDLPS). No lipomas were high polysomy. Conclusion: Polysomy is an uncommon, but distinct, finding in adipocytic neoplasms found across the spectrum of benign to malignant with little insight into the pathophysiology or prognosis. While low polysomy is also observed in benign adipocytic neoplasms, high polysomy is almost always seen in malignant adipocytic neoplasms and is uncommon in benign adipocytic neoplasms.
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Affiliation(s)
- Diane M Wilcock
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT
| | - Valarie McMurtry
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Joshua F Coleman
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Jong Taek Kim
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Parisa Khalili
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Georgios Deftereos
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Daniel Albertson
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Evin H Gulbahce
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Ting Liu
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
| | - Deepika Sirohi
- The Institute for Experimental Pathology® , ARUP Laboratories, Salt Lake City, UT.,14434University of Utah and ARUP Laboratories, Salt Lake City, UT
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27
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Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
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Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
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28
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Jeffery D, Lochhead M, Almouzni G. CENP-A: A Histone H3 Variant with Key Roles in Centromere Architecture in Healthy and Diseased States. Results Probl Cell Differ 2022; 70:221-261. [PMID: 36348109 DOI: 10.1007/978-3-031-06573-6_7] [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] [Indexed: 06/16/2023]
Abstract
Centromeres are key architectural components of chromosomes. Here, we examine their construction, maintenance, and functionality. Focusing on the mammalian centromere- specific histone H3 variant, CENP-A, we highlight its coevolution with both centromeric DNA and its chaperone, HJURP. We then consider CENP-A de novo deposition and the importance of centromeric DNA recently uncovered with the added value from new ultra-long-read sequencing. We next review how to ensure the maintenance of CENP-A at the centromere throughout the cell cycle. Finally, we discuss the impact of disrupting CENP-A regulation on cancer and cell fate.
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Affiliation(s)
- Daniel Jeffery
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Marina Lochhead
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Geneviève Almouzni
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France.
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Barbosa AC, Xu Z, Karari K, Williams W, Hauf S, Brown WRA. Mutation and selection explain why many eukaryotic centromeric DNA sequences are often A + T rich. Nucleic Acids Res 2021; 50:579-596. [PMID: 34928384 PMCID: PMC8754631 DOI: 10.1093/nar/gkab1219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/16/2021] [Accepted: 11/30/2021] [Indexed: 01/10/2023] Open
Abstract
We have used chromosome engineering to replace native centromeric DNA with different test sequences at native centromeres in two different strains of the fission yeast Schizosaccharomyces pombe and have discovered that A + T rich DNA, whether synthetic or of bacterial origin, will function as a centromere in this species. Using genome size as a surrogate for the inverse of effective population size (Ne) we also show that the relative A + T content of centromeric DNA scales with Ne across 43 animal, fungal and yeast (Opisthokonta) species. This suggests that in most of these species the A + T content of the centromeric DNA is determined by a balance between selection and mutation. Combining the experimental results and the evolutionary analyses allows us to conclude that A + T rich DNA of almost any sequence will function as a centromere in most Opisthokonta species. The fact that many G/C to A/T substitutions are unlikely to be selected against may contribute to the rapid evolution of centromeric DNA. We also show that a neo-centromere sequence is not simply a weak version of native centromeric DNA and suggest that neo-centromeres require factors either for their propagation or establishment in addition to those required by native centromeres.
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Affiliation(s)
- Anne C Barbosa
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Zhengyao Xu
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Kazhal Karari
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
| | - Wendi Williams
- Virginia Tech, Department of Biological Sciences, Fralin Life Sciences Institute, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Silke Hauf
- Virginia Tech, Department of Biological Sciences, Fralin Life Sciences Institute, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - William R A Brown
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, NG7 2UH, UK
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30
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Giannuzzi G, Logsdon GA, Chatron N, Miller DE, Reversat J, Munson KM, Hoekzema K, Bonnet-Dupeyron MN, Rollat-Farnier PA, Baker CA, Sanlaville D, Eichler EE, Schluth-Bolard C, Reymond A. Alpha Satellite Insertion Close to an Ancestral Centromeric Region. Mol Biol Evol 2021; 38:5576-5587. [PMID: 34464971 PMCID: PMC8662618 DOI: 10.1093/molbev/msab244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human centromeres are mainly composed of alpha satellite DNA hierarchically organized as higher-order repeats (HORs). Alpha satellite dynamics is shown by sequence homogenization in centromeric arrays and by its transfer to other centromeric locations, for example, during the maturation of new centromeres. We identified during prenatal aneuploidy diagnosis by fluorescent in situ hybridization a de novo insertion of alpha satellite DNA from the centromere of chromosome 18 (D18Z1) into cytoband 15q26. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by the lack of constriction and the absence of CENP-A binding. The insertion was associated with a 2.8-kbp deletion and likely occurred in the paternal germline. The site was enriched in long terminal repeats and located ∼10 Mbp from the location where a centromere was ancestrally seeded and became inactive in the common ancestor of humans and apes 20-25 million years ago. Long-read mapping to the T2T-CHM13 human genome assembly revealed that the insertion derives from a specific region of chromosome 18 centromeric 12-mer HOR array in which the monomer size follows a regular pattern. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the methylation status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name "alpha satellite insertion." It also expands our knowledge on alphoid DNA dynamics and conveys the possibility that alphoid arrays can relocate near vestigial centromeric sites.
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Affiliation(s)
- Giuliana Giannuzzi
- Department of Biosciences, University of Milan, Milan, Italy
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Nicolas Chatron
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institut NeuroMyoGène, University of Lyon, Lyon, France
| | - Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital, Seattle, WA
| | - Julie Reversat
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | - Pierre-Antoine Rollat-Farnier
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Cellule Bioinformatique, Hospices Civils de Lyon, Lyon, France
| | - Carl A Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Damien Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institut NeuroMyoGène, University of Lyon, Lyon, France
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Caroline Schluth-Bolard
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institut NeuroMyoGène, University of Lyon, Lyon, France
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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31
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Kim T. Epigenetic control of centromere: what can we learn from neocentromere? Genes Genomics 2021; 44:317-325. [PMID: 34843088 DOI: 10.1007/s13258-021-01193-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND The centromere is the special region on a chromosome, which serves as the site for assembly of kinetochore complex and is essential for maintaining genomic integrity. Neocentromeres are new centromeres that form on the non-centromeric regions of the chromosome when the natural centromere is disrupted or inactivated. Although neocentromeres lack the typical features found in centromeres, cells with neocentromeres divide normally during mitosis and meiosis. Neocentromeres not only arise naturally but their formation can also be induced experimentally. Therefore, neocentromeres are a great tool for studying functions and formation of centromeres. OBJECTIVE To study neocentromeres and use that knowledge to gain insights into the epigenetic regulation of canonical centromeres. DISCUSSION Here, we review the characteristics of naturally occurring centromeres and neocentromeres and those of experimentally induced neocentromeres. We also discuss the mechanism of centromere formation and epigenetic regulation of centromere function, which we learned from studying the neocentromeres. Although neocentromeres lack main features of centromeres, such as presence of repetitive ⍺-satellite DNA and pericentric heterochromatin, they behave quite similar to the canonical centromere, indicating the epigenetic nature of the centromere. Still, further investigation will help to understand the formation and maintenance of the centromere, and the correlation to human diseases. CONCLUSION Neocentromeres helped us to understand the formation of canonical centromeres. Also, since neocentromeres are associated with certain cancer types, knowledge about them could be helpful to treat cancer.
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Affiliation(s)
- Taekyung Kim
- Department of Biology Education, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Korea.
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32
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Abstract
The centromere performs a universally conserved function, to accurately partition genetic information upon cell division. Yet, centromeres are among the most rapidly evolving regions of the genome and are bound by a varying assortment of centromere-binding factors that are themselves highly divergent at the protein-sequence level. A common thread in most species is the dependence on the centromere-specific histone variant CENP-A for the specification of the centromere site. However, CENP-A is not universally required in all species or cell types, making the identification of a general mechanism for centromere specification challenging. In this review, we examine our current understanding of the mechanisms of centromere specification in CENP-A-dependent and independent systems, focusing primarily on recent work.
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Affiliation(s)
- Barbara G Mellone
- Department of Molecular and Cell Biology, and Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005 Paris, France.
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33
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Paixão VDS, Suárez P, Oliveira da Silva W, Geise L, Ferguson-Smith MA, O’Brien PCM, Mendes-Oliveira AC, Rossi RV, Pieczarka JC, Nagamachi CY. Comparative genomic mapping reveals mechanisms of chromosome diversification in Rhipidomys species (Rodentia, Thomasomyini) and syntenic relationship between species of Sigmodontinae. PLoS One 2021; 16:e0258474. [PMID: 34634084 PMCID: PMC8504764 DOI: 10.1371/journal.pone.0258474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Rhipidomys (Sigmodontinae, Thomasomyini) has 25 recognized species, with a wide distribution ranging from eastern Panama to northern Argentina. Cytogenetic data has been described for 13 species with 12 of them having 2n = 44 with a high level of autosomal fundamental number (FN) variation, ranging from 46 to 80, assigned to pericentric inversions. The species are grouped in groups with low FN (46-52) and high FN (72-80). In this work the karyotypes of Rhipidomys emiliae (2n = 44, FN = 50) and Rhipidomys mastacalis (2n = 44, FN = 74), were studied by classical cytogenetics and by fluorescence in situ hybridization using telomeric and whole chromosome probes (chromosome painting) of Hylaeamys megacephalus (HME). Chromosome painting revealed homology between 36 segments of REM and 37 of RMA. We tested the hypothesis that pericentric inversions are the predominant chromosomal rearrangements responsible for karyotypic divergence between these species, as proposed in literature. Our results show that the genomic diversification between the karyotypes of the two species resulted from translocations, centromeric repositioning and pericentric inversions. The chromosomal evolution in Rhipidomys was associated with karyotypical orthoselection. The HME probes revealed that seven syntenic probably ancestral blocks for Sigmodontinae are present in Rhipidomys. An additional syntenic block described here is suggested as part of the subfamily ancestral karyotype. We also define five synapomorphies that can be used as chromosomal signatures for Rhipidomys.
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Affiliation(s)
- Vergiana dos Santos Paixão
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Pablo Suárez
- Instituto de Biologia Subtropical (CONICET-UNAM), Puerto Iguazú, Misiones, Argentina
| | - Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Lena Geise
- Laboratório de Mastozoologia, Departamento de Zoologia, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Patricia Caroline Mary O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ana Cristina Mendes-Oliveira
- Laboratório de Zoologia e Ecologia de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
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34
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Lin Z, Xie Y, Nong W, Ren X, Li R, Zhao Z, Hui JHL, Yuen KWY. Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization. Nucleic Acids Res 2021; 49:9174-9193. [PMID: 34417622 PMCID: PMC8450109 DOI: 10.1093/nar/gkab690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 11/14/2022] Open
Abstract
To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.
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Affiliation(s)
- Zhongyang Lin
- School of Biological Sciences, the University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Yichun Xie
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Xiaoliang Ren
- Department of Biology, Baptist University of Hong Kong, Sir Run Run Shaw Building, Ho Sin Hang Campus, Kowloon Tong, Hong Kong
| | - Runsheng Li
- Department of Biology, Baptist University of Hong Kong, Sir Run Run Shaw Building, Ho Sin Hang Campus, Kowloon Tong, Hong Kong
| | - Zhongying Zhao
- Department of Biology, Baptist University of Hong Kong, Sir Run Run Shaw Building, Ho Sin Hang Campus, Kowloon Tong, Hong Kong
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, the University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
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35
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DeBose-Scarlett EM, Sullivan BA. Genomic and Epigenetic Foundations of Neocentromere Formation. Annu Rev Genet 2021; 55:331-348. [PMID: 34496611 DOI: 10.1146/annurev-genet-071719-020924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Centromeres are essential to genome inheritance, serving as the site of kinetochore assembly and coordinating chromosome segregation during cell division. Abnormal centromere function is associated with birth defects, infertility, and cancer. Normally, centromeres are assembled and maintained at the same chromosomal location. However, ectopic centromeres form spontaneously at new genomic locations and contribute to genome instability and developmental defects as well as to acquired and congenital human disease. Studies in model organisms have suggested that certain regions of the genome, including pericentromeres, heterochromatin, and regions of open chromatin or active transcription, support neocentromere activation. However, there is no universal mechanism that explains neocentromere formation. This review focuses on recent technological and intellectual advances in neocentromere research and proposes future areas of study. Understanding neocentromere biology will provide a better perspective on chromosome and genome organization and functional context for information generated from the Human Genome Project, ENCODE, and other large genomic consortia. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Evon M DeBose-Scarlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
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36
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Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Mol Ecol 2021; 30:2710-2723. [PMID: 33955064 DOI: 10.1111/mec.15936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023]
Abstract
A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.
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Affiliation(s)
- Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Alexander Suh
- School of Biological Sciences - Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Inês Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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37
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Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci 2021; 22:ijms22094309. [PMID: 33919233 PMCID: PMC8122249 DOI: 10.3390/ijms22094309] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
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Affiliation(s)
- Jitendra Thakur
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
- Correspondence:
| | - Jenika Packiaraj
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA 98109, USA
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38
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Lin Z, Yuen KWY. RbAp46/48LIN-53 and HAT-1 are required for initial CENP-AHCP-3 deposition and de novo holocentromere formation on artificial chromosomes in Caenorhabditis elegans embryos. Nucleic Acids Res 2021; 49:9154-9173. [PMID: 33872374 PMCID: PMC8450102 DOI: 10.1093/nar/gkab217] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
Foreign DNA microinjected into the Caenorhabditis elegans syncytial gonad forms episomal extra-chromosomal arrays, or artificial chromosomes (ACs), in embryos. Short, linear DNA fragments injected concatemerize into high molecular weight (HMW) DNA arrays that are visible as punctate DAPI-stained foci in oocytes, and they undergo chromatinization and centromerization in embryos. The inner centromere, inner kinetochore and spindle checkpoint components, including AIR-2, CENP-AHCP-3, Mis18BP1KNL-2 and BUB-1, respectively, assemble onto the nascent ACs during the first mitosis. The DNA replication efficiency of ACs improves over several cell cycles, which correlates with the improvement of kinetochore bi-orientation and proper segregation of ACs. Depletion of condensin II subunits, like CAPG-2 and SMC-4, but not the replicative helicase component, MCM-2, reduces de novo CENP-AHCP-3 level on nascent ACs. Furthermore, H3K9ac, H4K5ac and H4K12ac are highly enriched on newly chromatinized ACs. RbAp46/48LIN-53 and HAT-1, which affect the acetylation of histone H3 and H4, are essential for chromatinization, de novo centromere formation and segregation competency of nascent ACs. RbAp46/48LIN-53 or HAT-1 depletion causes the loss of both CENP-AHCP-3 and Mis18BP1KNL-2 initial deposition at de novo centromeres on ACs. This phenomenon is different from centromere maintenance on endogenous chromosomes, where Mis18BP1KNL-2 functions upstream of RbAp46/48LIN-53.
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Affiliation(s)
- Zhongyang Lin
- School of Biological Sciences, The University of Hong Kong. Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong. Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
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39
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Shrestha RL, Rossi A, Wangsa D, Hogan AK, Zaldana KS, Suva E, Chung YJ, Sanders CL, Difilippantonio S, Karpova TS, Karim B, Foltz DR, Fachinetti D, Aplan PD, Ried T, Basrai MA. CENP-A overexpression promotes aneuploidy with karyotypic heterogeneity. J Cell Biol 2021; 220:211820. [PMID: 33620383 PMCID: PMC7905998 DOI: 10.1083/jcb.202007195] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/15/2020] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosomal instability (CIN) is a hallmark of many cancers. Restricting the localization of centromeric histone H3 variant CENP-A to centromeres prevents CIN. CENP-A overexpression (OE) and mislocalization have been observed in cancers and correlate with poor prognosis; however, the molecular consequences of CENP-A OE on CIN and aneuploidy have not been defined. Here, we show that CENP-A OE leads to its mislocalization and CIN with lagging chromosomes and micronuclei in pseudodiploid DLD1 cells and xenograft mouse model. CIN is due to reduced localization of proteins to the kinetochore, resulting in defects in kinetochore integrity and unstable kinetochore–microtubule attachments. CENP-A OE contributes to reduced expression of cell adhesion genes and higher invasion of DLD1 cells. We show that CENP-A OE contributes to aneuploidy with karyotypic heterogeneity in human cells and xenograft mouse model. In summary, our results provide a molecular link between CENP-A OE and aneuploidy, and suggest that karyotypic heterogeneity may contribute to the aggressive phenotype of CENP-A–overexpressing cancers.
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Affiliation(s)
- Roshan L Shrestha
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Austin Rossi
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ann K Hogan
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL
| | - Kimberly S Zaldana
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Evelyn Suva
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Chelsea L Sanders
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD
| | - Simone Difilippantonio
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Baktiar Karim
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 144, Paris, France
| | - Peter D Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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40
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Nagpal H, Fierz B. The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity? J Mol Biol 2021; 433:166676. [PMID: 33065112 DOI: 10.1016/j.jmb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023]
Abstract
The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epigenetic mark defining the centromere. In this review, we discuss the role of CENP-A on the structure and dynamics of centromeric chromatin. We further discuss the impact of the CENP-A binding proteins CENP-C, CENP-N, and CENP-B on modulating centro-chromatin structure. Based on these findings we provide an overview of the higher order structure of the centromere.
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Affiliation(s)
- Harsh Nagpal
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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41
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Abstract
Murillo-Pineda and colleagues (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202007210) use CRISPR-Cas9-based genetic engineering in human cells to induce a new functional centromere at a naive chromosomal site. Long-read DNA sequencing at the neocentromere provides firm evidence that centromere establishment is a truly epigenetic event.
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Affiliation(s)
| | - Elaine M. Dunleavy
- Centre for Chromosome Biology, Biomedical Sciences, National University of Ireland Galway, Galway, Ireland
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42
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Murillo-Pineda M, Valente LP, Dumont M, Mata JF, Fachinetti D, Jansen LE. Induction of spontaneous human neocentromere formation and long-term maturation. J Cell Biol 2021; 220:e202007210. [PMID: 33443568 PMCID: PMC7812830 DOI: 10.1083/jcb.202007210] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/23/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Human centromeres form primarily on α-satellite DNA but sporadically arise de novo at naive ectopic loci, creating neocentromeres. Centromere inheritance is driven primarily by chromatin containing the histone H3 variant CENP-A. Here, we report a chromosome engineering system for neocentromere formation in human cells and characterize the first experimentally induced human neocentromere at a naive locus. The spontaneously formed neocentromere spans a gene-poor 100-kb domain enriched in histone H3 lysine 9 trimethylated (H3K9me3). Long-read sequencing revealed this neocentromere was formed by purely epigenetic means and assembly of a functional kinetochore correlated with CENP-A seeding, eviction of H3K9me3 and local accumulation of mitotic cohesin and RNA polymerase II. At formation, the young neocentromere showed markedly reduced chromosomal passenger complex (CPC) occupancy and poor sister chromatin cohesion. However, long-term tracking revealed increased CPC assembly and low-level transcription providing evidence for centromere maturation over time.
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Affiliation(s)
- Marina Murillo-Pineda
- Department of Biochemistry, University of Oxford, Oxford, UK
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Marie Dumont
- Institut Curie, Paris Sciences et Lettres, Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 144, Paris, France
| | - João F. Mata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Daniele Fachinetti
- Institut Curie, Paris Sciences et Lettres, Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 144, Paris, France
| | - Lars E.T. Jansen
- Department of Biochemistry, University of Oxford, Oxford, UK
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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43
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CENP-A nucleosome-a chromatin-embedded pedestal for the centromere: lessons learned from structural biology. Essays Biochem 2021; 64:205-221. [PMID: 32720682 PMCID: PMC7475651 DOI: 10.1042/ebc20190074] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 11/17/2022]
Abstract
The centromere is a chromosome locus that directs equal segregation of chromosomes during cell division. A nucleosome containing the histone H3 variant CENP-A epigenetically defines the centromere. Here, we summarize findings from recent structural biology studies, including several CryoEM structures, that contributed to elucidate specific features of the CENP-A nucleosome and molecular determinants of its interactions with CENP-C and CENP-N, the only two centromere proteins that directly bind to it. Based on those findings, we propose a role of the CENP-A nucleosome in the organization of centromeric chromatin beyond binding centromeric proteins.
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44
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Unequal contribution of two paralogous CENH3 variants in cowpea centromere function. Commun Biol 2020; 3:775. [PMID: 33319863 PMCID: PMC7738545 DOI: 10.1038/s42003-020-01507-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
In most diploids the centromere-specific histone H3 (CENH3), the assembly site of active centromeres, is encoded by a single copy gene. Persistance of two CENH3 paralogs in diploids species raises the possibility of subfunctionalization. Here we analysed both CENH3 genes of the diploid dryland crop cowpea. Phylogenetic analysis suggests that gene duplication of CENH3 occurred independently during the speciation of Vigna unguiculata. Both functional CENH3 variants are transcribed, and the corresponding proteins are intermingled in subdomains of different types of centromere sequences in a tissue-specific manner together with the kinetochore protein CENPC. CENH3.2 is removed from the generative cell of mature pollen, while CENH3.1 persists. CRISPR/Cas9-based inactivation of CENH3.1 resulted in delayed vegetative growth and sterility, indicating that this variant is needed for plant development and reproduction. By contrast, CENH3.2 knockout individuals did not show obvious defects during vegetative and reproductive development. Hence, CENH3.2 of cowpea is likely at an early stage of pseudogenization and less likely undergoing subfunctionalization.
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45
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MacKinnon RN, Peverall J, Campbell LJ, Wall M. Detailed molecular cytogenetic characterisation of the myeloid cell line U937 reveals the fate of homologous chromosomes and shows that centromere capture is a feature of genome instability. Mol Cytogenet 2020; 13:50. [PMID: 33317567 PMCID: PMC7737353 DOI: 10.1186/s13039-020-00517-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The U937 cell line is widely employed as a research tool. It has a complex karyotype. A PICALM-MLLT10 fusion gene formed by the recurrent t(10;11) translocation is present, and the myeloid common deleted region at 20q12 has been lost from its near-triploid karyotype. We carried out a detailed investigation of U937 genome reorganisation including the chromosome 20 rearrangements and other complex rearrangements. RESULTS SNP array, G-banding and Multicolour FISH identified chromosome segments resulting from unbalanced and balanced rearrangements. The organisation of the abnormal chromosomes containing these segments was then reconstructed with the strategic use of targeted metaphase FISH. This provided more accurate karyotype information for the evolving karyotype. Rearrangements involving the homologues of a chromosome pair could be differentiated in most instances. Centromere capture was demonstrated in an abnormal chromosome containing parts of chromosomes 16 and 20 which were stabilised by joining to a short section of chromosome containing an 11 centromere. This adds to the growing number of examples of centromere capture, which to date have a high incidence in complex karyotypes where the centromeres of the rearranged chromosomes are identified. There were two normal copies of one chromosome 20 homologue, and complex rearrangement of the other homologue including loss of the 20q12 common deleted region. This confirmed the previously reported loss of heterozygosity of this region in U937, and defined the rearrangements giving rise to this loss. CONCLUSIONS Centromere capture, stabilising chromosomes pieced together from multiple segments, may be a common feature of complex karyotypes. However, it has only recently been recognised, as this requires deliberate identification of the centromeres of abnormal chromosomes. The approach presented here is invaluable for studying complex reorganised genomes such as those produced by chromothripsis, and provides a more complete picture than can be obtained by microarray, karyotyping or FISH studies alone. One major advantage of SNP arrays for this process is that the two homologues can usually be distinguished when there is more than one rearrangement of a chromosome pair. Tracking the fate of each homologue and of highly repetitive DNA regions such as centromeres helps build a picture of genome evolution. Centromere- and telomere-containing elements are important to deducing chromosome structure. This study confirms and highlights ongoing evolution in cultured cell lines.
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Affiliation(s)
- Ruth N. MacKinnon
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital, PO Box 2900, Fitzroy, Melbourne, 3065 Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Parkville, Australia
| | - Joanne Peverall
- PathWest Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Australia
| | - Lynda J. Campbell
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital, PO Box 2900, Fitzroy, Melbourne, 3065 Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Parkville, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Services, Parkville, Melbourne, Australia
- Murdoch Children’s Research Institute, Parkville, Melbourne, Australia
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46
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Karyotype Evolution in 10 Pinniped Species: Variability of Heterochromatin versus High Conservatism of Euchromatin as Revealed by Comparative Molecular Cytogenetics. Genes (Basel) 2020; 11:genes11121485. [PMID: 33321928 PMCID: PMC7763226 DOI: 10.3390/genes11121485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 11/19/2022] Open
Abstract
Pinnipedia karyotype evolution was studied here using human, domestic dog, and stone marten whole-chromosome painting probes to obtain comparative chromosome maps among species of Odobenidae (Odobenus rosmarus), Phocidae (Phoca vitulina, Phoca largha, Phoca hispida, Pusa sibirica, Erignathus barbatus), and Otariidae (Eumetopias jubatus, Callorhinus ursinus, Phocarctos hookeri, and Arctocephalus forsteri). Structural and functional chromosomal features were assessed with telomere repeat and ribosomal-DNA probes and by CBG (C-bands revealed by barium hydroxide treatment followed by Giemsa staining) and CDAG (Chromomycin A3-DAPI after G-banding) methods. We demonstrated diversity of heterochromatin among pinniped karyotypes in terms of localization, size, and nucleotide composition. For the first time, an intrachromosomal rearrangement common for Otariidae and Odobenidae was revealed. We postulate that the order of evolutionarily conserved segments in the analyzed pinnipeds is the same as the order proposed for the ancestral Carnivora karyotype (2n = 38). The evolution of conserved genomes of pinnipeds has been accompanied by few fusion events (less than one rearrangement per 10 million years) and by novel intrachromosomal changes including the emergence of new centromeres and pericentric inversion/centromere repositioning. The observed interspecific diversity of pinniped karyotypes driven by constitutive heterochromatin variation likely has played an important role in karyotype evolution of pinnipeds, thereby contributing to the differences of pinnipeds’ chromosome sets.
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47
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Milagre I, Pereira C, Oliveira RA, Jansen LET. Reprogramming of human cells to pluripotency induces CENP-A chromatin depletion. Open Biol 2020; 10:200227. [PMID: 33081635 PMCID: PMC7653353 DOI: 10.1098/rsob.200227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells (PSCs) are central to development as they are the precursors of all cell types in the embryo. Therefore, maintaining a stable karyotype is essential, both for their physiological role as well as for their use in regenerative medicine. Karyotype abnormalities in PSCs in culture are common but the underlying causes remain unknown. To gain insight, we explore the composition of the centromere and kinetochore in human embryonic and induced PSCs. Centromere function depends on CENP-A nucleosome-defined chromatin. We show that while PSCs maintain abundant pools of CENP-A, CENP-C and CENP-T, these essential centromere components are strongly reduced at stem cell centromeres. Outer kinetochore recruitment is also impaired to a lesser extent, indicating an overall weaker kinetochore while the inner centromere protein Aurora B remains unaffected. We further show that, similar to differentiated human cells, CENP-A chromatin assembly in PSCs requires transition into G1 phase. Finally, reprogramming experiments indicate that reduction of centromeric CENP-A levels is an early event during dedifferentiation, coinciding with global chromatin remodelling. Our characterization of centromeres in human stem cells suggests a possible link between impaired centromere function and stem cell aneuploidies.
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Affiliation(s)
- Inês Milagre
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Carolina Pereira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Lars E T Jansen
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.,Department of Biochemistry, University of Oxford, OX1, 3QU, UK
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48
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Deakin JE, Potter S. Marsupial chromosomics: bridging the gap between genomes and chromosomes. Reprod Fertil Dev 2020; 31:1189-1202. [PMID: 30630589 DOI: 10.1071/rd18201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Sally Potter
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
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49
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Hoffmann S, Izquierdo HM, Gamba R, Chardon F, Dumont M, Keizer V, Hervé S, McNulty SM, Sullivan BA, Manel N, Fachinetti D. A genetic memory initiates the epigenetic loop necessary to preserve centromere position. EMBO J 2020; 39:e105505. [PMID: 32945564 PMCID: PMC7560200 DOI: 10.15252/embj.2020105505] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
Centromeres are built on repetitive DNA sequences (CenDNA) and a specific chromatin enriched with the histone H3 variant CENP‐A, the epigenetic mark that identifies centromere position. Here, we interrogate the importance of CenDNA in centromere specification by developing a system to rapidly remove and reactivate CENP‐A (CENP‐AOFF/ON). Using this system, we define the temporal cascade of events necessary to maintain centromere position. We unveil that CENP‐B bound to CenDNA provides memory for maintenance on human centromeres by promoting de novo CENP‐A deposition. Indeed, lack of CENP‐B favors neocentromere formation under selective pressure. Occasionally, CENP‐B triggers centromere re‐activation initiated by CENP‐C, but not CENP‐A, recruitment at both ectopic and native centromeres. This is then sufficient to initiate the CENP‐A‐based epigenetic loop. Finally, we identify a population of CENP‐A‐negative, CENP‐B/C‐positive resting CD4+ T cells capable to re‐express and reassembles CENP‐A upon cell cycle entry, demonstrating the physiological importance of the genetic memory.
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Affiliation(s)
| | | | - Riccardo Gamba
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Florian Chardon
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Marie Dumont
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Veer Keizer
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Solène Hervé
- Institut Curie, CNRS, UMR 144, PSL Research University, Paris, France
| | - Shannon M McNulty
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Nicolas Manel
- Institut Curie, PSL Research University, INSERM U932, Paris, France
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50
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Tolomeo D, Agostini A, Macchia G, L'Abbate A, Severgnini M, Cifola I, Frassanito MA, Racanelli V, Solimando AG, Haglund F, Mertens F, Storlazzi CT. BL1391: an established cell line from a human malignant peripheral nerve sheath tumor with unique genomic features. Hum Cell 2020; 34:238-245. [PMID: 32856169 DOI: 10.1007/s13577-020-00418-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022]
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive tumors, accounting for around 5% of all soft tissue sarcomas. A better understanding of the pathogenesis of these tumors and the development of effective treatments are needed. In this context, established tumor cell lines can be very informative, as they may be used for in-depth molecular analyses and improvement of treatment strategies. Here, we present the genomic and transcriptomic profiling analysis of a MPNST cell line (BL1391) that was spontaneously established in our laboratory from a primary tumor that had not been exposed to genotoxic treatment. This cell line shows peculiar genetic features, such as a large marker chromosome composed of high-copy number amplifications of regions from chromosomes 1 and 11 with an embedded neocentromere. Moreover, the transcriptome profiling revealed the presence of several fusion transcripts involving the CACHD1, TNMA4, MDM4, and YAP1 genes, all of which map to the amplified regions of the marker. BL1391 could be a useful tool to study genomic amplifications and neocentromere seeding in MPNSTs and to develop new therapeutic strategies.
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Affiliation(s)
- Doron Tolomeo
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy
| | - Antonio Agostini
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Gemma Macchia
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy
| | - Alberto L'Abbate
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy.,Institute of Biomembranes, Bioenergetics, and Molecular Biotechnologies, National Research Council (IBIOM-CNR), 70125, Bari, Italy
| | - Marco Severgnini
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, 20090, Milan, Italy
| | - Ingrid Cifola
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, 20090, Milan, Italy
| | - Maria Antonia Frassanito
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy.,IRCCS Istituto Tumori "Giovanni Paolo II", 70124, Bari, Italy
| | - Felix Haglund
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, Lund University and Skåne University Hospital, 221 85, Lund, Sweden
| | - Clelia Tiziana Storlazzi
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy.
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