1
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Kitaoka M, Smith OK, Straight AF, Heald R. Molecular conflicts disrupting centromere maintenance contribute to Xenopus hybrid inviability. Curr Biol 2022; 32:3939-3951.e6. [PMID: 35973429 PMCID: PMC9529917 DOI: 10.1016/j.cub.2022.07.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/15/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022]
Abstract
Although central to evolution, the causes of hybrid inviability that drive reproductive isolation are poorly understood. Embryonic lethality occurs when the eggs of the frog X. tropicalis are fertilized with either X. laevis or X. borealis sperm. We observed that distinct subsets of paternal chromosomes failed to assemble functional centromeres, causing their mis-segregation during embryonic cell divisions. Core centromere DNA sequence analysis revealed little conservation among the three species, indicating that epigenetic mechanisms that normally operate to maintain centromere integrity are disrupted on specific paternal chromosomes in hybrids. In vitro reactions combining X. tropicalis egg extract with either X. laevis or X. borealis sperm chromosomes revealed that paternally matched or overexpressed centromeric histone CENP-A and its chaperone HJURP could rescue centromere assembly on affected chromosomes in interphase nuclei. However, although the X. laevis chromosomes maintained centromeric CENP-A in metaphase, X. borealis chromosomes did not and also displayed ultra-thin regions containing ribosomal DNA. Both centromere assembly and morphology of X. borealis mitotic chromosomes could be rescued by inhibiting RNA polymerase I or preventing the collapse of stalled DNA replication forks. These results indicate that specific paternal centromeres are inactivated in hybrids due to the disruption of associated chromatin regions that interfere with CENP-A incorporation, at least in some cases due to conflicts between replication and transcription machineries. Thus, our findings highlight the dynamic nature of centromere maintenance and its susceptibility to disruption in vertebrate interspecies hybrids.
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Affiliation(s)
- Maiko Kitaoka
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Owen K Smith
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA.
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2
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Mitotic drive in asymmetric epigenetic inheritance. Biochem Soc Trans 2022; 50:675-688. [PMID: 35437581 PMCID: PMC9162470 DOI: 10.1042/bst20200267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 01/14/2023]
Abstract
Asymmetric cell division (ACD) produces two daughter cells with distinct cell fates. This division mode is widely used during development and by adult stem cells during tissue homeostasis and regeneration, which can be regulated by both extrinsic cues such as signaling molecules and intrinsic factors such as epigenetic information. While the DNA replication process ensures that the sequences of sister chromatids are identical, how epigenetic information is re-distributed during ACD has remained largely unclear in multicellular organisms. Studies of Drosophila male germline stem cells (GSCs) have revealed that sister chromatids incorporate pre-existing and newly synthesized histones differentially and segregate asymmetrically during ACD. To understand the underlying molecular mechanisms of this phenomenon, two key questions must be answered: first, how and when asymmetric histone information is established; and second, how epigenetically distinct sister chromatids are distinguished and segregated. Here, we discuss recent advances which help our understanding of this interesting and important cell division mode.
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3
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Toscani MA, Pigozzi MI, Papeschi AG, Bressa MJ. Histone H3 Methylation and Autosomal vs. Sex Chromosome Segregation During Male Meiosis in Heteroptera. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.836786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heteropteran insects exhibit a remarkable diversity of meiotic processes, including coexistence of different chromosomes types with different behavior during the first meiotic division, non-chiasmatic segregation, and inverted meiosis. Because of this diversity they represent suitable models to study fundamental questions about the mechanisms of chromosome behavior during cell division. All heteropteran species possess holokinetic chromosomes and in most of them the autosomal chromosomes synapse, recombine, and undergoe pre-reductional meiosis. In contrast, the sex chromosomes are achiasmatic, behave as univalents at metaphase I and present an inverted or post-reductional meiosis. An exception to this typical behavior is found in Pachylis argentinus, where both the autosomes and the X-chromosome divide reductionally at anaphase I and then divide equationally at anaphase II. In the present report, we analyzed the distribution of histones H3K9me2 and H3K9me3 in P. argentinus and in five species that have simple and multiple sex chromosome systems with typical chromosome segregation, Belostoma elegans, B. oxyurum, Holhymenia rubiginosa, Phthia picta, and Oncopeltus unifasciatellus. We found that H3K9me3 is a marker for sex-chromosomes from early prophase I to the end of the first division in all the species. H3K9me2 also marks the sex chromosomes since early prophase but shows different dynamics at metaphase I depending on the sex-chromosome segregation: it is lost in species with equationally dividing sex chromosomes but remains on one end of the X chromosome of P. argentinus, where chromatids migrate together at anaphase I. It is proposed that the loss of H3K9me2 from the sex chromosomes observed at metaphase I may be part of a set of epigenetic signals that lead to the reductional or equational division of autosomes and sex chromosomes observed in most Heteroptera. The present observations suggest that the histone modifications analyzed here evolved in Heteroptera as markers for asynaptic and achiasmatic sex chromosomes during meiosis to allow the distinction from the chiasmatic autosomal chromosomes.
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4
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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] [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, USA
| | - 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, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - 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, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - 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, USA
| | - 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, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - 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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5
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Li B, Li Z, Lu C, Chang L, Zhao D, Shen G, Kusakabe T, Xia Q, Zhao P. Heat Shock Cognate 70 Functions as A Chaperone for the Stability of Kinetochore Protein CENP-N in Holocentric Insect Silkworms. Int J Mol Sci 2019; 20:ijms20235823. [PMID: 31756960 PMCID: PMC6929194 DOI: 10.3390/ijms20235823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 01/09/2023] Open
Abstract
The centromere, in which kinetochore proteins are assembled, plays an important role in the accurate congression and segregation of chromosomes during cell mitosis. Although the function of the centromere and kinetochore is conserved from monocentric to holocentric, the DNA sequences of the centromere and components of the kinetochore are varied among different species. Given the lack of core centromere protein A (CENP-A) and CENP-C in the lepidopteran silkworm Bombyx mori, which possesses holocentric chromosomes, here we investigated the role of CENP-N, another important member of the centromere protein family essential for kinetochore assembly. For the first time, cellular localization and RNA interference against CENP-N have confirmed its kinetochore function in silkworms. To gain further insights into the regulation of CENP-N in the centromere, we analyzed the affinity-purified complex of CENP-N by mass spectrometry and identified 142 interacting proteins. Among these factors, we found that the chaperone protein heat shock cognate 70 (HSC70) is able to regulate the stability of CENP-N by prohibiting ubiquitin-proteasome pathway, indicating that HSC70 could control cell cycle-regulated degradation of CENP-N at centromeres. Altogether, the present work will provide a novel clue to understand the regulatory mechanism for the kinetochore activity of CENP-N during the cell cycle.
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Affiliation(s)
- Bingqian Li
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Zhiqing Li
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
- Correspondence:
| | - Chenchen Lu
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Li Chang
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Dongchao Zhao
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Guanwang Shen
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka 819-0395, Japan;
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Chongqing 400715, China; (B.L.); (C.L.); (L.C.); (D.Z.); (G.S.); (Q.X.); (P.Z.)
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
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6
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Imaging and Quantitation of Assembly Dynamics of the Centromeric Histone H3 Variant CENP-A in Drosophila melanogaster Spermatocytes by Immunofluorescence and Fluorescence In-Situ Hybridization (Immuno-FISH). Methods Mol Biol 2018. [PMID: 30073536 DOI: 10.1007/978-1-4939-8663-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter describes a method used to assay the cell cycle dynamics of the centromeric histone H3 variant CENP-A in meiosis using Drosophila males as the experimental system. Specifically, we describe a method that combines Immunofluorescence (IF) and Fluorescence in-situ Hybridization (FISH) protocols, performed on fixed Drosophila testes. An advantage of this protocol is the ability to localize individual centromeres on the four Drosophila homologous chromosomes that form distinct nuclear territories in spermatocytes. We also describe a method to quantify CENP-A focal intensities using Image J software.
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7
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Nergadze SG, Piras FM, Gamba R, Corbo M, Cerutti F, McCarter JGW, Cappelletti E, Gozzo F, Harman RM, Antczak DF, Miller D, Scharfe M, Pavesi G, Raimondi E, Sullivan KF, Giulotto E. Birth, evolution, and transmission of satellite-free mammalian centromeric domains. Genome Res 2018; 28:789-799. [PMID: 29712753 PMCID: PMC5991519 DOI: 10.1101/gr.231159.117] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/13/2018] [Indexed: 11/25/2022]
Abstract
Mammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain. Centromeres are epigenetically specified, and binding of the CENPA protein is their main determinant. In previous work, we described the first example of a natural satellite-free centromere on Equus caballus Chromosome 11. Here, we investigated the satellite-free centromeres of Equus asinus by using ChIP-seq with anti-CENPA antibodies. We identified an extraordinarily high number of centromeres lacking satellite DNA (16 of 31). All of them lay in LINE- and AT-rich regions. A subset of these centromeres is associated with DNA amplification. The location of CENPA binding domains can vary in different individuals, giving rise to epialleles. The analysis of epiallele transmission in hybrids (three mules and one hinny) showed that centromeric domains are inherited as Mendelian traits, but their position can slide in one generation. Conversely, centromere location is stable during mitotic propagation of cultured cells. Our results demonstrate that the presence of more than half of centromeres void of satellite DNA is compatible with genome stability and species survival. The presence of amplified DNA at some centromeres suggests that these arrays may represent an intermediate stage toward satellite DNA formation during evolution. The fact that CENPA binding domains can move within relatively restricted regions (a few hundred kilobases) suggests that the centromeric function is physically limited by epigenetic boundaries.
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Affiliation(s)
- Solomon G Nergadze
- 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
| | - Riccardo Gamba
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Marco Corbo
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Federico Cerutti
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Joseph G W McCarter
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland
| | - Eleonora Cappelletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Francesco Gozzo
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Rebecca M Harman
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Maren Scharfe
- Genomanalytik (GMAK), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Giulio Pavesi
- Department of Biosciences, University of Milano, 20122 Milano, Italy
| | - Elena Raimondi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Kevin F Sullivan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland
| | - Elena Giulotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
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8
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Cáceres-Gutiérrez R, Herrera LA. Centromeric Non-coding Transcription: Opening the Black Box of Chromosomal Instability? Curr Genomics 2017; 18:227-235. [PMID: 28603453 PMCID: PMC5439370 DOI: 10.2174/1389202917666161102095508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/01/2016] [Accepted: 10/27/2016] [Indexed: 02/05/2023] Open
Abstract
In eukaryotes, mitosis is tightly regulated to avoid the generation of numerical chromosome aberrations, or aneuploidies. The aneuploid phenotype is a consequence of chromosomal instability (CIN), i.e., an enhanced rate of chromosome segregation errors, which is frequently found in cancer cells and is associated with tumor aggressiveness and increased tumor cell survival potential. To avoid the generation of aneuploidies, cells rely on the spindle assembly checkpoint (SAC), a widely conserved mechanism that protects the genome against this type of error. This signaling pathway stops mitotic pro-gression before anaphase until all chromosomes are correctly attached to spindle microtubules. Howev-er, impairment of the SAC cannot account for the establishment of CIN because cells bearing this phe-notype have a functional SAC. Hence, in cells with CIN, anaphase is not triggered until all chromo-somes are correctly attached to spindle microtubules and congressed at the metaphase plate. Thus, an in-teresting question arises: What mechanisms actually mediate CIN in cancer cells? Recent research has shown that some pathways involved in chromosome segregation are closely associated to centromere-encoded non-coding RNA (cencRNA) and that these RNAs are deregulated in abnormal conditions, such as cancer. These mechanisms may provide new explanations for chromosome segregation errors. The present review discusses some of these findings and proposes novel mechanisms for the establish-ment of CIN based on regulation by cencRNA.
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Affiliation(s)
- Rodrigo Cáceres-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexicocity, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexicocity, Mexico
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9
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Giulotto E, Raimondi E, Sullivan KF. The Unique DNA Sequences Underlying Equine Centromeres. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:337-354. [PMID: 28840244 DOI: 10.1007/978-3-319-58592-5_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Centromeres are highly distinctive genetic loci whose function is specified largely by epigenetic mechanisms. Understanding the role of DNA sequences in centromere function has been a daunting task due to the highly repetitive nature of centromeres in animal chromosomes. The discovery of a centromere devoid of satellite DNA in the domestic horse consolidated observations on the epigenetic nature of centromere identity, showing that entirely natural chromosomes could function without satellite DNA cues. Horses belong to the genus Equus which exhibits a very high degree of evolutionary plasticity in centromere position and DNA sequence composition. Examination of horses has revealed that the position of the satellite-free centromere is variable among individuals. Analysis of centromere location and composition in other Equus species, including domestic donkey and zebras, confirms that the satellite-less configuration of centromeres is common in this group which has undergone particularly rapid karyotype evolution. These features have established the equids as a new mammalian system in which to investigate the molecular organization, dynamics and evolutionary behaviour of centromeres.
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Affiliation(s)
- Elena Giulotto
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Elena Raimondi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Kevin F Sullivan
- National University of Ireland Galway, University Road, Galway, Ireland
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10
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Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. eLife 2014; 3. [PMID: 25247700 DOI: 10.7554/elife.03676.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/25/2014] [Indexed: 05/24/2023] Open
Abstract
Faithful chromosome segregation in all eukaryotes relies on centromeres, the chromosomal sites that recruit kinetochore proteins and mediate spindle attachment during cell division. The centromeric histone H3 variant, CenH3, is the defining chromatin component of centromeres in most eukaryotes, including animals, fungi, plants, and protists. In this study, using detailed genomic and transcriptome analyses, we show that CenH3 was lost independently in at least four lineages of insects. Each of these lineages represents an independent transition from monocentricity (centromeric determinants localized to a single chromosomal region) to holocentricity (centromeric determinants extended over the entire chromosomal length) as ancient as 300 million years ago. Holocentric insects therefore contain a CenH3-independent centromere, different from almost all the other eukaryotes. We propose that ancient transitions to holocentricity in insects obviated the need to maintain CenH3, which is otherwise essential in most eukaryotes, including other holocentrics.
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Affiliation(s)
- Ines A Drinnenberg
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Dakota deYoung
- Department of Biology, University of Washington, Seattle, United States
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Harmit Singh Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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11
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Drinnenberg IA, deYoung D, Henikoff S, Malik HS. Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. eLife 2014; 3:e03676. [PMID: 25247700 PMCID: PMC4359364 DOI: 10.7554/elife.03676] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/25/2014] [Indexed: 01/15/2023] Open
Abstract
Faithful chromosome segregation in all eukaryotes relies on centromeres, the chromosomal sites that recruit kinetochore proteins and mediate spindle attachment during cell division. The centromeric histone H3 variant, CenH3, is the defining chromatin component of centromeres in most eukaryotes, including animals, fungi, plants, and protists. In this study, using detailed genomic and transcriptome analyses, we show that CenH3 was lost independently in at least four lineages of insects. Each of these lineages represents an independent transition from monocentricity (centromeric determinants localized to a single chromosomal region) to holocentricity (centromeric determinants extended over the entire chromosomal length) as ancient as 300 million years ago. Holocentric insects therefore contain a CenH3-independent centromere, different from almost all the other eukaryotes. We propose that ancient transitions to holocentricity in insects obviated the need to maintain CenH3, which is otherwise essential in most eukaryotes, including other holocentrics.
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Affiliation(s)
- Ines A Drinnenberg
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Dakota deYoung
- Department of Biology, University of Washington, Seattle, United States
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Harmit Singh Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
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12
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Abstract
The centromere is the chromosomal locus essential for chromosome inheritance and genome stability. Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Contiguous alpha satellite DNA sequence is absent from the assembled reference genome, limiting current understanding of centromere organization and function. Here, we review the progress in centromere genomics spanning the discovery of the sequence to its molecular characterization and the work done during the Human Genome Project era to elucidate alpha satellite structure and sequence variation. We discuss exciting recent advances in alpha satellite sequence assembly that have provided important insight into the abundance and complex organization of this sequence on human chromosomes. In light of these new findings, we offer perspectives for future studies of human centromere assembly and function.
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Affiliation(s)
- Megan E. Aldrup-MacDonald
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; E-Mail:
- Division of Human Genetics, Duke University, Durham, NC 27710, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; E-Mail:
- Division of Human Genetics, Duke University, Durham, NC 27710, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-919-684-9038
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13
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Panchenko T, Sorensen TC, Woodcock CL, Kan ZY, Wood S, Resch MG, Luger K, Englander SW, Hansen JC, Black BE. Replacement of histone H3 with CENP-A directs global nucleosome array condensation and loosening of nucleosome superhelical termini. Proc Natl Acad Sci U S A 2011; 108:16588-93. [PMID: 21949362 PMCID: PMC3189058 DOI: 10.1073/pnas.1113621108] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Centromere protein A (CENP-A) is a histone H3 variant that marks centromere location on the chromosome. To study the subunit structure and folding of human CENP-A-containing chromatin, we generated a set of nucleosomal arrays with canonical core histones and another set with CENP-A substituted for H3. At the level of quaternary structure and assembly, we find that CENP-A arrays are composed of octameric nucleosomes that assemble in a stepwise mechanism, recapitulating conventional array assembly with canonical histones. At intermediate structural resolution, we find that CENP-A-containing arrays are globally condensed relative to arrays with the canonical histones. At high structural resolution, using hydrogen-deuterium exchange coupled to mass spectrometry (H/DX-MS), we find that the DNA superhelical termini within each nucleosome are loosely connected to CENP-A, and we identify the key amino acid substitution that is largely responsible for this behavior. Also the C terminus of histone H2A undergoes rapid hydrogen exchange relative to canonical arrays and does so in a manner that is independent of nucleosomal array folding. These findings have implications for understanding CENP-A-containing nucleosome structure and higher-order chromatin folding at the centromere.
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Affiliation(s)
- Tanya Panchenko
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Graduate Group in Cell and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Troy C. Sorensen
- Department of Biochemistry and Molecular Biology, Colorado State University, Ft. Collins, CO 80523; and
| | | | - Zhong-yuan Kan
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Stacey Wood
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael G. Resch
- Department of Biochemistry and Molecular Biology, Colorado State University, Ft. Collins, CO 80523; and
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Ft. Collins, CO 80523; and
| | - S. Walter Englander
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jeffrey C. Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Ft. Collins, CO 80523; and
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Graduate Group in Cell and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104
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14
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Verdaasdonk JS, Bloom K. Centromeres: unique chromatin structures that drive chromosome segregation. Nat Rev Mol Cell Biol 2011; 12:320-32. [PMID: 21508988 DOI: 10.1038/nrm3107] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fidelity during chromosome segregation is essential to prevent aneuploidy. The proteins and chromatin at the centromere form a unique site for kinetochore attachment and allow the cell to sense and correct errors during chromosome segregation. Centromeric chromatin is characterized by distinct chromatin organization, epigenetics, centromere-associated proteins and histone variants. These include the histone H3 variant centromeric protein A (CENPA), the composition and deposition of which have been widely investigated. Studies have examined the structural and biophysical properties of the centromere and have suggested that the centromere is not simply a 'landing pad' for kinetochore formation, but has an essential role in mitosis by assembling and directing the organization of the kinetochore.
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Affiliation(s)
- Jolien S Verdaasdonk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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15
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Lee SH, Itkin-Ansari P, Levine F. CENP-A, a protein required for chromosome segregation in mitosis, declines with age in islet but not exocrine cells. Aging (Albany NY) 2011; 2:785-90. [PMID: 21068465 PMCID: PMC3006021 DOI: 10.18632/aging.100220] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta-cell replication dramatically declines with age. Here, we report that the level of CENP-A, a protein required for cell division, declines precipitously with age in an islet-specific manner. CENP-A is essentially undetectable after age 29 in humans. However, exocrine cells retain CENP-A expression. The decline in islet-cell CENP-A expression is more striking in humans than in mice, where CENP-A expression continues to be detectable at low levels even in elderly mice. The mechanism by which CENP-A declines appears to be post-transcriptional, as there was no correlation between CENP-A mRNA levels and age or islet purity. This finding has implications for efforts to induce beta-cell replication as a treatment for diabetes.
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Affiliation(s)
- Seung-Hee Lee
- Sanford Children's Health Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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16
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Abstract
Nucleosomes containing histone variant H2A.Z (Htz1) serve to poise quiescent genes for activation and transcriptional initiation. However, little is known about their role in transcription elongation. Here we show that dominant mutations in the elongation genes SPT5 and SPT16 suppress the hypersensitivity of htz1Δ strains to drugs that inhibit elongation, indicating that Htz1 functions at the level of transcription elongation. Direct kinetic measurements of RNA polymerase II (Pol II) movement across the 9.5-kb GAL10p-VPS13 gene revealed that the elongation rate of polymerase is 24% slower in the absence of Htz1. We provide evidence for two nonexclusive mechanisms. First, we observed that both the phospho-Ser2 levels in the elongating isoform of Pol II and the loading of Spt5 and Elongator over the GAL1 open reading frame (ORF) depend on Htz1. Second, in the absence of Htz1, the density of nucleosome occupancy is increased over the GAL10p-VPS13 ORF and the chromatin is refractory to remodeling during active transcription. These results establish a mechanistic role for Htz1 in transcription elongation and suggest that Htz1-containing nucleosomes facilitate Pol II passage by affecting the correct assembly and modification status of Pol II elongation complexes and by favoring efficient nucleosome remodeling over the gene.
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Koren A, Tsai HJ, Tirosh I, Burrack LS, Barkai N, Berman J. Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase. PLoS Genet 2010; 6:e1001068. [PMID: 20808889 PMCID: PMC2924309 DOI: 10.1371/journal.pgen.1001068] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 07/14/2010] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic centromeres are maintained at specific chromosomal sites over many generations. In the budding yeast Saccharomyces cerevisiae, centromeres are genetic elements defined by a DNA sequence that is both necessary and sufficient for function; whereas, in most other eukaryotes, centromeres are maintained by poorly characterized epigenetic mechanisms in which DNA has a less definitive role. Here we use the pathogenic yeast Candida albicans as a model organism to study the DNA replication properties of centromeric DNA. By determining the genome-wide replication timing program of the C. albicans genome, we discovered that each centromere is associated with a replication origin that is the first to fire on its respective chromosome. Importantly, epigenetic formation of new ectopic centromeres (neocentromeres) was accompanied by shifts in replication timing, such that a neocentromere became the first to replicate and became associated with origin recognition complex (ORC) components. Furthermore, changing the level of the centromere-specific histone H3 isoform led to a concomitant change in levels of ORC association with centromere regions, further supporting the idea that centromere proteins determine origin activity. Finally, analysis of centromere-associated DNA revealed a replication-dependent sequence pattern characteristic of constitutively active replication origins. This strand-biased pattern is conserved, together with centromere position, among related strains and species, in a manner independent of primary DNA sequence. Thus, inheritance of centromere position is correlated with a constitutively active origin of replication that fires at a distinct early time. We suggest a model in which the distinct timing of DNA replication serves as an epigenetic mechanism for the inheritance of centromere position. Centromeres form at the same chromosomal position from generation to generation, yet in most species this inheritance occurs in a DNA sequence–independent manner that is not well understood. Here, we determine the timing of DNA replication across the genome of the human fungal pathogen Candida albicans and find that centromeric DNA is the first locus to replicate on each chromosome. Furthemore, this unique replication timing may be important for centromere inheritance, based on several observations. First, DNA sequence patterns at centromeres indicate that, despite high levels of primary sequence divergence, the region has served as a replication origin for millions of years; second, formation of a neocentromere (a new centromere formed at an ectopic locus following deletion of the native centromere DNA) results in the establishment of a new, early-firing origin of replication; and third, a centromere-specific protein, Cse4p, recruits origin replication complex proteins in a concentration-dependent manner. Thus, centromere position is inherited by an epigenetic mechanism that appears to be defined by a distinctively early firing DNA replication origin.
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Affiliation(s)
- Amnon Koren
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Hung-Ji Tsai
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Itay Tirosh
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Laura S. Burrack
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Naama Barkai
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
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Buscaino A, Allshire R, Pidoux A. Building centromeres: home sweet home or a nomadic existence? Curr Opin Genet Dev 2010; 20:118-26. [PMID: 20206496 DOI: 10.1016/j.gde.2010.01.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/20/2010] [Accepted: 01/22/2010] [Indexed: 12/26/2022]
Abstract
Centromere assembly and propagation is governed by genetic and epigenetic mechanisms. A centromere-specific histone H3 variant, CENP-A is strongly favored as the epigenetic mark that specifies centromere identity. Despite the critical importance of centromere function, centromeric sequences are not conserved. This has prompted exploration of other genomic and chromatin features to gain an understanding of where CENP-A is deposited. In this review we highlight recent papers that advance our understanding of how the cell builds a centromere. We focus on what influences the choice of site for CENP-A deposition and therefore the site of centromere formation. We then briefly discuss how centromeres are propagated once the site of centromere assembly is chosen.
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Affiliation(s)
- Alessia Buscaino
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Scotland, UK
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