1
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Lim KK, Lam UTF, Li Y, Zeng YB, Yang H, Chen ES. Set2 regulates Ccp1 and Swc2 to ensure centromeric stability by retargeting CENP-A. Nucleic Acids Res 2024; 52:4198-4214. [PMID: 38442274 PMCID: PMC11077061 DOI: 10.1093/nar/gkae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/07/2024] Open
Abstract
Precise positioning of the histone-H3 variant, CENP-A, ensures centromere stability and faithful chromosomal segregation. Mislocalization of CENP-A to extra-centromeric loci results in aneuploidy and compromised cell viability associated with formation of ectopic kinetochores. The mechanism that retargets mislocalized CENP-A back to the centromere is unclarified. We show here that the downregulation of the histone H3 lysine 36 (H3K36) methyltransferase Set2 can preserve centromere localization of a temperature-sensitive mutant cnp1-1 Schizosaccharomyces pombe CENP-A (SpCENP-A) protein and reverse aneuploidy by redirecting mislocalized SpCENP-A back to centromere from ribosomal DNA (rDNA) loci, which serves as a sink for the delocalized SpCENP-A. Downregulation of set2 augments Swc2 (SWR1 complex DNA-binding module) expression and releases histone chaperone Ccp1 from the centromeric reservoir. Swc2 and Ccp1 are directed to the rDNA locus to excavate the SpCENP-Acnp1-1, which is relocalized to the centromere in a manner dependent on canonical SpCENP-A loaders, including Mis16, Mis17 and Mis18, thereby conferring cell survival and safeguarding chromosome segregation fidelity. Chromosome missegregation is a severe genetic instability event that compromises cell viability. This mechanism thus promotes CENP-A presence at the centromere to maintain genomic stability.
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Affiliation(s)
- Kim Kiat Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ulysses Tsz Fung Lam
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ying Li
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yi Bing Zeng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Henry Yang
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
- Integrative Sciences & Engineering Programme, National University of Singapore, Singapore
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2
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Cao J, Hori T, Ariyoshi M, Fukagawa T. Artificial tethering of constitutive centromere-associated network proteins induces CENP-A deposition without Knl2 in DT40 cells. J Cell Sci 2024; 137:jcs261639. [PMID: 38319136 DOI: 10.1242/jcs.261639] [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: 09/10/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
The kinetochore is an essential structure for chromosome segregation. Although the kinetochore is usually formed on a centromere locus, it can be artificially formed at a non-centromere locus by protein tethering. An artificial kinetochore can be formed by tethering of CENP-C or CENP-I, members of the constitutive centromere-associated network (CCAN). However, how CENP-C or CENP-I recruit the centromere-specific histone CENP-A to form an artificial kinetochore remains unclear. In this study, we analyzed this issue using the tethering assay combined with an auxin-inducible degron (AID)-based knockout method in chicken DT40 cells. We found that tethering of CENP-C or CENP-I induced CENP-A incorporation at the non-centromeric locus in the absence of Knl2 (or MIS18BP1), a component of the Mis18 complex, and that Knl2 tethering recruited CENP-A in the absence of CENP-C. We also showed that CENP-C coimmunoprecipitated with HJURP, independently of Knl2. Considering these results, we propose that CENP-C recruits CENP-A by HJURP binding to form an artificial kinetochore. Our results suggest that CENP-C or CENP-I exert CENP-A recruitment activity, independently of Knl2, for artificial kinetochore formation in chicken DT40 cells. This gives us a new insight into mechanisms for CENP-A incorporation.
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Affiliation(s)
- JingHui Cao
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mariko Ariyoshi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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3
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Puchta H, Houben A. Plant chromosome engineering - past, present and future. THE NEW PHYTOLOGIST 2024; 241:541-552. [PMID: 37984056 DOI: 10.1111/nph.19414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
Spontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X-ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double-strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing.
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Affiliation(s)
- Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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4
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Meyer CM, Goldman IL, Krysan PJ. Chromosome-level changes and genome elimination by manipulation of CENH3 in carrot ( Daucus carota). FRONTIERS IN PLANT SCIENCE 2023; 14:1294551. [PMID: 38034555 PMCID: PMC10684906 DOI: 10.3389/fpls.2023.1294551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023]
Abstract
Hybrid cultivars are valuable in many crop species due to their high yield, uniformity, and other desirable traits. Doubled haploids, which have two identical sets of chromosomes, are valuable for hybrid breeding because they can be produced in one generation, in comparison to the multigenerational process typically used to produce inbred parents for hybrid production. One method to produce haploid plants is manipulation of centromeric histone H3 (CENH3). This method of producing haploids has so far been successful in Arabidopsis, maize (Zea mays), and wheat (Triticum aestivum). Here we describe modification of CENH3 in carrot (Daucus carota) to test for the ability of these modifications to induce uniparental genome elimination, which is the basis for haploid induction. Base editing was used to make cenh3 mutant plants with amino acid substitutions in the region of CENH3 encoding the histone fold domain. These cenh3 mutant plants were then outcrossed with CENH3 wild-type plants. Using PCR-based genotyping assays, we identified two candidates for genome elimination. One candidate was classified as a putative aneuploid plant in which chromosome 7 is in a single copy state. The other candidate was characterized as a putative tetraploid that was likely haploid during its genesis. Our results suggest that this putative tetraploid inherited all of its chromosomes from the CENH3 wild-type parent and that the genome of the cenh3 mutant plant was lost. This study provides evidence that modification of CENH3 in carrot has the potential to induce genome elimination and ploidy changes in carrot.
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Affiliation(s)
| | | | - Patrick J. Krysan
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
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5
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Melters DP, Neuman KC, Bentahar RS, Rakshit T, Dalal Y. Single molecule analysis of CENP-A chromatin by high-speed atomic force microscopy. eLife 2023; 12:e86709. [PMID: 37728600 PMCID: PMC10511241 DOI: 10.7554/elife.86709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
Chromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated of the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamics in vitro inform us about transcriptional potential in vivo. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the mean square displacement and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, we found that an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. From these data, we speculate that factors altering nucleosome mobility in vitro, also correspondingly alter transcription in vivo. Subsequently, we propose a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance nucleosome mobility.
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Affiliation(s)
- Daniël P Melters
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
| | - Keir C Neuman
- National Heart, Lung, and Blood Institute, Laboratory of Single Molecule BiophysicsBethesdaUnited States
| | - Reda S Bentahar
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
| | - Tatini Rakshit
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
- Department of Chemistry, Shiv Nadar UniversityDadriIndia
| | - Yamini Dalal
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
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6
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Das A, Boese KG, Tachibana K, Baek SH, Lampson MA, Black BE. Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly. Curr Biol 2023; 33:3759-3765.e3. [PMID: 37582374 PMCID: PMC10528140 DOI: 10.1016/j.cub.2023.07.032] [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: 04/21/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023]
Abstract
Centromeres direct genetic inheritance but are not themselves genetically encoded. Instead, centromeres are defined epigenetically by the presence of a histone H3 variant, CENP-A.1 In cultured somatic cells, an established paradigm of cell-cycle-coupled propagation maintains centromere identity: CENP-A is partitioned between sisters during replication and replenished by new assembly, which is restricted to G1. The mammalian female germ line challenges this model because of the cell-cycle arrest between pre-meiotic S phase and the subsequent G1, which can last for the entire reproductive lifespan (months to decades). New CENP-A chromatin assembly maintains centromeres during prophase I in worm and starfish oocytes,2,3 suggesting that a similar process may be required for centromere inheritance in mammals. To test this hypothesis, we developed an oocyte-specific conditional knockout (cKO) mouse for Mis18α, an essential component of the assembly machinery. We find that embryos derived from Mis18α knockout oocytes fail to assemble CENP-A nucleosomes prior to zygotic genome activation (ZGA), validating the knockout model. We show that deletion of Mis18α in the female germ line at the time of birth has no impact on centromeric CENP-A nucleosome abundance, even after 6-8 months of aging. In addition, there is no detectable detriment to fertility. Thus, centromere chromatin is maintained long-term, independent of new assembly during the extended prophase I arrest in mouse oocytes.
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Affiliation(s)
- Arunika Das
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katelyn G Boese
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kikue Tachibana
- Department of Totipotency, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, Seoul National University, Seoul 08826, Republic of Korea
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Raipuria RK, Watts A, Sharma BB, Watts A, Bhattacharya R. Decoding allelic diversity, transcript variants and transcriptional complexity of CENH3 gene in Brassica oleracea var. botrytis. PROTOPLASMA 2023; 260:1149-1162. [PMID: 36705736 DOI: 10.1007/s00709-023-01837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 01/07/2023] [Indexed: 06/07/2023]
Abstract
Histone proteins play a critical role in the primary organization of nucleosomes, which is the fundamental unit of chromatin. Among the five types of the histones, histone H3 has multiple variants, and the number differs among the species. Amongst histone H3 variants, centromeric histone H3 (CENH3) is crucial for centromere identification and proper chromosomal segregation during cell division. In the present study, we have identified 17 putative histone H3 genes of Brassica oleracea. Furthermore, we have done a detailed characterization of the CENH3 gene of B. oleracea. We showed that a single CENH3 gene exhibits allelic diversity with at least two alleles and alternative splicing pattern. Also, we have identified a CENH3 gene-specific co-dominant cleaved amplified polymorphic sequence marker SNP34(A/C) to distinguish CENH3 alleles and follow their expression in leaf and flower tissues. The gene structure analysis of the CENH3 gene revealed the conserved 5'-CAGCAG-3' sequence at the intron 3-exon 4 junction in B. oleracea, which serves as an alternative splicing site with one-codon (alanine) addition/deletion. However, this one-codon alternative splicing feature is not conserved in the CENH3 genes of wild allied Brassica species. Our finding suggests that transcriptional complexity and alternative splicing might play a key role in the transcriptional regulation and function of the CENH3 gene in B. oleracea. Altogether, data generated from the present study can serve as a primary information resource and can be used to engineer CENH3 gene towards developing haploid inducer lines in B. oleracea.
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Affiliation(s)
- Ritesh Kumar Raipuria
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Anshul Watts
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
| | - Brij Bihari Sharma
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Archana Watts
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
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8
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van den Berg SJW, East S, Mitra S, Jansen LET. p97/VCP drives turnover of SUMOylated centromeric CCAN proteins and CENP-A. Mol Biol Cell 2023; 34:br6. [PMID: 36989032 PMCID: PMC10162411 DOI: 10.1091/mbc.e23-01-0035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
The centromere is a unique chromatin domain that links sister chromatids and forms the attachment site for spindle microtubules in mitosis. Centromere inheritance is largely DNA sequence-independent but strongly reliant on a self-propagating chromatin domain featuring nucleosomes containing the H3 variant CENP-A. Unlike other histones, CENP-A is maintained with unusually high stability in chromatin. Previously, we have shown that mitotic maintenance of CENP-A and other constitutive centromere-associated network (CCAN) proteins is controlled by a dynamic SUMO cycle and that the deSUMOylase SENP6 is necessary for stable maintenance of CENP-A at the centromere. Here, we discover that the removal of SENP6 leads to a rapid loss of the CCAN, followed by a delayed loss of centromeric CENP-A, indicating that the CCAN is the primary SUMO target. We found that the ATP-dependent segregase p97/VCP removes centromeric CENP-A in a SUMO-dependent manner and interacts physically with the CCAN and CENP-A chromatin. Our data suggest a direct role of p97 in removing centromeric CENP-A via SUMOylated CCAN proteins, thereby ensuring centromere homeostasis and potentially preventing ectopic CENP-A accumulation.
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Affiliation(s)
- Sebastiaan J. W. van den Berg
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Instituto Gulbenkian de Ciencia, 2780-156 Oeiras, Portugal
| | - Samuel East
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sreyoshi Mitra
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Lars E. T. Jansen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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9
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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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10
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Ding W, Zhu Y, Han J, Zhang H, Xu Z, Khurshid H, Liu F, Hasterok R, Shen X, Wang K. Characterization of centromeric DNA of Gossypium anomalum reveals sequence-independent enrichment dynamics of centromeric repeats. Chromosome Res 2023; 31:12. [PMID: 36971835 DOI: 10.1007/s10577-023-09721-z] [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: 01/07/2023] [Revised: 02/20/2023] [Accepted: 03/04/2023] [Indexed: 03/29/2023]
Abstract
Centromeres in eukaryotes are composed of highly repetitive DNAs, which evolve rapidly and are thought to achieve a favorable structure in mature centromeres. However, how the centromeric repeat evolves into an adaptive structure is largely unknown. We characterized the centromeric sequences of Gossypium anomalum through chromatin immunoprecipitation against CENH3 antibodies. We revealed that the G. anomalum centromeres contained only retrotransposon-like repeats but were depleted in long arrays of satellites. These retrotransposon-like centromeric repeats were present in the African-Asian and Australian lineage species, suggesting that they might have arisen in the common ancestor of these diploid species. Intriguingly, we observed a substantial increase and decrease in copy numbers among African-Asian and Australian lineages, respectively, for the retrotransposon-derived centromeric repeats without apparent structure or sequence variation in cotton. This result indicates that the sequence content is not a decisive aspect of the adaptive evolution of centromeric repeats or at least retrotransposon-like centromeric repeats. In addition, two active genes with potential roles in gametogenesis or flowering were identified in CENH3 nucleosome-binding regions. Our results provide new insights into the constitution of centromeric repetitive DNA and the adaptive evolution of centromeric repeats in plants.
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Affiliation(s)
- Wenjie Ding
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Yuanbin Zhu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, the Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Haris Khurshid
- Oilseeds Research Program, National Agricultural Research Centre, Islamabad, 44500, Pakistan
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, 40-032, Poland.
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, the Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China.
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11
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Dawe RK, Gent JI, Zeng Y, Zhang H, Fu FF, Swentowsky KW, Kim DW, Wang N, Liu J, Piri RD. Synthetic maize centromeres transmit chromosomes across generations. NATURE PLANTS 2023; 9:433-441. [PMID: 36928774 DOI: 10.1038/s41477-023-01370-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/10/2023] [Indexed: 05/18/2023]
Abstract
Centromeres are long, often repetitive regions of genomes that bind kinetochore proteins and ensure normal chromosome segregation. Engineering centromeres that function in vivo has proven to be difficult. Here we describe a tethering approach that activates functional maize centromeres at synthetic sequence arrays. A LexA-CENH3 fusion protein was used to recruit native Centromeric Histone H3 (CENH3) to long arrays of LexO repeats on a chromosome arm. Newly recruited CENH3 was sufficient to organize functional kinetochores that caused chromosome breakage, releasing chromosome fragments that were passed through meiosis and into progeny. Several fragments formed independent neochromosomes with centromeres localized over the LexO repeat arrays. The new centromeres were self-sustaining and transmitted neochromosomes to subsequent generations in the absence of the LexA-CENH3 activator. Our results demonstrate the feasibility of using synthetic centromeres for karyotype engineering applications.
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Affiliation(s)
- R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, USA.
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Han Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Fang-Fang Fu
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | | | - Dong Won Kim
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Rebecca D Piri
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
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12
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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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13
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Dong Q, Li F. Cell cycle control of kinetochore assembly. Nucleus 2022; 13:208-220. [PMID: 36037227 PMCID: PMC9427032 DOI: 10.1080/19491034.2022.2115246] [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] [Indexed: 10/28/2022] Open
Abstract
The kinetochore is a large proteinaceous structure assembled on the centromeres of chromosomes. The complex machinery links chromosomes to the mitotic spindle and is essential for accurate chromosome segregation during cell division. The kinetochore is composed of two submodules: the inner and outer kinetochore. The inner kinetochore is assembled on centromeric chromatin and persists with centromeres throughout the cell cycle. The outer kinetochore attaches microtubules to the inner kinetochore, and assembles only during mitosis. The review focuses on recent advances in our understanding of the mechanisms governing the proper assembly of the outer kinetochore during mitosis and highlights open questions for future investigation.
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Affiliation(s)
- Qianhua Dong
- Department of Biology, New York University, New York, NY, USA
| | - Fei Li
- Department of Biology, New York University, New York, NY, USA
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14
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Urban JA, Ranjan R, Chen X. Asymmetric Histone Inheritance: Establishment, Recognition, and Execution. Annu Rev Genet 2022; 56:113-143. [PMID: 35905975 PMCID: PMC10054593 DOI: 10.1146/annurev-genet-072920-125226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of biased histone inheritance in asymmetrically dividing Drosophila melanogaster male germline stem cells demonstrates one means to produce two distinct daughter cells with identical genetic material. This inspired further studies in different systems, which revealed that this phenomenon may be a widespread mechanism to introduce cellular diversity. While the extent of asymmetric histone inheritance could vary among systems, this phenomenon is proposed to occur in three steps: first, establishment of histone asymmetry between sister chromatids during DNA replication; second, recognition of sister chromatids carrying asymmetric histone information during mitosis; and third, execution of this asymmetry in the resulting daughter cells. By compiling the current knowledge from diverse eukaryotic systems, this review comprehensively details and compares known chromatin factors, mitotic machinery components, and cell cycle regulators that may contribute to each of these three steps. Also discussed are potential mechanisms that introduce and regulate variable histone inheritance modes and how these different modes may contribute to cell fate decisions in multicellular organisms.
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Affiliation(s)
- Jennifer A Urban
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA;
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
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15
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Hill HJ, Golic KG. Chromosome Tug of War: Dicentric Chromosomes and the Centromere Strength Hypothesis. Cells 2022; 11:3550. [PMID: 36428979 PMCID: PMC9688759 DOI: 10.3390/cells11223550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
It has been 70 years since the concept of varied centromere strengths was introduced based on the behavior of dicentric chromosomes. One of the key conclusions from those early experiments was that some centromeres could pull with sufficient force to break a dicentric chromosome bridge, while others could not. In the ensuing decades there have been numerous studies to characterize strengths of the various components involved, such as the spindle, the kinetochore, and the chromosome itself. We review these various measurements to determine if the conclusions about centromere strength are supported by current evidence, with special attention to characterization of Drosophila melanogaster kinetochores upon which the original conclusions were based.
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Affiliation(s)
| | - Kent G. Golic
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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16
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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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17
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McVey SL, Olson MA, Pawlowski WP, Nannas NJ. Beyond Editing, CRISPR/Cas9 For Protein Localization: An Educational Primer for Use with "A dCas9-Based System Identifies a Central Role for Ctf19 in Kinetochore-Derived Suppression of Meiotic Recombination". Genetics 2022; 222:6650694. [PMID: 35894926 PMCID: PMC9434236 DOI: 10.1093/genetics/iyac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/07/2022] [Indexed: 11/14/2022] Open
Abstract
CRISPR/Cas9 has dramatically changed how we conduct genetic research, providing a tool for precise sequence editing. However, new applications of CRISPR/Cas9 have emerged that do not involve nuclease activity. In the accompanying article "A dCas9-Based System Identifies a Central Role for Ctf19 in Kinetochore-Derived Suppression of Meiotic Recombination", Kuhl and colleagues utilize a catalytically dead Cas9 to localize proteins at specific genomic locations. The authors seek to understand the role of kinetochore proteins in the suppression of meiotic recombination, a phenomenon that has been observed in centromere regions. By harnessing the power of CRISPR/Cas9 to bind specific genomic sequences, Kuhl et al. localized individual kinetochore proteins to areas of high meiotic recombination and assessed their role in suppression. This primer article provides undergraduate students with background information on chromosomes, meiosis, recombination and CRISPR/Cas9 to support their reading of the Kuhl et al. study. This primer is intended to help students and instructors navigate the study's experimental design, interpret the results, and appreciate the broader scope of meiotic recombination and CRISPR/Cas9. Questions are included to facilitate discussion of the study.
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Affiliation(s)
- Shelby L McVey
- Department of Biology, Hamilton College, Clinton, NY 13323, USA
| | - Mischa A Olson
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | - Wojciech P Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA.,Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
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18
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Senaratne AP, Cortes-Silva N, Drinnenberg IA. Evolution of holocentric chromosomes: Drivers, diversity, and deterrents. Semin Cell Dev Biol 2022; 127:90-99. [PMID: 35031207 DOI: 10.1016/j.semcdb.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/14/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Centromeres are specialized chromosomal regions that recruit kinetochore proteins and mediate spindle microtubule attachment to ensure faithful chromosome segregation during mitosis and meiosis. Centromeres can be restricted to one region of the chromosome. Named "monocentromere", this type represents the most commonly found centromere organization across eukaryotes. Alternatively, centromeres can also be assembled at sites chromosome-wide. This second type is called "holocentromere". Despite their early description over 100 years ago, research on holocentromeres has lagged behind that of monocentromeres. Nevertheless, the application of next generation sequencing approaches and advanced microscopic technologies enabled recent advances understanding the molecular organization and regulation of holocentromeres in different organisms. Here we review the current state of research on holocentromeres focusing on evolutionary considerations. First, we provide a brief historical perspective on the discovery of holocentric chromosomes. We then discuss models/drivers that have been proposed over the years to explain the evolutionary transition from mono- to holocentric chromosomes. We continue to review the description of holocentric chromosomes in diverse eukaryotic groups and then focus our discussion on a specific and recently characterized type of holocentromere organization in insects that functions independently of the otherwise essential centromeric marker protein CenH3, thus providing novel insights into holocentromere evolution in insects. Finally, we propose reasons to explain why the holocentric trait is not more frequent across eukaryotes despite putative selective advantages.
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Affiliation(s)
| | - Nuria Cortes-Silva
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ines A Drinnenberg
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France.
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19
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Patchigolla VS, Mellone BG. Enrichment of Non-B-Form DNA at D. melanogaster Centromeres. Genome Biol Evol 2022; 14:evac054. [PMID: 35441684 PMCID: PMC9070824 DOI: 10.1093/gbe/evac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 11/17/2022] Open
Abstract
Centromeres are essential chromosomal regions that mediate the accurate inheritance of genetic information during eukaryotic cell division. Despite their conserved function, centromeres do not contain conserved DNA sequences and are instead epigenetically marked by the presence of the centromere-specific histone H3 variant centromeric protein A. The functional contribution of centromeric DNA sequences to centromere identity remains elusive. Previous work found that dyad symmetries with a propensity to adopt noncanonical secondary DNA structures are enriched at the centromeres of several species. These findings lead to the proposal that noncanonical DNA structures may contribute to centromere specification. Here, we analyze the predicted secondary structures of the recently identified centromere DNA sequences of Drosophila melanogaster. Although dyad symmetries are only enriched on the Y centromere, we find that other types of noncanonical DNA structures, including melted DNA and G-quadruplexes, are common features of all D. melanogaster centromeres. Our work is consistent with previous models suggesting that noncanonical DNA secondary structures may be conserved features of centromeres with possible implications for centromere specification.
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Affiliation(s)
| | - Barbara G. Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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20
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Lam E, Michael TP. Wolffia, a minimalist plant and synthetic biology chassis. TRENDS IN PLANT SCIENCE 2022; 27:430-439. [PMID: 34920947 DOI: 10.1016/j.tplants.2021.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
A highly simplified species for genome engineering would facilitate rational design of a synthetic plant. A candidate species is the aquatic, non-grass monocot wolffia (Wolffia australiana) in the Lemnaceae family. Commonly known as watermeal, wolffia is a rootless ball of several thousand cells the size of a pinhead and the fastest growing plant known on Earth. Its extreme morphological reduction is coupled to transposon-mediated streamlining of its transcriptome, which represents a core set of nonredundant protein coding genes. Despite its body plan and transcriptome being highly specialized for continuous growth, wolffia retains cell types relevant to higher plants. Systems level studies with this species could enable the creation of a defined biological chassis for synthetic plant construction.
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Affiliation(s)
- Eric Lam
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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21
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The ins and outs of CENP-A: Chromatin dynamics of the centromere-specific histone. Semin Cell Dev Biol 2022; 135:24-34. [PMID: 35422390 DOI: 10.1016/j.semcdb.2022.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 01/08/2023]
Abstract
Centromeres are highly specialised chromosome domains defined by the presence of an epigenetic mark, the specific histone H3 variant called CENP-A (centromere protein A). They constitute the genomic regions on which kinetochores form and when defective cause segregation defects that can lead to aneuploidy and cancer. Here, we discuss how CENP-A is established and maintained to propagate centromere identity while subjected to dynamic chromatin remodelling during essential cellular processes like DNA repair, replication, and transcription. We highlight parallels and identify conserved mechanisms between different model organism with a particular focus on 1) the establishment of CENP-A at centromeres, 2) CENP-A maintenance during transcription and replication, and 3) the mechanisms that help preventing CENP-A localization at non-centromeric sites. We then give examples of how timely loading of new CENP-A to the centromere, maintenance of old CENP-A during S-phase and transcription, and removal of CENP-A at non-centromeric sites are coordinated and controlled by an intricate network of factors whose identity is slowly being unravelled.
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22
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Ghosh S, Lehner CF. Incorporation of CENP-A/CID into centromeres during early Drosophila embryogenesis does not require RNA polymerase II-mediated transcription. Chromosoma 2022; 131:1-17. [PMID: 35015118 PMCID: PMC9079035 DOI: 10.1007/s00412-022-00767-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 11/24/2022]
Abstract
In many species, centromere identity is specified epigenetically by special nucleosomes containing a centromere-specific histone H3 variant, designated as CENP-A in humans and CID in Drosophila melanogaster. After partitioning of centromere-specific nucleosomes onto newly replicated sister centromeres, loading of additional CENP-A/CID into centromeric chromatin is required for centromere maintenance in proliferating cells. Analyses with cultured cells have indicated that transcription of centromeric DNA by RNA polymerase II is required for deposition of new CID into centromere chromatin. However, a dependence of centromeric CID loading on transcription is difficult to reconcile with the notion that the initial embryonic stages appear to proceed in the absence of transcription in Drosophila, as also in many other animal species. To address the role of RNA polymerase II–mediated transcription for CID loading in early Drosophila embryos, we have quantified the effects of alpha-amanitin and triptolide on centromeric CID-EGFP levels. Our analyses demonstrate that microinjection of these two potent inhibitors of RNA polymerase II–mediated transcription has at most a marginal effect on centromeric CID deposition during progression through the early embryonic cleavage cycles. Thus, we conclude that at least during early Drosophila embryogenesis, incorporation of CID into centromeres does not depend on RNA polymerase II–mediated transcription.
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Affiliation(s)
- Samadri Ghosh
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Christian F Lehner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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23
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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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24
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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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25
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Salinas-Luypaert C, Allu PK, Logsdon GA, Dawicki-McKenna JM, Gambogi CW, Fachinetti D, Black BE. Gene replacement strategies validate the use of functional tags on centromeric chromatin and invalidate an essential role for CENP-A K124ub. Cell Rep 2021; 37:109924. [PMID: 34731637 PMCID: PMC8643106 DOI: 10.1016/j.celrep.2021.109924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 12/17/2022] Open
Abstract
Functional tags are ubiquitous in cell biology, and for studies of one chromosomal locus, the centromere, tags have been remarkably useful. The centromere directs chromosome inheritance at cell division. The location of the centromere is defined by a histone H3 variant, CENP-A. The regulation of the chromatin assembly pathway essential for centromere inheritance and function includes posttranslational modification (PTM) of key components, including CENP-A itself. Others have recently called into question the use of functional tags, with the claim that at least two widely used tags obscured the essentiality of one particular PTM, CENP-AK124 ubiquitination (ub). Here, we employ three independent gene replacement strategies that eliminate large, lysine-containing tags to interrogate these claims. Using these approaches, we find no evidence to support an essential function of CENP-AK124ub. Our general methodology will be useful to validate discoveries permitted by powerful functional tagging schemes at the centromere and other cellular locations. Using three gene replacement strategies, Salinas-Luypaert et al. demonstrate that CENP-AK124ub is not essential for CENP-A function at centromeres. Thus, functional tags do not mask the role of K124 when it is mutated. These strategies can be employed to interrogate posttranslational modifications at the centromere and other cellular locations.
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Affiliation(s)
| | - Praveen Kumar Allu
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jennine M Dawicki-McKenna
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Craig W Gambogi
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniele Fachinetti
- Institut Curie, PSL University, CNRS, UMR 144, 26 rue d'Ulm, 75005, Paris, France.
| | - Ben E Black
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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26
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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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27
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Dong Q, Yang J, Gao J, Li F. Recent insights into mechanisms preventing ectopic centromere formation. Open Biol 2021; 11:210189. [PMID: 34493071 PMCID: PMC8424319 DOI: 10.1098/rsob.210189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The centromere is a specialized chromosomal structure essential for chromosome segregation. Centromere dysfunction leads to chromosome segregation errors and genome instability. In most eukaryotes, centromere identity is specified epigenetically by CENP-A, a centromere-specific histone H3 variant. CENP-A replaces histone H3 in centromeres, and nucleates the assembly of the kinetochore complex. Mislocalization of CENP-A to non-centromeric regions causes ectopic assembly of CENP-A chromatin, which has a devastating impact on chromosome segregation and has been linked to a variety of human cancers. How non-centromeric regions are protected from CENP-A misincorporation in normal cells is largely unexplored. Here, we review the most recent advances on the mechanisms underlying the prevention of ectopic centromere formation, and discuss the implications in human disease.
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Affiliation(s)
- Qianhua Dong
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Jinpu Yang
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Jinxin Gao
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Fei Li
- Department of Biology, New York University, New York, NY 10003-6688, USA
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28
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Pajpach F, Wu T, Shearwin-Whyatt L, Jones K, Grützner F. Flavors of Non-Random Meiotic Segregation of Autosomes and Sex Chromosomes. Genes (Basel) 2021; 12:genes12091338. [PMID: 34573322 PMCID: PMC8471020 DOI: 10.3390/genes12091338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Segregation of chromosomes is a multistep process occurring both at mitosis and meiosis to ensure that daughter cells receive a complete set of genetic information. Critical components in the chromosome segregation include centromeres, kinetochores, components of sister chromatid and homologous chromosomes cohesion, microtubule organizing centres, and spindles. Based on the cytological work in the grasshopper Brachystola, it has been accepted for decades that segregation of homologs at meiosis is fundamentally random. This ensures that alleles on chromosomes have equal chance to be transmitted to progeny. At the same time mechanisms of meiotic drive and an increasing number of other examples of non-random segregation of autosomes and sex chromosomes provide insights into the underlying mechanisms of chromosome segregation but also question the textbook dogma of random chromosome segregation. Recent advances provide a better understanding of meiotic drive as a prominent force where cellular and chromosomal changes allow autosomes to bias their segregation. Less understood are mechanisms explaining observations that autosomal heteromorphism may cause biased segregation and regulate alternating segregation of multiple sex chromosome systems or translocation heterozygotes as an extreme case of non-random segregation. We speculate that molecular and cytological mechanisms of non-random segregation might be common in these cases and that there might be a continuous transition between random and non-random segregation which may play a role in the evolution of sexually antagonistic genes and sex chromosome evolution.
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Affiliation(s)
- Filip Pajpach
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Tianyu Wu
- Department of Central Laboratory, Clinical Laboratory, Jing’an District Centre Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Keith Jones
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK;
| | - Frank Grützner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
- Correspondence:
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29
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Leo L, Colonna Romano N. Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease. Int J Mol Sci 2021; 22:ijms22168809. [PMID: 34445507 PMCID: PMC8395756 DOI: 10.3390/ijms22168809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. The latter can lead to detrimental alterations in gene transcription, as well as pathological conditions such as cancer. Epigenetic marks regulate the transcriptional output of cells. Centromeres are chromosome structures that are epigenetically regulated and are crucial for accurate segregation. The advent of single-cell epigenetic profiling has provided finer analytical resolution, exposing the intrinsic peculiarities of different cells within an apparently homogenous population. In this review, we discuss recent advances in methodologies applied to epigenetics, such as CUT&RUN and CUT&TAG. Then, we compare standard and emerging single-cell techniques and their relevance for investigating human diseases. Finally, we describe emerging methodologies that investigate centromeric chromatin specification and neocentromere formation.
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30
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Joshi A, Musicante MJ, Wheeler BS. Defining the consequences of endogenous genetic variation within a novel family of Schizosaccharomyces pombe heterochromatin nucleating sequences. G3 GENES|GENOMES|GENETICS 2021; 11:6291246. [PMID: 34849813 PMCID: PMC8496282 DOI: 10.1093/g3journal/jkab185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/20/2021] [Indexed: 11/13/2022]
Abstract
Centromeres are essential for genetic inheritance—they prevent aneuploidy by providing a physical link between DNA and chromosome segregation machinery. In many organisms, centromeres form at sites of repetitive DNAs that help establish the chromatin architecture required for centromere function. These repeats are often rapidly evolving and subject to homogenization, which causes the expansion of novel repeats and sequence turnover. Thus, centromere sequence varies between individuals and across species. This variation can affect centromere function. We utilized Schizosaccharomyces pombe to assess the relationship between centromere sequence and chromatin structure and determine how sensitive this relationship is to genetic variation. In S. pombe, nucleating sequences within centromere repeats recruit heterochromatin via multiple mechanisms, which include RNA-interference (RNAi) . Heterochromatin, in turn, contributes to centromere function through its participation in three essential processes; establishment of a kinetochore, cohesion of sister chromatids, and suppression of recombination. Here, we show that a centromere element containing RevCen, a target of the RNAi pathway, establishes heterochromatin and gene silencing when relocated to a chromosome arm. Within this RevCen-containing element (RCE), a highly conserved domain is necessary for full heterochromatin nucleation but cannot establish heterochromatin independently. We characterize the 10 unique RCEs in the S. pombe centromere assembly, which range from 60% to 99.6% identical, and show that all are sufficient to establish heterochromatin. These data affirm the importance of centromere repeats in establishing heterochromatin and suggest there is flexibility within the sequences that mediate this process. Such flexibility may preserve centromere function despite the rapid evolution of centromere repeats.
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Affiliation(s)
- Arati Joshi
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | | | - Bayly S Wheeler
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
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31
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Morrison O, Thakur J. Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin. Int J Mol Sci 2021; 22:6922. [PMID: 34203193 PMCID: PMC8268097 DOI: 10.3390/ijms22136922] [Citation(s) in RCA: 42] [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: 06/11/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/19/2023] Open
Abstract
Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves a network of interactions among molecular complexes that modify chromatin structure and organization to affect the accessibility of DNA to transcription factors leading to the activation or repression of the transcription of target DNA loci. Based on its structure and compaction state, chromatin is categorized into euchromatin, heterochromatin, and centromeric chromatin. In this review, we discuss distinct chromatin factors and molecular complexes that constitute euchromatin-open chromatin structure associated with active transcription; heterochromatin-less accessible chromatin associated with silencing; centromeric chromatin-the site of spindle binding in chromosome segregation.
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Affiliation(s)
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd #2006, Atlanta, GA 30322, USA;
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32
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Carty BL, Dattoli AA, Dunleavy EM. CENP-C functions in centromere assembly, the maintenance of CENP-A asymmetry and epigenetic age in Drosophila germline stem cells. PLoS Genet 2021; 17:e1009247. [PMID: 34014920 PMCID: PMC8136707 DOI: 10.1371/journal.pgen.1009247] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/16/2021] [Indexed: 01/08/2023] Open
Abstract
Germline stem cells divide asymmetrically to produce one new daughter stem cell and one daughter cell that will subsequently undergo meiosis and differentiate to generate the mature gamete. The silent sister hypothesis proposes that in asymmetric divisions, the selective inheritance of sister chromatids carrying specific epigenetic marks between stem and daughter cells impacts cell fate. To facilitate this selective inheritance, the hypothesis specifically proposes that the centromeric region of each sister chromatid is distinct. In Drosophila germ line stem cells (GSCs), it has recently been shown that the centromeric histone CENP-A (called CID in flies)—the epigenetic determinant of centromere identity—is asymmetrically distributed between sister chromatids. In these cells, CID deposition occurs in G2 phase such that sister chromatids destined to end up in the stem cell harbour more CENP-A, assemble more kinetochore proteins and capture more spindle microtubules. These results suggest a potential mechanism of ‘mitotic drive’ that might bias chromosome segregation. Here we report that the inner kinetochore protein CENP-C, is required for the assembly of CID in G2 phase in GSCs. Moreover, CENP-C is required to maintain a normal asymmetric distribution of CID between stem and daughter cells. In addition, we find that CID is lost from centromeres in aged GSCs and that a reduction in CENP-C accelerates this loss. Finally, we show that CENP-C depletion in GSCs disrupts the balance of stem and daughter cells in the ovary, shifting GSCs toward a self-renewal tendency. Ultimately, we provide evidence that centromere assembly and maintenance via CENP-C is required to sustain asymmetric divisions in female Drosophila GSCs. Stem cells can divide in an asymmetric fashion giving rise to two daughter cells with different fates. One daughter remains a stem cell, while the other can differentiate and adopt a new cell fate. Germline stem cells in the testes and ovaries give rise to differentiating daughter cells that eventually form the gametes, eggs and sperm. Here we investigate mechanisms controlling germline stem cell divisions occurring in the ovary of the fruit fly Drosophila melanogaster. Centromeres are epigenetically specified loci on chromosomes that make essential connections to the cell division machinery. Our study is focused on the centromere component CENP-C. We show that CENP-C is critical for the correct assembly of centromeres that occurs prior to cell division in germline stem cells. In addition, we find that CENP-C is asymmetrically distributed between stem and daughter cells, with more CENP-C at stem cell centromeres. Finally, we show that CENP-C depletion in germline stem cells disrupts the balance of stem and daughter cells in the developing ovary, impacting on cell fate. Taken together, we propose that CENP-C level and function at centromeres plays an important role in determining cell fate upon asymmetric division occurring in stem cells.
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Affiliation(s)
- Ben L. Carty
- Centre for Chromosome Biology, Biomedical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Anna A. Dattoli
- Centre for Chromosome Biology, Biomedical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Elaine M. Dunleavy
- Centre for Chromosome Biology, Biomedical Sciences, National University of Ireland Galway, Galway, Ireland
- * E-mail:
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33
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Stajic D, Jansen LET. Empirical evidence for epigenetic inheritance driving evolutionary adaptation. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200121. [PMID: 33866813 DOI: 10.1098/rstb.2020.0121] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The cellular machinery that regulates gene expression can be self-propagated across cell division cycles and even generations. This renders gene expression states and their associated phenotypes heritable, independently of genetic changes. These phenotypic states, in turn, can be subject to selection and may influence evolutionary adaptation. In this review, we will discuss the molecular basis of epigenetic inheritance, the extent of its transmission and mechanisms of evolutionary adaptation. The current work shows that heritable gene expression can facilitate the process of adaptation through the increase of survival in a novel environment and by enlarging the size of beneficial mutational targets. Moreover, epigenetic control of gene expression enables stochastic switching between different phenotypes in populations that can potentially facilitate adaptation in rapidly fluctuating environments. Ecological studies of the variation of epigenetic markers (e.g. DNA methylation patterns) in wild populations show a potential contribution of this mode of inheritance to local adaptation in nature. However, the extent of the adaptive contribution of the naturally occurring variation in epi-alleles compared to genetic variation remains unclear. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Dragan Stajic
- Department of Zoology, University of Stockholm, 106 91 Stockholm, Sweden
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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34
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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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35
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Navarro AP, Cheeseman IM. Kinetochore assembly throughout the cell cycle. Semin Cell Dev Biol 2021; 117:62-74. [PMID: 33753005 DOI: 10.1016/j.semcdb.2021.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/29/2022]
Abstract
The kinetochore plays an essential role in facilitating chromosome segregation during cell division. This massive protein complex assembles onto the centromere of chromosomes and enables their attachment to spindle microtubules during mitosis. The kinetochore also functions as a signaling hub to regulate cell cycle progression, and is crucial to ensuring the fidelity of chromosome segregation. Despite the fact that kinetochores are large and robust molecular assemblies, they are also highly dynamic structures that undergo structural and organizational changes throughout the cell cycle. This review will highlight our current understanding of kinetochore structure and function, focusing on the dynamic processes that underlie kinetochore assembly.
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Affiliation(s)
- Alexandra P Navarro
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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36
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Centromere assembly and non-random sister chromatid segregation in stem cells. Essays Biochem 2021; 64:223-232. [PMID: 32406510 DOI: 10.1042/ebc20190066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/21/2020] [Accepted: 04/30/2020] [Indexed: 01/17/2023]
Abstract
Asymmetric cell division (ACD) produces daughter cells with separate distinct cell fates and is critical for the development and regulation of multicellular organisms. Epigenetic mechanisms are key players in cell fate determination. Centromeres, epigenetically specified loci defined by the presence of the histone H3-variant, centromere protein A (CENP-A), are essential for chromosome segregation at cell division. ACDs in stem cells and in oocyte meiosis have been proposed to be reliant on centromere integrity for the regulation of the non-random segregation of chromosomes. It has recently been shown that CENP-A is asymmetrically distributed between the centromeres of sister chromatids in male and female Drosophila germline stem cells (GSCs), with more CENP-A on sister chromatids to be segregated to the GSC. This imbalance in centromere strength correlates with the temporal and asymmetric assembly of the mitotic spindle and potentially orientates the cell to allow for biased sister chromatid retention in stem cells. In this essay, we discuss the recent evidence for asymmetric sister centromeres in stem cells. Thereafter, we discuss mechanistic avenues to establish this sister centromere asymmetry and how it ultimately might influence cell fate.
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37
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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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38
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Senaratne AP, Muller H, Fryer KA, Kawamoto M, Katsuma S, Drinnenberg IA. Formation of the CenH3-Deficient Holocentromere in Lepidoptera Avoids Active Chromatin. Curr Biol 2020; 31:173-181.e7. [PMID: 33125865 DOI: 10.1016/j.cub.2020.09.078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022]
Abstract
Despite the essentiality for faithful chromosome segregation, centromere architectures are diverse among eukaryotes1,2 and embody two main configurations: mono- and holocentromeres, referring, respectively, to localized or unrestricted distribution of centromeric activity. Of the two, some holocentromeres offer the curious condition of having arisen independently in multiple insects, most of which have lost the otherwise essential centromere-specifying factor CenH33 (first described as CENP-A in humans).4-7 The loss of CenH3 raises intuitive questions about how holocentromeres are organized and regulated in CenH3-lacking insects. Here, we report the first chromatin-level description of CenH3-deficient holocentromeres by leveraging recently identified centromere components6,7 and genomics approaches to map and characterize the holocentromeres of the silk moth Bombyx mori, a representative lepidopteran insect lacking CenH3. This uncovered a robust correlation between the distribution of centromere sites and regions of low chromatin activity along B. mori chromosomes. Transcriptional perturbation experiments recapitulated the exclusion of B. mori centromeres from active chromatin. Based on reciprocal centromere occupancy patterns observed along differentially expressed orthologous genes of Lepidoptera, we further found that holocentromere formation in a manner that is recessive to chromatin dynamics is evolutionarily conserved. Our results help us discuss the plasticity of centromeres in the context of a role for the chromosome-wide chromatin landscape in conferring centromere identity rather than the presence of CenH3. Given the co-occurrence of CenH3 loss and holocentricity in insects,7 we further propose that the evolutionary establishment of holocentromeres in insects was facilitated through the loss of a CenH3-specified centromere.
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Affiliation(s)
- Aruni P Senaratne
- Institut Curie, PSL Research University, CNRS, UMR3664, 75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, 75005 Paris, France
| | - Héloïse Muller
- Institut Curie, PSL Research University, CNRS, UMR3664, 75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, 75005 Paris, France
| | - Kelsey A Fryer
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA 94305-5307, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
| | - Munetaka Kawamoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ines A Drinnenberg
- Institut Curie, PSL Research University, CNRS, UMR3664, 75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, 75005 Paris, France.
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39
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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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40
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van den Berg SJ, Jansen LE. Centromeres: genetic input to calibrate an epigenetic feedback loop. EMBO J 2020; 39:e106638. [PMID: 32959893 DOI: 10.15252/embj.2020106638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Centromeres are chromatin domains maintained by a self-templating feedback loop based on nucleosomes bearing the histone H3 variant CENP-A. The underlying centromeric DNA sequence is largely dispensable, yet paradoxically, it has highly conserved features. Hoffmann et al (2020) now uncover that when the epigenetic chromatin cycle falters, a genetically hardwired mechanism offers robustness to a dynamic epigenetic feedback loop ensuring long-term centromere inheritance.
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Affiliation(s)
- Sebastiaan Jw van den Berg
- Department of Biochemistry, University of Oxford, Oxford, UK.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Lars Et Jansen
- Department of Biochemistry, University of Oxford, Oxford, UK
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41
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Mitra S, Srinivasan B, Jansen LE. Stable inheritance of CENP-A chromatin: Inner strength versus dynamic control. J Cell Biol 2020; 219:e202005099. [PMID: 32931551 PMCID: PMC7659725 DOI: 10.1083/jcb.202005099] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022] Open
Abstract
Chromosome segregation during cell division is driven by mitotic spindle attachment to the centromere region on each chromosome. Centromeres form a protein scaffold defined by chromatin featuring CENP-A, a conserved histone H3 variant, in a manner largely independent of local DNA cis elements. CENP-A nucleosomes fulfill two essential criteria to epigenetically identify the centromere. They undergo self-templated duplication to reestablish centromeric chromatin following DNA replication. More importantly, CENP-A incorporated into centromeric chromatin is stably transmitted through consecutive cell division cycles. CENP-A nucleosomes have unique structural properties and binding partners that potentially explain their long lifetime in vivo. However, rather than a static building block, centromeric chromatin is dynamically regulated throughout the cell cycle, indicating that CENP-A stability is also controlled by external factors. We discuss recent insights and identify the outstanding questions on how dynamic control of the long-term stability of CENP-A ensures epigenetic centromere inheritance.
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Affiliation(s)
- Sreyoshi Mitra
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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42
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Boopathi R, Danev R, Khoshouei M, Kale S, Nahata S, Ramos L, Angelov D, Dimitrov S, Hamiche A, Petosa C, Bednar J. Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends. Nucleic Acids Res 2020; 48:5735-5748. [PMID: 32313946 PMCID: PMC7261176 DOI: 10.1093/nar/gkaa246] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/11/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
The histone H3 variant CENP-A marks centromeres epigenetically and is essential for mitotic fidelity. Previous crystallographic studies of the CENP-A nucleosome core particle (NCP) reconstituted with a human α-satellite DNA derivative revealed both DNA ends to be highly flexible, a feature important for CENP-A mitotic functions. However, recent cryo-EM studies of CENP-A NCP complexes comprising primarily Widom 601 DNA reported well-ordered DNA ends. Here, we report the cryo-EM structure of the CENP-A 601 NCP determined by Volta phase-plate imaging. The data reveal that one (‘left’) 601 DNA end is well ordered whereas the other (‘right’) end is flexible and partly detached from the histone core, suggesting sequence-dependent dynamics of the DNA termini. Indeed, a molecular dynamics simulation of the CENP-A 601 NCP confirmed the distinct dynamics of the two DNA extremities. Reprocessing the image data using two-fold symmetry yielded a cryo-EM map in which both DNA ends appeared well ordered, indicating that such an artefact may inadvertently arise if NCP asymmetry is lost during image processing. These findings enhance our understanding of the dynamic features that discriminate CENP-A from H3 nucleosomes by revealing that DNA end flexibility can be fine-tuned in a sequence-dependent manner.
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Affiliation(s)
- Ramachandran Boopathi
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Radostin Danev
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Maryam Khoshouei
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Seyit Kale
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Sunil Nahata
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Lorrie Ramos
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule (LBMC), CNRS/ ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
- Correspondence may also be addressed to Stefan Dimitrov.
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/ CNRS/INSERM, 67404 Illkirch Cedex, France
- Correspondence may also be addressed to Ali Hamiche.
| | - Carlo Petosa
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
- Correspondence may also be addressed to Carlo Petosa.
| | - Jan Bednar
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
- Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General Teaching Hospital, 128 00 Prague, Czech Republic
- To whom correspondence should be addressed. Tel: +33 4 76 54 94 73;
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43
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Balzano E, Giunta S. Centromeres under Pressure: Evolutionary Innovation in Conflict with Conserved Function. Genes (Basel) 2020; 11:E912. [PMID: 32784998 PMCID: PMC7463522 DOI: 10.3390/genes11080912] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Centromeres are essential genetic elements that enable spindle microtubule attachment for chromosome segregation during mitosis and meiosis. While this function is preserved across species, centromeres display an array of dynamic features, including: (1) rapidly evolving DNA; (2) wide evolutionary diversity in size, shape and organization; (3) evidence of mutational processes to generate homogenized repetitive arrays that characterize centromeres in several species; (4) tolerance to changes in position, as in the case of neocentromeres; and (5) intrinsic fragility derived by sequence composition and secondary DNA structures. Centromere drive underlies rapid centromere DNA evolution due to the "selfish" pursuit to bias meiotic transmission and promote the propagation of stronger centromeres. Yet, the origins of other dynamic features of centromeres remain unclear. Here, we review our current understanding of centromere evolution and plasticity. We also detail the mutagenic processes proposed to shape the divergent genetic nature of centromeres. Changes to centromeres are not simply evolutionary relics, but ongoing shifts that on one side promote centromere flexibility, but on the other can undermine centromere integrity and function with potential pathological implications such as genome instability.
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Affiliation(s)
- Elisa Balzano
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, 00185 Roma, Italy;
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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Palladino J, Chavan A, Sposato A, Mason TD, Mellone BG. Targeted De Novo Centromere Formation in Drosophila Reveals Plasticity and Maintenance Potential of CENP-A Chromatin. Dev Cell 2020; 52:379-394.e7. [PMID: 32049040 DOI: 10.1016/j.devcel.2020.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/17/2019] [Accepted: 01/06/2020] [Indexed: 11/25/2022]
Abstract
Centromeres are essential for accurate chromosome segregation and are marked by centromere protein A (CENP-A) nucleosomes. Mis-targeted CENP-A chromatin has been shown to seed centromeres at non-centromeric DNA. However, the requirements for such de novo centromere formation and transmission in vivo remain unknown. Here, we employ Drosophila melanogaster and the LacI/lacO system to investigate the ability of targeted de novo centromeres to assemble and be inherited through development. De novo centromeres form efficiently at six distinct genomic locations, which include actively transcribed chromatin and heterochromatin, and cause widespread chromosomal instability. During tethering, de novo centromeres sometimes prevail, causing the loss of the endogenous centromere via DNA breaks and HP1-dependent epigenetic inactivation. Transient induction of de novo centromeres and chromosome healing in early embryogenesis show that, once established, these centromeres can be maintained through development. Our results underpin the ability of CENP-A chromatin to establish and sustain mitotic centromere function in Drosophila.
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Affiliation(s)
- Jason Palladino
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Ankita Chavan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Anthony Sposato
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Timothy D Mason
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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45
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Martins NMC, Cisneros-Soberanis F, Pesenti E, Kochanova NY, Shang WH, Hori T, Nagase T, Kimura H, Larionov V, Masumoto H, Fukagawa T, Earnshaw WC. H3K9me3 maintenance on a human artificial chromosome is required for segregation but not centromere epigenetic memory. J Cell Sci 2020; 133:jcs242610. [PMID: 32576667 PMCID: PMC7390644 DOI: 10.1242/jcs.242610] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
Most eukaryotic centromeres are located within heterochromatic regions. Paradoxically, heterochromatin can also antagonize de novo centromere formation, and some centromeres lack it altogether. In order to investigate the importance of heterochromatin at centromeres, we used epigenetic engineering of a synthetic alphoidtetO human artificial chromosome (HAC), to which chimeric proteins can be targeted. By tethering the JMJD2D demethylase (also known as KDM4D), we removed heterochromatin mark H3K9me3 (histone 3 lysine 9 trimethylation) specifically from the HAC centromere. This caused no short-term defects, but long-term tethering reduced HAC centromere protein levels and triggered HAC mis-segregation. However, centromeric CENP-A was maintained at a reduced level. Furthermore, HAC centromere function was compatible with an alternative low-H3K9me3, high-H3K27me3 chromatin signature, as long as residual levels of H3K9me3 remained. When JMJD2D was released from the HAC, H3K9me3 levels recovered over several days back to initial levels along with CENP-A and CENP-C centromere levels, and mitotic segregation fidelity. Our results suggest that a minimal level of heterochromatin is required to stabilize mitotic centromere function but not for maintaining centromere epigenetic memory, and that a homeostatic pathway maintains heterochromatin at centromeres.This article has an associated First Person interview with the first authors of the paper.
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Affiliation(s)
| | | | - Elisa Pesenti
- Wellcome Trust Centre for Cell Biology, Edinburgh, UK
| | | | - Wei-Hao Shang
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Vladimir Larionov
- National Cancer Institute, National Institutes of Health, Bethesda, USA
| | | | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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46
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Mahlke MA, Nechemia-Arbely Y. Guarding the Genome: CENP-A-Chromatin in Health and Cancer. Genes (Basel) 2020; 11:genes11070810. [PMID: 32708729 PMCID: PMC7397030 DOI: 10.3390/genes11070810] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
Faithful chromosome segregation is essential for the maintenance of genomic integrity and requires functional centromeres. Centromeres are epigenetically defined by the histone H3 variant, centromere protein A (CENP-A). Here we highlight current knowledge regarding CENP-A-containing chromatin structure, specification of centromere identity, regulation of CENP-A deposition and possible contribution to cancer formation and/or progression. CENP-A overexpression is common among many cancers and predicts poor prognosis. Overexpression of CENP-A increases rates of CENP-A deposition ectopically at sites of high histone turnover, occluding CCCTC-binding factor (CTCF) binding. Ectopic CENP-A deposition leads to mitotic defects, centromere dysfunction and chromosomal instability (CIN), a hallmark of cancer. CENP-A overexpression is often accompanied by overexpression of its chaperone Holliday Junction Recognition Protein (HJURP), leading to epigenetic addiction in which increased levels of HJURP and CENP-A become necessary to support rapidly dividing p53 deficient cancer cells. Alterations in CENP-A posttranslational modifications are also linked to chromosome segregation errors and CIN. Collectively, CENP-A is pivotal to genomic stability through centromere maintenance, perturbation of which can lead to tumorigenesis.
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Affiliation(s)
- Megan A. Mahlke
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA;
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yael Nechemia-Arbely
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA;
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence: ; Tel.: +1-412-623-3228; Fax: +1-412-623-7828
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47
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Das A, Black BE, Lampson MA. Maternal inheritance of centromeres through the germline. Curr Top Dev Biol 2020; 140:35-54. [PMID: 32591081 DOI: 10.1016/bs.ctdb.2020.03.004] [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: 03/18/2023]
Abstract
The centromere directs chromosome segregation but is not itself genetically encoded. In most species, centromeres are epigenetically defined by the presence of a histone H3 variant CENP-A, independent of the underlying DNA sequence. Therefore, to maintain centromeres and ensure accurate chromosome segregation, CENP-A nucleosomes must be inherited across generations through the germline. In this chapter we discuss three aspects of maternal centromere inheritance. First, we propose mechanisms for maintaining CENP-A nucleosomes through the prolonged prophase arrest in mammalian oocytes. Second, we review mechanisms by which selfish centromeres bias their transmission through female meiosis. Third, we discuss regulation of centromere size through early embryonic development.
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Affiliation(s)
- Arunika Das
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States.
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48
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Abundant expression of maternal siRNAs is a conserved feature of seed development. Proc Natl Acad Sci U S A 2020; 117:15305-15315. [PMID: 32541052 DOI: 10.1073/pnas.2001332117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa, RdDM is required in the maternal sporophyte for successful seed development. Here, we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during B. rapa seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in diverse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together, these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.
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49
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Wong CYY, Ling YH, Mak JKH, Zhu J, Yuen KWY. "Lessons from the extremes: Epigenetic and genetic regulation in point monocentromere and holocentromere establishment on artificial chromosomes". Exp Cell Res 2020; 390:111974. [PMID: 32222413 DOI: 10.1016/j.yexcr.2020.111974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 02/08/2023]
Abstract
The formation of de novo centromeres on artificial chromosomes in humans (HACs) and fission yeast (SpYACs) has provided much insights to the epigenetic and genetic control on regional centromere establishment and maintenance. Similarly, the use of artificial chromosomes in point centromeric budding yeast Saccharomyces cerevisiae (ScYACs) and holocentric Caenorhabditis elegans (WACs) has revealed epigenetic regulation in the originally thought purely genetically-determined point centromeres and some centromeric DNA sequence features in holocentromeres, respectively. These relatively extreme and less characterized centromere organizations, on the endogenous chromosomes and artificial chromosomes, will be discussed and compared to the more well-studied regional centromere systems. This review will highlight some of the common epigenetic and genetic features in different centromere architectures, including the presence of the centromeric histone H3 variant, CENP-A or CenH3, centromeric and pericentric transcription, AT-richness and repetitiveness of centromeric DNA sequences.
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Affiliation(s)
- Charmaine Yan Yu Wong
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yick Hin Ling
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Jason Ka Ho Mak
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Jing Zhu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong.
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50
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Demirdizen E, Spiller-Becker M, Förtsch A, Wilhelm A, Corless S, Bade D, Bergner A, Hessling B, Erhardt S. Localization of Drosophila CENP-A to non-centromeric sites depends on the NuRD complex. Nucleic Acids Res 2020; 47:11589-11608. [PMID: 31713634 PMCID: PMC7145711 DOI: 10.1093/nar/gkz962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 09/12/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Centromere function requires the presence of the histone H3 variant CENP-A in most eukaryotes. The precise localization and protein amount of CENP-A are crucial for correct chromosome segregation, and misregulation can lead to aneuploidy. To characterize the loading of CENP-A to non-centromeric chromatin, we utilized different truncation- and localization-deficient CENP-A mutant constructs in Drosophila melanogaster cultured cells, and show that the N-terminus of Drosophila melanogaster CENP-A is required for nuclear localization and protein stability, and that CENP-A associated proteins, rather than CENP-A itself, determine its localization. Co-expression of mutant CENP-A with its loading factor CAL1 leads to exclusive centromere loading of CENP-A whereas co-expression with the histone-binding protein RbAp48 leads to exclusive non-centromeric CENP-A incorporation. Mass spectrometry analysis of non-centromeric CENP-A interacting partners identified the RbAp48-containing NuRD chromatin remodeling complex. Further analysis confirmed that NuRD is required for ectopic CENP-A incorporation, and RbAp48 and MTA1-like subunits of NuRD together with the N-terminal tail of CENP-A mediate the interaction. In summary, our data show that Drosophila CENP-A has no intrinsic specificity for centromeric chromatin and utilizes separate loading mechanisms for its incorporation into centromeric and ectopic sites. This suggests that the specific association and availability of CENP-A interacting factors are the major determinants of CENP-A loading specificity.
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Affiliation(s)
- Engin Demirdizen
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Matthias Spiller-Becker
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Arion Förtsch
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Alexander Wilhelm
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Samuel Corless
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Debora Bade
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Andrea Bergner
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Bernd Hessling
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Sylvia Erhardt
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks - Cluster of Excellence, University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- To whom correspondence should be addressed. Tel: +49 6221 54 6898; Fax: +49 6221 54 5892;
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