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Chen YL, Jones AN, Crawford A, Sattler M, Ettinger A, Torres-Padilla ME. Determinants of minor satellite RNA function in chromosome segregation in mouse embryonic stem cells. J Cell Biol 2024; 223:e202309027. [PMID: 38625077 PMCID: PMC11022885 DOI: 10.1083/jcb.202309027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/06/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
The centromere is a fundamental higher-order structure in chromosomes ensuring their faithful segregation upon cell division. Centromeric transcripts have been described in several species and suggested to participate in centromere function. However, low sequence conservation of centromeric repeats appears inconsistent with a role in recruiting highly conserved centromeric proteins. Here, we hypothesized that centromeric transcripts may function through a secondary structure rather than sequence conservation. Using mouse embryonic stem cells (ESCs), we show that an imbalance in the levels of forward or reverse minor satellite (MinSat) transcripts leads to severe chromosome segregation defects. We further show that MinSat RNA adopts a stem-loop secondary structure, which is conserved in human α-satellite transcripts. We identify an RNA binding region in CENPC and demonstrate that MinSat transcripts function through the structured region of the RNA. Importantly, mutants that disrupt MinSat secondary structure do not cause segregation defects. We propose that the conserved role of centromeric transcripts relies on their secondary RNA structure.
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Affiliation(s)
- Yung-Li Chen
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
| | - Alisha N. Jones
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Amy Crawford
- Department of Chemistry, New York University, New York, NY, USA
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, Bavarian NMR Center, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Andreas Ettinger
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany
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2
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Khurana S, Varma D, Foltz DR. Contribution of CENP-F to FOXM1-Mediated Discordant Centromere and Kinetochore Transcriptional Regulation. Mol Cell Biol 2024; 44:209-225. [PMID: 38779933 PMCID: PMC11204039 DOI: 10.1080/10985549.2024.2350543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
Proper chromosome segregation is required to ensure chromosomal stability. The centromere (CEN) is a unique chromatin domain defined by CENP-A and is responsible for recruiting the kinetochore (KT) during mitosis, ultimately regulating microtubule spindle attachment and mitotic checkpoint function. Upregulation of many CEN/KT genes is commonly observed in cancer. Here, we show that although FOXM1 occupies promoters of many CEN/KT genes with MYBL2, FOXM1 overexpression alone is insufficient to drive the FOXM1-correlated transcriptional program. CENP-F is canonically an outer kinetochore component; however, it functions with FOXM1 to coregulate G2/M transcription and proper chromosome segregation. Loss of CENP-F results in altered chromatin accessibility at G2/M genes and reduced FOXM1-MBB complex formation. We show that coordinated CENP-FFOXM1 transcriptional regulation is a cancer-specific function. We observe a small subset of CEN/KT genes including CENP-C, that are not regulated by FOXM1. Upregulation of CENP-C in the context of CENP-A overexpression leads to increased chromosome missegregation and cell death suggesting that escape of CENP-C from FOXM1 regulation is a cancer survival mechanism. Together, we show that FOXM1 and CENP-F coordinately regulate G2/M genes, and this coordination is specific to a subset of genes to allow for maintenance of chromosome instability levels and subsequent cell survival.
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Affiliation(s)
- Sakshi Khurana
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Dileep Varma
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Cellular and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Daniel R. Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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3
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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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Ramakrishnan Chandra J, Kalidass M, Demidov D, Dabravolski SA, Lermontova I. The role of centromeric repeats and transcripts in kinetochore assembly and function. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:982-996. [PMID: 37665331 DOI: 10.1111/tpj.16445] [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: 01/20/2023] [Revised: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Centromeres are the chromosomal domains, where the kinetochore protein complex is formed, mediating proper segregation of chromosomes during cell division. Although the function of centromeres has remained conserved during evolution, centromeric DNA is highly variable, even in closely related species. In addition, the composition of the kinetochore complexes varies among organisms. Therefore, it is assumed that the centromeric position is determined epigenetically, and the centromeric histone H3 (CENH3) serves as an epigenetic marker. The loading of CENH3 onto centromeres depends on centromere-licensing factors, chaperones, and transcription of centromeric repeats. Several proteins that regulate CENH3 loading and kinetochore assembly interact with the centromeric transcripts and DNA in a sequence-independent manner. However, the functional aspects of these interactions are not fully understood. This review discusses the variability of centromeric sequences in different organisms and the regulation of their transcription through the RNA Pol II and RNAi machinery. The data suggest that the interaction of proteins involved in CENH3 loading and kinetochore assembly with centromeric DNA and transcripts plays a role in centromere, and possibly neocentromere, formation in a sequence-independent manner.
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Affiliation(s)
| | - Manikandan Kalidass
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Dmitri Demidov
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Siarhei A Dabravolski
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Snunit 51, Karmiel, 2161002, Israel
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
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Zipple MN, Southworth CA, Zipple SP, Archie EA, Tung J, Alberts SC. Infant spatial relationships with adult males in a wild primate: males as mitigators or magnifiers of intergenerational effects of early adversity? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.590770. [PMID: 38712182 PMCID: PMC11071619 DOI: 10.1101/2024.04.25.590770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Adult male mammals can provide infants with protection and enhance their access to resources. They can also pose a risk to infants, either directly through infanticide or other aggression, or indirectly by placing infants at increased risk of conspecific or heterospecific conflict. Both benefits and costs may be especially important for offspring born to mothers in poor condition. Here we present the most detailed analysis to date of the influence of adult non-human primate males on a wide range of infant behaviors, and a description of the predictors of individual infants' proximity to adult males. We show that the number of adult males near an infant predicts many infant behavioral traits, including aspects of the mother-infant relationship, infant activity budgets, and the frequency of social interactions with non-mothers. Infant exposure to adult males is statistically significantly repeatable over time (R = 0.16). This repeatability is partially explained by whether the infant's mother experienced early life adversity: offspring of high-adversity mothers spent time in close proximity to more males during the first months of life. Our results are consistent with the possibility that the effects of maternal early life adversity can be mitigated or magnified by relationships with adult males.
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Yurchenko A, Pšenička T, Mora P, Ortega JAM, Baca AS, Rovatsos M. Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos. Genes (Basel) 2024; 15:429. [PMID: 38674364 PMCID: PMC11049218 DOI: 10.3390/genes15040429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel's leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther's flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested.
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Affiliation(s)
- Alona Yurchenko
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Tomáš Pšenička
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Pablo Mora
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Juan Alberto Marchal Ortega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Antonio Sánchez Baca
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
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Folco H, Xiao H, Wheeler D, Feng H, Bai Y, Grewal SS. The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity. Nucleic Acids Res 2024; 52:1688-1701. [PMID: 38084929 PMCID: PMC10899784 DOI: 10.1093/nar/gkad1182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 02/29/2024] Open
Abstract
Centromeric chromatin plays a crucial role in kinetochore assembly and chromosome segregation. Centromeres are specified through the loading of the histone H3 variant CENP-A by the conserved chaperone Scm3/HJURP. The N-terminus of Scm3/HJURP interacts with CENP-A, while the C-terminus facilitates centromere localization by interacting with the Mis18 holocomplex via a small domain, called the Mis16-binding domain (Mis16-BD) in fission yeast. Fungal Scm3 proteins contain an additional conserved cysteine-rich domain (CYS) of unknown function. Here, we find that CYS binds zinc in vitro and is essential for the localization and function of fission yeast Scm3. Disrupting CYS by deletion or introduction of point mutations within its zinc-binding motif prevents Scm3 centromere localization and compromises kinetochore integrity. Interestingly, CYS alone can localize to the centromere, albeit weakly, but its targeting is greatly enhanced when combined with Mis16-BD. Expressing a truncated protein containing both Mis16-BD and CYS, but lacking the CENP-A binding domain, causes toxicity and is accompanied by considerable chromosome missegregation and kinetochore loss. These effects can be mitigated by mutating the CYS zinc-binding motif. Collectively, our findings establish the essential role of the cysteine-rich domain in fungal Scm3 proteins and provide valuable insights into the mechanism of Scm3 centromere targeting.
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Affiliation(s)
- H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Packiaraj J, Thakur J. DNA satellite and chromatin organization at mouse centromeres and pericentromeres. Genome Biol 2024; 25:52. [PMID: 38378611 PMCID: PMC10880262 DOI: 10.1186/s13059-024-03184-z] [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: 06/02/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Centromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of satellite DNA and chromatin at mouse centromeres and pericentromeres is poorly understood due to the challenges of assembling repetitive genomic regions. RESULTS Using recently available PacBio long-read sequencing data from the C57BL/6 strain, we find that contrary to the previous reports of their homogeneous nature, both centromeric minor satellites and pericentromeric major satellites exhibit a high degree of variation in sequence and organization within and between arrays. While most arrays are continuous, a significant fraction is interspersed with non-satellite sequences, including transposable elements. Using chromatin immunoprecipitation sequencing (ChIP-seq), we find that the occupancy of CENP-A and H3K9me3 chromatin at centromeric and pericentric regions, respectively, is associated with increased sequence enrichment and homogeneity at these regions. The transposable elements at centromeric regions are not part of functional centromeres as they lack significant CENP-A enrichment. Furthermore, both CENP-A and H3K9me3 nucleosomes occupy minor and major satellites spanning centromeric-pericentric junctions and a low yet significant amount of CENP-A spreads locally at centromere junctions on both pericentric and telocentric sides. Finally, while H3K9me3 nucleosomes display a well-phased organization on major satellite arrays, CENP-A nucleosomes on minor satellite arrays are poorly phased. Interestingly, the homogeneous class of major satellites also phase CENP-A and H3K27me3 nucleosomes, indicating that the nucleosome phasing is an inherent property of homogeneous major satellites. CONCLUSIONS Our findings reveal that mouse centromeres and pericentromeres display a high diversity in satellite sequence, organization, and chromatin structure.
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Affiliation(s)
- Jenika Packiaraj
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA, 30322, USA
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA, 30322, USA.
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Khurana S, Foltz DR. Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573453. [PMID: 38234763 PMCID: PMC10793414 DOI: 10.1101/2023.12.27.573453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Proper chromosome segregation is required to ensure genomic and chromosomal stability. The centromere is a unique chromatin domain present throughout the cell cycle on each chromosome defined by the CENP-A nucleosome. Centromeres (CEN) are responsible for recruiting the kinetochore (KT) during mitosis, ultimately regulating spindle attachment and mitotic checkpoint function. Upregulation of many genes that encode the CEN/KT proteins is commonly observed in cancer. Here, we show although that FOXM1 occupies the promoters of many CEN/KT genes with MYBL2, occupancy is insufficient alone to drive the FOXM1 correlated transcriptional program. We show that CENP-F, a component of the outer kinetochore, functions with FOXM1 to coregulate G2/M transcription and proper chromosome segregation. Loss of CENP-F results in alteration of chromatin accessibility at G2/M genes, including CENP-A, and leads to reduced FOXM1-MBB complex formation. The FOXM1-CENP-F transcriptional coordination is a cancer-specific function. We observed that a few CEN/KT genes escape FOXM1 regulation such as CENP-C which when upregulated with CENP-A, leads to increased chromosome misegregation and cell death. Together, we show that the FOXM1 and CENP-F coordinately regulate G2/M gene expression, and this coordination is specific to a subset of genes to allow for proliferation and maintenance of chromosome stability for cancer cell survival.
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Affiliation(s)
- Sakshi Khurana
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Simpsom Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Daniel R. Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Simpsom Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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Wong VA, Dinh KN, Chen G, Wrenshall LE. IL-2RαKO mice exhibit maternal microchimerism and reveal nuclear localization of IL-2Rα in lymphoid and non-lymphoid cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565571. [PMID: 37961725 PMCID: PMC10635137 DOI: 10.1101/2023.11.03.565571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
IL-2Rα KO mice have been instrumental to discovering the immunoregulatory properties of IL-2Rα. While initially thought of only as a stimulatory cytokine, IL-2 and IL-2Rα knock out (KO) mice revealed that this cytokine-receptor system controls immune responses through restimulation-induced cell death and by promoting the survival of T regulatory cells. Although described mostly in the context of lymphocytes, recent studies by our laboratory showed that IL-2R is expressed in smooth muscle cells. Given this finding, we sought to use IL-2Rα knock mice to determine the function of this receptor in vascular smooth muscle cells. Surprisingly, we found that IL-2Rα knock out vascular smooth muscle cells had detectable IL-2Rα. Further studies suggested that the source of IL-2Rα protein was likely maternal heterozygous cells present in KO offspring due to maternal microchimerism. Because the KO was generated by using a neomycin resistance gene insert, we treated cells with G418 and were able to eliminate the majority of IL-2Rα expressing cells. This elimination revealed that IL-2Rα KO vascular smooth muscle cells exhibited increased proliferation, decreased size, and hypodiploid DNA content when compared to wildtype cells. Our findings suggest that the phenotype of complete IL-2Rα loss is more severe than demonstrated by IL-2Rα KO mice, and that IL-2Rα plays a here-to-fore unrecognized role in regulating cell proliferation in non-lymphoid cells.
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11
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Sidhwani P, Straight AF. Epigenetic inheritance and boundary maintenance at human centromeres. Curr Opin Struct Biol 2023; 82:102694. [PMID: 37657353 PMCID: PMC10530090 DOI: 10.1016/j.sbi.2023.102694] [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: 02/27/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/03/2023]
Abstract
Centromeres are chromosomal regions that provide the foundation for microtubule attachment during chromosome segregation. Centromeres are epigenetically defined by nucleosomes containing the histone H3 variant centromere protein A (CENP-A) and, in many organisms, are surrounded by transcriptionally repressed pericentromeric chromatin marked by trimethylation of histone H3 lysine 9 (H3K9me3). Pericentromeric regions facilitate sister chromatid cohesion during mitosis, thereby supporting centromere function. Heterochromatin has a known propensity to spread into adjacent euchromatic domains unless it is properly bounded. Heterochromatin spreading into the centromere can disrupt kinetochore function, perturbing chromosome segregation and genome stability. In the fission yeast Schizosaccharomyces pombe, tRNA genes provide barriers to heterochromatin spread at the centromere, the absence of which results in abnormal meiotic chromosome segregation. How heterochromatin-centromere boundaries are established in humans is not understood. We propose models for stable epigenetic inheritance of centromeric domains in humans and discuss advances that will enable the discovery of novel regulators of this process.
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Affiliation(s)
- Pragya Sidhwani
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States. https://twitter.com/@pra_sidh
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States.
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12
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Ninomiya K, Yamazaki T, Hirose T. Satellite RNAs: emerging players in subnuclear architecture and gene regulation. EMBO J 2023; 42:e114331. [PMID: 37526230 PMCID: PMC10505914 DOI: 10.15252/embj.2023114331] [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: 04/20/2023] [Revised: 07/13/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Satellite DNA is characterized by long, tandemly repeated sequences mainly found in centromeres and pericentromeric chromosomal regions. The recent advent of telomere-to-telomere sequencing data revealed the complete sequences of satellite regions, including centromeric α-satellites and pericentromeric HSat1-3, which together comprise ~ 5.7% of the human genome. Despite possessing constitutive heterochromatin features, these regions are transcribed to produce long noncoding RNAs with highly repetitive sequences that associate with specific sets of proteins to play various regulatory roles. In certain stress or pathological conditions, satellite RNAs are induced to assemble mesoscopic membraneless organelles. Specifically, under heat stress, nuclear stress bodies (nSBs) are scaffolded by HSat3 lncRNAs, which sequester hundreds of RNA-binding proteins. Upon removal of the stressor, nSBs recruit additional regulatory proteins, including protein kinases and RNA methylases, which modify the previously sequestered nSB components. The sequential recruitment of substrates and enzymes enables nSBs to efficiently regulate the splicing of hundreds of pre-mRNAs under limited temperature conditions. This review discusses the structural features and regulatory roles of satellite RNAs in intracellular architecture and gene regulation.
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Affiliation(s)
- Kensuke Ninomiya
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
| | | | - Tetsuro Hirose
- Graduate School of Frontier BiosciencesOsaka UniversitySuitaJapan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI)Osaka UniversitySuitaJapan
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13
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Packiaraj J, Thakur J. DNA satellite and chromatin organization at house mouse centromeres and pericentromeres. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549612. [PMID: 37503200 PMCID: PMC10370071 DOI: 10.1101/2023.07.18.549612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Centromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of satellite DNA and chromatin at mouse centromeres and pericentromeres is poorly understood due to the challenges of sequencing and assembling repetitive genomic regions. Using recently available PacBio long-read sequencing data from the C57BL/6 strain and chromatin profiling, we found that contrary to the previous reports of their highly homogeneous nature, centromeric and pericentromeric satellites display varied sequences and organization. We find that both centromeric minor satellites and pericentromeric major satellites exhibited sequence variations within and between arrays. While most arrays are continuous, a significant fraction is interspersed with non-satellite sequences, including transposable elements. Additionally, we investigated CENP-A and H3K9me3 chromatin organization at centromeres and pericentromeres using Chromatin immunoprecipitation sequencing (ChIP-seq). We found that the occupancy of CENP-A and H3K9me3 chromatin at centromeric and pericentric regions, respectively, is associated with increased sequence abundance and homogeneity at these regions. Furthermore, the transposable elements at centromeric regions are not part of functional centromeres as they lack CENP-A enrichment. Finally, we found that while H3K9me3 nucleosomes display a well-phased organization on major satellite arrays, CENP-A nucleosomes on minor satellite arrays lack phased organization. Interestingly, the homogeneous class of major satellites phase CENP-A and H3K27me3 nucleosomes as well, indicating that the nucleosome phasing is an inherent property of homogeneous major satellites. Overall, our findings reveal that house mouse centromeres and pericentromeres, which were previously thought to be highly homogenous, display significant diversity in satellite sequence, organization, and chromatin structure.
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Affiliation(s)
- Jenika Packiaraj
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA 30322
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA 30322
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Manna S, Mishra J, Baral T, Kirtana R, Nandi P, Roy A, Chakraborty S, Niharika, Patra SK. Epigenetic signaling and crosstalk in regulation of gene expression and disease progression. Epigenomics 2023; 15:723-740. [PMID: 37661861 DOI: 10.2217/epi-2023-0235] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
Chromatin modifications - including DNA methylation, modification of histones and recruitment of noncoding RNAs - are essential epigenetic events. Multiple sequential modifications converge into a complex epigenetic landscape. For example, promoter DNA methylation is recognized by MeCP2/methyl CpG binding domain proteins which further recruit SETDB1/SUV39 to attain a higher order chromatin structure by propagation of inactive epigenetic marks like H3K9me3. Many studies with new information on different epigenetic modifications and associated factors are available, but clear maps of interconnected pathways are also emerging. This review deals with the salient epigenetic crosstalk mechanisms that cells utilize for different cellular processes and how deregulation or aberrant gene expression leads to disease progression.
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Affiliation(s)
- Soumen Manna
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Jagdish Mishra
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Tirthankar Baral
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - R Kirtana
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Piyasa Nandi
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Ankan Roy
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Subhajit Chakraborty
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Niharika
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Samir K Patra
- Epigenetics & Cancer Research Laboratory, Biochemistry & Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
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15
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Xiang M, Gao Y, Zhou Y, Wang M, Yao X. A novel nomogram based on cell cycle-related genes for predicting overall survival in early-onset colorectal cancer. BMC Cancer 2023; 23:595. [PMID: 37370046 DOI: 10.1186/s12885-023-11075-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Although the incidence of late-onset colorectal cancer (LOCRC) has decreased, the incidence of early-onset colorectal cancer (EOCRC) is still rising dramatically. Heterogeneity in the genomic, biological, and clinicopathological characteristics between EOCRC and LOCRC has been revealed. Therefore, the previous prognostic models based on the total CRC patient population might not be suitable for EOCRC patients. Here, we constructed a prognostic classifier to enhance the precision of individualized treatment and management of EOCRC patients. METHODS EOCRC expression data were downloaded from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. The regulatory pathways were explored by gene set enrichment analysis (GSEA). The prognostic model was developed by univariate Cox-LASSO-multivariate Cox regression analyses of GEO samples. TCGA samples were used to verify the model. The expression and mutation profiles and immune landscape of the high-risk and low-risk cohorts were analyzed and compared. Finally, the expression and prognostic value of the model genes were verified by immunohistochemistry and qRT‒PCR analysis. RESULTS The cell cycle was identified as the most significantly enriched oncological signature of EOCRC. Then, a 4-gene prognostic signature comprising MCM2, INHBA, CGREF1, and KLF9 was constructed. The risk score was an independent predictor of overall survival. The area under the curve values of the classifier for 1-, 3-, and 5-year survival were 0.856, 0.893, and 0.826, respectively, in the training set and 0.749, 0.858, and 0.865, respectively, in the validation set. Impaired DNA damage repair capability (p < 0.05) and frequent PIK3CA mutations (p < 0.05) were found in the high-risk cohort. CD8 T cells (p < 0.05), activated memory CD4 T cells (p < 0.01), and activated dendritic cells (p < 0.05) were clustered in the low-risk group. Finally, we verified the expression of MCM2, INHBA, CGREF1, and KLF9. Their prognostic value was closely related to age. CONCLUSION In this study, a robust prognostic classifier for EOCRC was established and validated. The findings may provide a reference for individualized treatment and medical decision-making for patients with EOCRC.
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Affiliation(s)
- Meijuan Xiang
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Department of Gastrointestinal Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
- Department of General Surgery, Guangdong Provincial People's Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou, 341000, China
- Department of General Surgery, Foresea Life Insurance Shaoguan Hospital, Shaoguan, 512000, China
| | - Yuan Gao
- Department of Gastrointestinal Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
- Department of General Surgery, Guangdong Provincial People's Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou, 341000, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yue Zhou
- Department of Gastrointestinal Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
- Department of General Surgery, Guangdong Provincial People's Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou, 341000, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Muqing Wang
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Xueqing Yao
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.
- Department of Gastrointestinal Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China.
- Department of General Surgery, Guangdong Provincial People's Hospital Ganzhou Hospital (Ganzhou Municipal Hospital), Ganzhou, 341000, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China.
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16
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A View on Uterine Leiomyoma Genesis through the Prism of Genetic, Epigenetic and Cellular Heterogeneity. Int J Mol Sci 2023; 24:ijms24065752. [PMID: 36982825 PMCID: PMC10056617 DOI: 10.3390/ijms24065752] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Uterine leiomyomas (ULs), frequent benign tumours of the female reproductive tract, are associated with a range of symptoms and significant morbidity. Despite extensive research, there is no consensus on essential points of UL initiation and development. The main reason for this is a pronounced inter- and intratumoral heterogeneity resulting from diverse and complicated mechanisms underlying UL pathobiology. In this review, we comprehensively analyse risk and protective factors for UL development, UL cellular composition, hormonal and paracrine signalling, epigenetic regulation and genetic abnormalities. We conclude the need to carefully update the concept of UL genesis in light of the current data. Staying within the framework of the existing hypotheses, we introduce a possible timeline for UL development and the associated key events—from potential prerequisites to the beginning of UL formation and the onset of driver and passenger changes.
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17
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Gordon H, Schafer ZT, Smith CJ. A paradox promoted by microglia cannibalism shortens the lifespan of developmental microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532426. [PMID: 36993267 PMCID: PMC10055159 DOI: 10.1101/2023.03.15.532426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The overproduction of cells and subsequent production of debris is a universal principle of neurodevelopment. Here we show an additional feature of the developing nervous system that causes neural debris - promoted by the sacrificial nature of embryonic microglia that irreversibly become phagocytic after clearing other neural debris. Described as long-lived, microglia colonize the embryonic brain and persist into adulthood. Using transgenic zebrafish to investigate the microglia debris during brain construction, we identified that unlike other neural cell-types that die in developmental stages after they have expanded, necroptotic-dependent microglial debris is prevalent when microglia are expanding in the zebrafish brain. Time-lapse imaging of microglia demonstrates that this debris is cannibalized by other microglia. To investigate features that promote microglia death and cannibalism, we used time-lapse imaging and fate-mapping strategies to track the lifespan of individual developmental microglia. These approaches revealed that instead of embryonic microglia being long-lived cells that completely digest their phagocytic debris, once most developmental microglia in zebrafish become phagocytic they eventually die, including ones that are cannibalistic. These results establish a paradox -- which we tested by increasing neural debris and manipulating phagocytosis -- that once most microglia in the embryo become phagocytic, they die, create debris and then are cannibalized by other microglia, resulting in more phagocytic microglia that are destined to die.
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Affiliation(s)
- Hannah Gordon
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN
- The Center for Stem Cells and Regenerative Medicine at the University of Notre Dame, Notre Dame, IN
| | - Zachary T. Schafer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN
| | - Cody J. Smith
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN
- The Center for Stem Cells and Regenerative Medicine at the University of Notre Dame, Notre Dame, IN
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18
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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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19
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Kitaoka M, Smith OK, Straight AF, Heald R. Molecular conflicts disrupting centromere maintenance contribute to Xenopus hybrid inviability. Curr Biol 2022; 32:3939-3951.e6. [PMID: 35973429 PMCID: PMC9529917 DOI: 10.1016/j.cub.2022.07.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/15/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022]
Abstract
Although central to evolution, the causes of hybrid inviability that drive reproductive isolation are poorly understood. Embryonic lethality occurs when the eggs of the frog X. tropicalis are fertilized with either X. laevis or X. borealis sperm. We observed that distinct subsets of paternal chromosomes failed to assemble functional centromeres, causing their mis-segregation during embryonic cell divisions. Core centromere DNA sequence analysis revealed little conservation among the three species, indicating that epigenetic mechanisms that normally operate to maintain centromere integrity are disrupted on specific paternal chromosomes in hybrids. In vitro reactions combining X. tropicalis egg extract with either X. laevis or X. borealis sperm chromosomes revealed that paternally matched or overexpressed centromeric histone CENP-A and its chaperone HJURP could rescue centromere assembly on affected chromosomes in interphase nuclei. However, although the X. laevis chromosomes maintained centromeric CENP-A in metaphase, X. borealis chromosomes did not and also displayed ultra-thin regions containing ribosomal DNA. Both centromere assembly and morphology of X. borealis mitotic chromosomes could be rescued by inhibiting RNA polymerase I or preventing the collapse of stalled DNA replication forks. These results indicate that specific paternal centromeres are inactivated in hybrids due to the disruption of associated chromatin regions that interfere with CENP-A incorporation, at least in some cases due to conflicts between replication and transcription machineries. Thus, our findings highlight the dynamic nature of centromere maintenance and its susceptibility to disruption in vertebrate interspecies hybrids.
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Affiliation(s)
- Maiko Kitaoka
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Owen K Smith
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA.
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20
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Jamasbi E, Hamelian M, Hossain MA, Varmira K. The cell cycle, cancer development and therapy. Mol Biol Rep 2022; 49:10875-10883. [PMID: 35931874 DOI: 10.1007/s11033-022-07788-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/11/2022] [Indexed: 10/16/2022]
Abstract
The process of cell division plays a vital role in cancer progression. Cell proliferation and error-free chromosomes segregation during mitosis are central events in life cycle. Mistakes during cell division generate changes in chromosome content and alter the balances of chromosomes number. Any defects in expression of TIF1 family proteins, SAC proteins network, mitotic checkpoint proteins involved in chromosome mis-segregation and cancer development. Here we discuss the function of organelles deal with the chromosome segregation machinery, proteins and correction mechanisms involved in the accurate chromosome segregation during mitosis.
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Affiliation(s)
- Elaheh Jamasbi
- Research Center of Oils and Fats (RCOF), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mona Hamelian
- Research Center of Oils and Fats (RCOF), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammed Akhter Hossain
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Kambiz Varmira
- Research Center of Oils and Fats (RCOF), Kermanshah University of Medical Sciences, Kermanshah, Iran.
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21
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Wu W, McHugh T, Kelly DA, Pidoux AL, Allshire RC. Establishment of centromere identity is dependent on nuclear spatial organization. Curr Biol 2022; 32:3121-3136.e6. [PMID: 35830853 PMCID: PMC9616734 DOI: 10.1016/j.cub.2022.06.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/24/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022]
Abstract
The establishment of centromere-specific CENP-A chromatin is influenced by epigenetic and genetic processes. Central domain sequences from fission yeast centromeres are preferred substrates for CENP-ACnp1 incorporation, but their use is context dependent, requiring adjacent heterochromatin. CENP-ACnp1 overexpression bypasses heterochromatin dependency, suggesting that heterochromatin ensures exposure to conditions or locations permissive for CENP-ACnp1 assembly. Centromeres cluster around spindle-pole bodies (SPBs). We show that heterochromatin-bearing minichromosomes localize close to SPBs, consistent with this location promoting CENP-ACnp1 incorporation. We demonstrate that heterochromatin-independent de novo CENP-ACnp1 chromatin assembly occurs when central domain DNA is placed near, but not far from, endogenous centromeres or neocentromeres. Moreover, direct tethering of central domain DNA at SPBs permits CENP-ACnp1 assembly, suggesting that the nuclear compartment surrounding SPBs is permissive for CENP-ACnp1 incorporation because target sequences are exposed to high levels of CENP-ACnp1 and associated assembly factors. Thus, nuclear spatial organization is a key epigenetic factor that influences centromere identity.
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Affiliation(s)
- Weifang Wu
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Toni McHugh
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - David A Kelly
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Alison L Pidoux
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK.
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22
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Sundararajan K, Straight AF. Centromere Identity and the Regulation of Chromosome Segregation. Front Cell Dev Biol 2022; 10:914249. [PMID: 35721504 PMCID: PMC9203049 DOI: 10.3389/fcell.2022.914249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Eukaryotes segregate their chromosomes during mitosis and meiosis by attaching chromosomes to the microtubules of the spindle so that they can be distributed into daughter cells. The complexity of centromeres ranges from the point centromeres of yeast that attach to a single microtubule to the more complex regional centromeres found in many metazoans or holocentric centromeres of some nematodes, arthropods and plants, that bind to dozens of microtubules per kinetochore. In vertebrates, the centromere is defined by a centromere specific histone variant termed Centromere Protein A (CENP-A) that replaces histone H3 in a subset of centromeric nucleosomes. These CENP-A nucleosomes are distributed on long stretches of highly repetitive DNA and interspersed with histone H3 containing nucleosomes. The mechanisms by which cells control the number and position of CENP-A nucleosomes is unknown but likely important for the organization of centromeric chromatin in mitosis so that the kinetochore is properly oriented for microtubule capture. CENP-A chromatin is epigenetically determined thus cells must correct errors in CENP-A organization to prevent centromere dysfunction and chromosome loss. Recent improvements in sequencing complex centromeres have paved the way for defining the organization of CENP-A nucleosomes in centromeres. Here we discuss the importance and challenges in understanding CENP-A organization and highlight new discoveries and advances enabled by recent improvements in the human genome assembly.
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23
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Okazaki K, Nakano M, Ohzeki JI, Otake K, Kugou K, Larionov V, Earnshaw WC, Masumoto H. Combination of CENP-B Box Positive and Negative Synthetic Alpha Satellite Repeats Improves De Novo Human Artificial Chromosome Formation. Cells 2022; 11:cells11091378. [PMID: 35563684 PMCID: PMC9105310 DOI: 10.3390/cells11091378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 01/11/2023] Open
Abstract
Human artificial chromosomes (HACs) can be formed de novo by introducing large (>30 kb) centromeric sequences consisting of highly repeated 171-bp alpha satellite (alphoid) DNA into HT1080 cells. However, only a subset of transformed cells successfully establishes HACs. CENP-A chromatin and heterochromatin assemble on the HACs and play crucial roles in chromosome segregation. The CENP-B protein, which binds a 17-bp motif (CENP-B box) in the alphoid DNA, functions in the formation of alternative CENP-A chromatin or heterochromatin states. A balance in the coordinated assembly of these chromatin states on the introduced alphoid DNA is important for HAC formation. To obtain information about the relationship between chromatin architecture and de novo HAC formation efficiency, we tested combinations of two 60-kb synthetic alphoid sequences containing either tetO or lacO plus a functional or mutated CENP-B box combined with a multiple fusion protein tethering system. The combination of mutated and wild-type CENP-B box alphoid repeats significantly enhanced HAC formation. Both CENP-A and HP1α were enriched in the wild-type alphoid DNA, whereas H3K27me3 was enriched on the mutant alphoid array. The presence or absence of CENP-B binding resulted in differences in the assembly of CENP-A chromatin on alphoid arrays and the formation of H3K9me3 or H3K27me3 heterochromatin.
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Affiliation(s)
- Koei Okazaki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan; (M.N.); (J.-i.O.); (K.O.); (K.K.)
- Public Relations and Research Promotion Group, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
- Correspondence: (K.O.); (H.M.); Tel.: +81-438-52-3930 (K.O.); +81-438-52-3952 (H.M.)
| | - Megumi Nakano
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan; (M.N.); (J.-i.O.); (K.O.); (K.K.)
| | - Jun-ichirou Ohzeki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan; (M.N.); (J.-i.O.); (K.O.); (K.K.)
| | - Koichiro Otake
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan; (M.N.); (J.-i.O.); (K.O.); (K.K.)
| | - Kazuto Kugou
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan; (M.N.); (J.-i.O.); (K.O.); (K.K.)
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA;
| | | | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan; (M.N.); (J.-i.O.); (K.O.); (K.K.)
- Correspondence: (K.O.); (H.M.); Tel.: +81-438-52-3930 (K.O.); +81-438-52-3952 (H.M.)
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24
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Zhou K, Gebala M, Woods D, Sundararajan K, Edwards G, Krzizike D, Wereszczynski J, Straight AF, Luger K. CENP-N promotes the compaction of centromeric chromatin. Nat Struct Mol Biol 2022; 29:403-413. [PMID: 35422519 PMCID: PMC9010303 DOI: 10.1038/s41594-022-00758-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/08/2022] [Indexed: 12/14/2022]
Abstract
The histone variant CENP-A is the epigenetic determinant for the centromere, where it is interspersed with canonical H3 to form a specialized chromatin structure that nucleates the kinetochore. How nucleosomes at the centromere arrange into higher order structures is unknown. Here we demonstrate that the human CENP-A-interacting protein CENP-N promotes the stacking of CENP-A-containing mononucleosomes and nucleosomal arrays through a previously undefined interaction between the α6 helix of CENP-N with the DNA of a neighboring nucleosome. We describe the cryo-EM structures and biophysical characterization of such CENP-N-mediated nucleosome stacks and nucleosomal arrays and demonstrate that this interaction is responsible for the formation of densely packed chromatin at the centromere in the cell. Our results provide first evidence that CENP-A, together with CENP-N, promotes specific chromatin higher order structure at the centromere.
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Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Magdalena Gebala
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Dustin Woods
- Department of Chemistry and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA
| | | | - Garrett Edwards
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Dan Krzizike
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, CA, USA.
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, USA.
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25
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Abstract
The centromere performs a universally conserved function, to accurately partition genetic information upon cell division. Yet, centromeres are among the most rapidly evolving regions of the genome and are bound by a varying assortment of centromere-binding factors that are themselves highly divergent at the protein-sequence level. A common thread in most species is the dependence on the centromere-specific histone variant CENP-A for the specification of the centromere site. However, CENP-A is not universally required in all species or cell types, making the identification of a general mechanism for centromere specification challenging. In this review, we examine our current understanding of the mechanisms of centromere specification in CENP-A-dependent and independent systems, focusing primarily on recent work.
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Affiliation(s)
- Barbara G Mellone
- Department of Molecular and Cell Biology, and Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005 Paris, France.
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26
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Wu H, Zhou Y, Wu H, Xu L, Yan Y, Tong X, Yan H. CENPN Acts as a Novel Biomarker that Correlates With the Malignant Phenotypes of Glioma Cells. Front Genet 2021; 12:732376. [PMID: 34646306 PMCID: PMC8502822 DOI: 10.3389/fgene.2021.732376] [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: 06/29/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Gliomas are the most common intracranial malignant neoplasms and have high recurrence and mortality rates. Recent literatures have reported that centromere protein N (CENPN) participates in tumor development. However, the clinicopathologic significance and biological functions of CENPN in glioma are still unclear. Methods: Clinicopathologic data and gene expression profiles of glioma cases downloaded from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases were utilized to determine the associations between the expression of CENPN and clinical features of glioma. Kaplan-Meier and ROC curves were plotted for prognostic analysis. Gene set enrichment analysis (GSEA) and single sample gene set enrichment analysis (ssGSEA) were applied to identify immune-related functions and pathways associated with CENPN’ differential expression. In vitro experiments were conducted to investigate the impacts of CENPN on human glioma cells. Results: Elevated CENPN expression was associated with unfavorable clinical variables of glioma patients, which was validated in clinical specimens obtained from our institution by immunohistochemical staining (IHC). The GSEA and ssGSEA results revealed that CENPN expression was strongly correlated with inflammatory activities, immune-related signaling pathways and the infiltration of immune cells. Cell experiments showed that CENPN deficiency impaired cell proliferation, migration and invasion ability and increased glioma apoptosis. Conclusion: CENPN could be a promising therapeutic target for glioma.
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Affiliation(s)
- Hailong Wu
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China.,Department of Neurosurgery, Shijiazhuang Third Hospital, Hebei, China
| | - Yan Zhou
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China
| | - Haiyang Wu
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China
| | - Lixia Xu
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin Huanhu Hospital, Tianjin, China
| | - Yan Yan
- Clinical Laboratory, Tianjin Huanhu Hospital, Tianjin, China
| | - Xiaoguang Tong
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin Huanhu Hospital, Tianjin, China.,Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin, China
| | - Hua Yan
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin Huanhu Hospital, Tianjin, China
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27
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The synaptonemal complex imposes crossover interference and heterochiasmy in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2023613118. [PMID: 33723072 PMCID: PMC8000504 DOI: 10.1073/pnas.2023613118] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Meiotic recombination promotes genetic diversity by shuffling parental chromosomes. As observed by the very first geneticists, crossovers inhibit the formation of another crossover nearby, an elusive phenomenon called crossover interference. Another intriguing observation is heterochiasmy, the marked difference in male and female crossover rates observed in many species. Here, we show that the synaptonemal complex, a structure that zips homologous chromosomes together during meiosis, is essential for crossover interference in Arabidopsis. This suggests that a signal that inhibits crossover formation nearby a first crossover propagates along this specific structure. Furthermore, in the absence of the synaptonemal complex, crossover frequencies become identical in both sexes, suggesting that heterochiasmy is due to variation of crossover interference imposed by the synaptonemal complex. Meiotic crossovers (COs) have intriguing patterning properties, including CO interference, the tendency of COs to be well-spaced along chromosomes, and heterochiasmy, the marked difference in male and female CO rates. During meiosis, transverse filaments transiently associate the axes of homologous chromosomes, a process called synapsis that is essential for CO formation in many eukaryotes. Here, we describe the spatial organization of the transverse filaments in Arabidopsis (ZYP1) and show it to be evolutionary conserved. We show that in the absence of ZYP1 (zyp1a zyp1b null mutants), chromosomes associate in pairs but do not synapse. Unexpectedly, in absence of ZYP1, CO formation is not prevented but increased. Furthermore, genome-wide analysis of recombination revealed that CO interference is abolished, with the frequent observation of close COs. In addition, heterochiasmy was erased, with identical CO rates in males and females. This shows that the tripartite synaptonemal complex is dispensable for CO formation and has a key role in regulating their number and distribution, imposing CO interference and heterochiasmy.
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28
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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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29
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Liu X, Wang H, Zhao G. Centromere Protein A Goes Far Beyond the Centromere in Cancers. Mol Cancer Res 2021; 20:3-10. [PMID: 34465586 DOI: 10.1158/1541-7786.mcr-21-0311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
Centromere dysfunctions leading to numerical chromosome alterations are believed to be closely related to human cancers. As a centromere-specific protein, centromere protein A (CENP-A) replaces the histone H3 in centromeres and is therefore considered a key factor of centromere identity. Researches have shown that CENP-A is overexpressed in many types of human cancers. However, the behavior and function of CENP-A in tumorigenesis have not yet been systematically summarized. In this article, we describe the pleiotropic roles of CENP-A in human cells. Moreover, we provide a comprehensive review of the current knowledge on the relationship between aberrant expression and ectopic localization of CENP-A and tumorigenesis, and the mechanism of the ectopic deposition of CENP-A in cancers. Furthermore, we note that some oncogenic viruses can modulate the expression and localization of this centromere protein along with its chaperone. At last, we also discuss the therapeutic potential of targeting CENP-A for cancer therapy.
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Affiliation(s)
- Xiaolan Liu
- Affiliated Wuhan Mental Health Center, Tongji Medical College of Huazhong University of Science & Technology, Wuhan, Hubei, China. .,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, China
| | - Haiping Wang
- School of Medicine, Jianghan University, Wuhan, Hubei, China
| | - Guojun Zhao
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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30
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Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci 2021; 22:ijms22094309. [PMID: 33919233 PMCID: PMC8122249 DOI: 10.3390/ijms22094309] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
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Affiliation(s)
- Jitendra Thakur
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
- Correspondence:
| | - Jenika Packiaraj
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA 98109, USA
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31
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Centromeric chromatin integrity is compromised by loss of Cdk5rap2, a transcriptional activator of CENP-A. Biomed Pharmacother 2021; 138:111463. [PMID: 33725591 DOI: 10.1016/j.biopha.2021.111463] [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: 11/04/2020] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
Centromeres are chromosomal loci where kinetochores assemble to ensure faithful chromosome segregation during mitosis. CENP-A defines the loci by serving as an epigenetic marker that recruits other centromere components for a functional structure. However, the mechanism that controls CENP-A regulation of centromeric chromatin integrity remains to be explored. Separate studies have shown that loss of CENP-A or the Cdk5 regulatory subunit associated protein 2 (Cdk5rap2), a key player in mitotic progression, triggers the occurrence of lagging chromosomes. This prompted us to investigate a potential link between CENP-A and Cdk5rap2 in the maintenance of centromeric chromatin integrity. Here, we demonstrate that loss of Cdk5rap2 causes reduced CENP-A expression while exogenous Cdk5rap2 expression in cells depleted of endogenous Cdk5rap2 restores CENP-A expression. Indeed, we show that Cdk5rap2 is a nuclear protein that acts as a positive transcriptional regulator of CENP-A. Cdk5rap2 interacts with the CENP-A promoter and upregulates CENP-A transcription. Accordingly, loss of Cdk5rap2 causes reduced level of centromeric CENP-A. Exogenous CENP-A expression partially inhibits the occurrence of lagging chromosomes in Cdk5rap2 knockdown cells, indicating that lagging chromosomes induced by loss of Cdk5rap2 is due, in part, to loss of CENP-A. Aside from manifesting lagging chromosomes, cells depleted of Cdk5rap2, and thus CENP-A, show increased micronuclei and chromatin bridge formation. Altogether, our findings indicate that Cdk5rap2 serves to maintain centromeric chromatin integrity partly through CENP-A.
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32
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Peretti D, Smith HL, Verity N, Humoud I, de Weerd L, Swinden DP, Hayes J, Mallucci GR. TrkB signaling regulates the cold-shock protein RBM3-mediated neuroprotection. Life Sci Alliance 2021; 4:4/4/e202000884. [PMID: 33563652 PMCID: PMC7893816 DOI: 10.26508/lsa.202000884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 02/02/2023] Open
Abstract
Increasing levels of the cold-shock protein, RNA-binding motif 3 (RBM3), either through cooling or by ectopic over-expression, prevents synapse and neuronal loss in mouse models of neurodegeneration. To exploit this process therapeutically requires an understanding of mechanisms controlling cold-induced RBM3 expression. Here, we show that cooling increases RBM3 through activation of TrkB via PLCγ1 and pCREB signaling. RBM3, in turn, has a hitherto unrecognized negative feedback on TrkB-induced ERK activation through induction of its specific phosphatase, DUSP6. Thus, RBM3 mediates structural plasticity through a distinct, non-canonical activation of TrkB signaling, which is abolished in RBM3-null neurons. Both genetic reduction and pharmacological antagonism of TrkB and its downstream mediators abrogate cooling-induced RBM3 induction and prevent structural plasticity, whereas TrkB inhibition similarly prevents RBM3 induction and the neuroprotective effects of cooling in prion-diseased mice. Conversely, TrkB agonism induces RBM3 without cooling, preventing synapse loss and neurodegeneration. TrkB signaling is, therefore, necessary for the induction of RBM3 and related neuroprotective effects and provides a target by which RBM3-mediated synapse-regenerative therapies in neurodegenerative disorders can be used therapeutically without the need for inducing hypothermia.
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Affiliation(s)
- Diego Peretti
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Heather L Smith
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Nicholas Verity
- MRC Toxicology Unit at the University of Cambridge, Leicester, UK
| | - Ibrahim Humoud
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Lis de Weerd
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Dean P Swinden
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Joseph Hayes
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Giovanna R Mallucci
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
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33
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Thakur J, Henikoff S. Architectural RNA in chromatin organization. Biochem Soc Trans 2020; 48:1967-1978. [PMID: 32897323 PMCID: PMC7609026 DOI: 10.1042/bst20191226] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022]
Abstract
RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether or not RNA can act as an architectural molecule for chromatin remains unclear, partly because dissecting the architectural role of RNA from its regulatory role remains challenging. Studies that have addressed RNA's architectural role in chromatin organization rely on in situ RNA depletion using Ribonuclease A (RNase A) and suggest that RNA plays a major direct architectural role in chromatin organization. In this review, we will discuss these findings, candidate chromatin architectural long non-coding RNAs and possible mechanisms by which RNA, along with RNA binding proteins might be mediating chromatin organization.
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Affiliation(s)
- Jitendra Thakur
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, U.S.A
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34
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Otake K, Ohzeki JI, Shono N, Kugou K, Okazaki K, Nagase T, Yamakawa H, Kouprina N, Larionov V, Kimura H, Earnshaw WC, Masumoto H. CENP-B creates alternative epigenetic chromatin states permissive for CENP-A or heterochromatin assembly. J Cell Sci 2020; 133:jcs243303. [PMID: 32661090 PMCID: PMC7438015 DOI: 10.1242/jcs.243303] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/29/2020] [Indexed: 01/03/2023] Open
Abstract
CENP-B binds to CENP-B boxes on centromeric satellite DNAs (known as alphoid DNA in humans). CENP-B maintains kinetochore function through interactions with CENP-A nucleosomes and CENP-C. CENP-B binding to transfected alphoid DNA can induce de novo CENP-A assembly, functional centromere and kinetochore formation, and subsequent human artificial chromosome (HAC) formation. Furthermore, CENP-B also facilitates H3K9 (histone H3 lysine 9) trimethylation on alphoid DNA, mediated by Suv39h1, at ectopic alphoid DNA integration sites. Excessive heterochromatin invasion into centromere chromatin suppresses CENP-A assembly. It is unclear how CENP-B controls such different chromatin states. Here, we show that the CENP-B acidic domain recruits histone chaperones and many chromatin modifiers, including the H3K36 methylase ASH1L, as well as the heterochromatin components Suv39h1 and HP1 (HP1α, β and γ, also known as CBX5, CBX1 and CBX3, respectively). ASH1L facilitates the formation of open chromatin competent for CENP-A assembly on alphoid DNA. These results indicate that CENP-B is a nexus for histone modifiers that alternatively promote or suppress CENP-A assembly by mutually exclusive mechanisms. Besides the DNA-binding domain, the CENP-B acidic domain also facilitates CENP-A assembly de novo on transfected alphoid DNA. CENP-B therefore balances CENP-A assembly and heterochromatin formation on satellite DNA.
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Affiliation(s)
- Koichiro Otake
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Jun-Ichirou Ohzeki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Nobuaki Shono
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Kazuto Kugou
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Koei Okazaki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Takahiro Nagase
- Public Relations and Research Promotion Group, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Hisashi Yamakawa
- Clinical Analysis Team, Department of Omics Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
| | - Natalay Kouprina
- Genome Structure and Function Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Genome Structure and Function Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu 292-0818, Japan
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35
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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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36
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Kim JH, Youn Y, Lee JC, Kim J, Hwang JH. Involvement of the NF-κB signaling pathway in proliferation and invasion inhibited by Zwint-1 deficiency in Pancreatic Cancer Cells. J Cancer 2020; 11:5601-5611. [PMID: 32913455 PMCID: PMC7477444 DOI: 10.7150/jca.46173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/17/2020] [Indexed: 01/02/2023] Open
Abstract
Pancreatic cancer (PC) is an intractable cancer that is difficult to diagnose early and has a 5-year survival rate of less than 8%. ZW10-interacting kinetochore protein (ZWINT) is a crucial gene that contributes to chromosome instability and is essential for spindle assembly and kinetochore-microtubule attachment during meiosis and mitosis. However, the mechanism through which Zwint-1 promotes PC progression is yet to be elucidated. Here, we report that Zwint-1 is highly expressed in clinical PC specimens (based on analysis of the Gene Expression Profiling Interactive Analysis database) and various PC cell lines. Importantly, Zwint-1-deficient PC cells showed reduced nuclear factor-kappa B (NF-κB) (Ser536) phosphorylation along with inhibited proliferation and colony formation due to downregulation of NF-κB-regulated genes such as CCND1, cIAP1/2, and XIAP. In addition, Zwint-1-deficient PC cells showed reduced invasion and migration abilities, and decreased expression levels of the metalloproteinases MMP2 and MMP9. Furthermore, Zwint-1 deficiency arrested the PC cell cycle at the G2/M phase because the chromosomes failed to segregate properly, and the apoptosis rate in these cells gradually increased, accompanied by increased caspase-3 activation and anti-poly (ADP ribose) polymerase cleavage. Apoptosis caused by Zwint-1 deficiency was demonstrated to occur through caspase-dependent pathways based on experiments involving treatment with a pan-caspase inhibitor (Z-VAD-Fmk). Thus, Zwint-1 contributes to cell growth, invasion, and survival through NF-κB signaling pathways, suggesting that it could serve as a PC biomarker and new therapeutic target.
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Affiliation(s)
- Jae Hyeong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Yuna Youn
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Jong-chan Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jaihwan Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
| | - Jin-Hyeok Hwang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 13620, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
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37
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Shatskikh AS, Kotov AA, Adashev VE, Bazylev SS, Olenina LV. Functional Significance of Satellite DNAs: Insights From Drosophila. Front Cell Dev Biol 2020; 8:312. [PMID: 32432114 PMCID: PMC7214746 DOI: 10.3389/fcell.2020.00312] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
Since their discovery more than 60 years ago, satellite repeats are still one of the most enigmatic parts of eukaryotic genomes. Being non-coding DNA, satellites were earlier considered to be non-functional “junk,” but recently this concept has been extensively revised. Satellite DNA contributes to the essential processes of formation of crucial chromosome structures, heterochromatin establishment, dosage compensation, reproductive isolation, genome stability and development. Genomic abundance of satellites is under stabilizing selection owing of their role in the maintenance of vital regions of the genome – centromeres, pericentromeric regions, and telomeres. Many satellites are transcribed with the generation of long or small non-coding RNAs. Misregulation of their expression is found to lead to various defects in the maintenance of genomic architecture, chromosome segregation and gametogenesis. This review summarizes our current knowledge concerning satellite functions, the mechanisms of regulation and evolution of satellites, focusing on recent findings in Drosophila. We discuss here experimental and bioinformatics data obtained in Drosophila in recent years, suggesting relevance of our analysis to a wide range of eukaryotic organisms.
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Affiliation(s)
- Aleksei S Shatskikh
- Laboratory of Analysis of Clinical and Model Tumor Pathologies on the Organismal Level, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexei A Kotov
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir E Adashev
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergei S Bazylev
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ludmila V Olenina
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Wang Y, Fan LH, Yue W, Ouyang YC, Wang ZB, Hou Y, Schatten H, Sun QY. CENP-W regulates kinetochore-microtubule attachment and meiotic progression of mouse oocytes. Biochem Biophys Res Commun 2020; 527:8-14. [PMID: 32446395 DOI: 10.1016/j.bbrc.2020.04.078] [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: 03/30/2020] [Accepted: 04/05/2020] [Indexed: 10/24/2022]
Abstract
Oocyte meiotic maturation failure and unfaithful chromosome segregation are major causes for female infertility. Here, we showed that CENP-W, a relatively novel member of the kinetochore protein family, was expressed in mouse oocytes from the germinal vesicle (GV) to metaphase II (MII) stages. Confocal microscopy revealed that CENP-W was localized in the germinal vesicle in the GV stage, and then became concentrated on kinetochores during oocyte maturation. Knockdown of CENP-W by specific siRNA injection in vitro caused kinetochore-microtubule detachment, resulting in severely defective spindles and misaligned chromosomes, leading to metaphase I arrest and failure of first polar body (PB1) extrusion. Correspondingly, spindle assembly checkpoint (SAC) activation was observed in CENP-W knockdown oocytes even after 10h of culture. Our results suggest that CENP-W acts as a kinetochore protein, which takes part in kinetochore-microtubule attachment, thus mediating the progression of oocyte meiotic maturation.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Hua Fan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Yue
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Chun Ouyang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA
| | - Qing-Yuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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39
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Medina‐Pritchard B, Lazou V, Zou J, Byron O, Abad MA, Rappsilber J, Heun P, Jeyaprakash AA. Structural basis for centromere maintenance by Drosophila CENP-A chaperone CAL1. EMBO J 2020; 39:e103234. [PMID: 32134144 PMCID: PMC7110144 DOI: 10.15252/embj.2019103234] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/25/2020] [Accepted: 02/11/2020] [Indexed: 01/08/2023] Open
Abstract
Centromeres are microtubule attachment sites on chromosomes defined by the enrichment of histone variant CENP-A-containing nucleosomes. To preserve centromere identity, CENP-A must be escorted to centromeres by a CENP-A-specific chaperone for deposition. Despite this essential requirement, many eukaryotes differ in the composition of players involved in centromere maintenance, highlighting the plasticity of this process. In humans, CENP-A recognition and centromere targeting are achieved by HJURP and the Mis18 complex, respectively. Using X-ray crystallography, we here show how Drosophila CAL1, an evolutionarily distinct CENP-A histone chaperone, binds both CENP-A and the centromere receptor CENP-C without the requirement for the Mis18 complex. While an N-terminal CAL1 fragment wraps around CENP-A/H4 through multiple physical contacts, a C-terminal CAL1 fragment directly binds a CENP-C cupin domain dimer. Although divergent at the primary structure level, CAL1 thus binds CENP-A/H4 using evolutionarily conserved and adaptive structural principles. The CAL1 binding site on CENP-C is strategically positioned near the cupin dimerisation interface, restricting binding to just one CAL1 molecule per CENP-C dimer. Overall, by demonstrating how CAL1 binds CENP-A/H4 and CENP-C, we provide key insights into the minimalistic principles underlying centromere maintenance.
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Affiliation(s)
| | - Vasiliki Lazou
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Juan Zou
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Olwyn Byron
- School of Life SciencesUniversity of GlasgowGlasgowUK
| | - Maria A Abad
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Juri Rappsilber
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK,Institute of BiotechnologyTechnische Universität BerlinBerlinGermany
| | - Patrick Heun
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
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40
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Migl D, Kschonsak M, Arthur CP, Khin Y, Harrison SC, Ciferri C, Dimitrova YN. Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 Å Resolution. Structure 2020; 28:363-370.e3. [PMID: 32004465 PMCID: PMC7166091 DOI: 10.1016/j.str.2019.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/17/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022]
Abstract
Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, containing the histone variant Cse4CENP-A instead of H3, with a single microtubule. Conservation of most kinetochore components from yeast to metazoans suggests that the yeast kinetochore represents a module of the more complex metazoan arrangements. We describe here a streamlined protocol for reconstituting a yeast centromeric nucleosome and a systematic exploration of cryo-grid preparation. These developments allowed us to obtain a high-resolution cryoelectron microscopy reconstruction. As suggested by previous work, fewer base pairs are in tight association with the histone octamer than there are in canonical nucleosomes. Weak binding of the end DNA sequences may contribute to specific recognition by other inner kinetochore components. The centromeric nucleosome structure and the strategies we describe will facilitate studies of many other aspects of kinetochore assembly and chromatin biochemistry.
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Affiliation(s)
- David Migl
- Harvard Medical School, Boston, MA 02115, USA; Biophysics Program, Harvard University, Boston, MA 02115, USA
| | - Marc Kschonsak
- Structural Biology, Genentech, South San Francisco, CA, USA
| | | | - Yadana Khin
- Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C Harrison
- Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Claudio Ciferri
- Structural Biology, Genentech, South San Francisco, CA, USA.
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Melters DP, Pitman M, Rakshit T, Dimitriadis EK, Bui M, Papoian GA, Dalal Y. Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners. Proc Natl Acad Sci U S A 2019; 116:24066-24074. [PMID: 31712435 PMCID: PMC6883791 DOI: 10.1073/pnas.1911880116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Histone variants fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether and how nucleosome variants encode unique mechanical properties to their cognate chromatin structures remains elusive. Here, using in silico and in vitro nanoindentation methods, extending to in vivo dissections, we report that histone variant nucleosomes are intrinsically more elastic than their canonical counterparts. Furthermore, binding proteins, which discriminate between histone variant nucleosomes, suppress this innate elasticity and also compact chromatin. Interestingly, when we overexpress the binding proteins in vivo, we also observe increased compaction of chromatin enriched for histone variant nucleosomes, correlating with diminished access. Taken together, these data suggest a plausible link between innate mechanical properties possessed by histone variant nucleosomes, the adaptability of chromatin states in vivo, and the epigenetic plasticity of the underlying locus.
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Affiliation(s)
- Daniël P Melters
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Mary Pitman
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742
| | - Tatini Rakshit
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Emilios K Dimitriadis
- Scanning Probe Microscopy Unit, Biomedical Engineering and Physical Science Shared Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Minh Bui
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Garegin A Papoian
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742;
| | - Yamini Dalal
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892;
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Huang A, Kremser L, Schuler F, Wilflingseder D, Lindner H, Geley S, Lusser A. Phosphorylation of Drosophila CENP-A on serine 20 regulates protein turn-over and centromere-specific loading. Nucleic Acids Res 2019; 47:10754-10770. [PMID: 31535131 PMCID: PMC6847487 DOI: 10.1093/nar/gkz809] [Citation(s) in RCA: 10] [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: 05/14/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022] Open
Abstract
Centromeres are specialized chromosomal regions epigenetically defined by the presence of the histone H3 variant CENP-A. CENP-A is required for kinetochore formation which is essential for chromosome segregation during mitosis. Spatial restriction of CENP-A to the centromere is tightly controlled. Its overexpression results in ectopic incorporation and the formation of potentially deleterious neocentromeres in yeast, flies and in various human cancers. While the contribution of posttranslational modifications of CENP-A to these processes has been studied in yeast and mammals to some extent, very little is known about Drosophila melanogaster. Here, we show that CENP-A is phosphorylated at serine 20 (S20) by casein kinase II and that in mitotic cells, the phosphorylated form is enriched on chromatin. Importantly, our results reveal that S20 phosphorylation regulates the turn-over of prenucleosomal CENP-A by the SCFPpa-proteasome pathway and that phosphorylation promotes removal of CENP-A from ectopic but not from centromeric sites in chromatin. We provide multiple lines of evidence for a crucial role of S20 phosphorylation in controlling restricted incorporation of CENP-A into centromeric chromatin in flies. Modulation of the phosphorylation state of S20 may provide the cells with a means to fine-tune CENP-A levels in order to prevent deleterious loading to extra-centromeric sites.
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Affiliation(s)
- Anming Huang
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Austria
| | - Leopold Kremser
- Institute of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Fabian Schuler
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Doris Wilflingseder
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria
| | - Herbert Lindner
- Institute of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Austria
| | - Stephan Geley
- Institute of Pathophysiology, Biocenter, Medical University of Innsbruck, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Austria
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43
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Centromere repositioning causes inversion of meiosis and generates a reproductive barrier. Proc Natl Acad Sci U S A 2019; 116:21580-21591. [PMID: 31597736 PMCID: PMC6815110 DOI: 10.1073/pnas.1911745116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mutations in inner kinetochore components induce centromere repositioning without alteration in the centromeric DNA sequence, revealing a feedback mechanism underlying the high epigenetic stability of the centromere. This also provides a desirable experimental system to explore the functional significance of centromere positioning in meiosis. We discovered that in a heterozygotic meiosis, a repositioned centromere generates a reproductive barrier, suggesting a functional role of evolutionary new centromeres in speciation; furthermore, in a homozygotic meiosis, chromosomes carrying repositioned centromeres frequently undergo the 2 stages of meiotic segregation in an inverted order, demonstrating high flexibility in the meiotic process. The chromosomal position of each centromere is determined epigenetically and is highly stable, whereas incremental cases have supported the occurrence of centromere repositioning on an evolutionary time scale (evolutionary new centromeres, ENCs), which is thought to be important in speciation. The mechanisms underlying the high stability of centromeres and its functional significance largely remain an enigma. Here, in the fission yeast Schizosaccharomyces pombe, we identify a feedback mechanism: The kinetochore, whose assembly is guided by the centromere, in turn, enforces centromere stability. Upon going through meiosis, specific inner kinetochore mutations induce centromere repositioning—inactivation of the original centromere and formation of a new centromere elsewhere—in 1 of the 3 chromosomes at random. Repositioned centromeres reside asymmetrically in the pericentromeric regions and cells carrying them are competent in mitosis and homozygotic meiosis. However, when cells carrying a repositioned centromere are crossed with those carrying the original centromere, the progeny suffer severe lethality due to defects in meiotic chromosome segregation. Thus, repositioned centromeres constitute a reproductive barrier that could initiate genetic divergence between 2 populations with mismatched centromeres, documenting a functional role of ENCs in speciation. Surprisingly, homozygotic repositioned centromeres tend to undergo meiosis in an inverted order—that is, sister chromatids segregate first, and homologous chromosomes separate second—whereas the original centromeres on other chromosomes in the same cell undergo meiosis in the canonical order, revealing hidden flexibility in the perceived rigid process of meiosis.
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Asymmetric Centromeres Differentially Coordinate with Mitotic Machinery to Ensure Biased Sister Chromatid Segregation in Germline Stem Cells. Cell Stem Cell 2019; 25:666-681.e5. [PMID: 31564548 DOI: 10.1016/j.stem.2019.08.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/25/2019] [Accepted: 08/19/2019] [Indexed: 12/29/2022]
Abstract
Many stem cells utilize asymmetric cell division (ACD) to produce a self-renewed stem cell and a differentiating daughter cell. How non-genic information could be inherited differentially to establish distinct cell fates is not well understood. Here, we report a series of spatiotemporally regulated asymmetric components, which ensure biased sister chromatid attachment and segregation during ACD of Drosophila male germline stem cells (GSCs). First, sister centromeres are differentially enriched with proteins involved in centromere specification and kinetochore function. Second, temporally asymmetric microtubule activities and polarized nuclear envelope breakdown allow for the preferential recognition and attachment of microtubules to asymmetric sister kinetochores and sister centromeres. Abolishment of either the asymmetric sister centromeres or the asymmetric microtubule activities results in randomized sister chromatid segregation. Together, these results provide the cellular basis for partitioning epigenetically distinct sister chromatids during stem cell ACDs, which opens new directions to study these mechanisms in other biological contexts.
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45
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Abstract
Magnaporthe oryzae is an important fungal pathogen that causes a loss of 10% to 30% of the annual rice crop due to the devastating blast disease. In most organisms, kinetochores are clustered together or arranged at the metaphase plate to facilitate synchronized anaphase separation of sister chromatids in mitosis. In this study, we showed that the initially clustered kinetochores separate and position randomly prior to anaphase in M. oryzae. Centromeres in M. oryzae occupy large genomic regions and form on AT-rich DNA without any common sequence motifs. Overall, this study identified atypical kinetochore dynamics and mapped functional centromeres in M. oryzae to define the roles of centromeric and pericentric boundaries in kinetochore assembly on epigenetically specified centromere loci. This study should pave the way for further understanding of the contribution of heterochromatin in genome stability and virulence of the blast fungus and its related species of high economic importance. Precise kinetochore-microtubule interactions ensure faithful chromosome segregation in eukaryotes. Centromeres, identified as scaffolding sites for kinetochore assembly, are among the most rapidly evolving chromosomal loci in terms of the DNA sequence and length and organization of intrinsic elements. Neither the centromere structure nor the kinetochore dynamics is well studied in plant-pathogenic fungi. Here, we sought to understand the process of chromosome segregation in the rice blast fungus Magnaporthe oryzae. High-resolution imaging of green fluorescent protein (GFP)-tagged inner kinetochore proteins CenpA and CenpC revealed unusual albeit transient declustering of centromeres just before anaphase separation of chromosomes in M. oryzae. Strikingly, the declustered centromeres positioned randomly at the spindle midzone without an apparent metaphase plate per se. Using CenpA chromatin immunoprecipitation followed by deep sequencing, all seven centromeres in M. oryzae were found to be regional, spanning 57-kb to 109-kb transcriptionally poor regions. Highly AT-rich and heavily methylated DNA sequences were the only common defining features of all the centromeres in rice blast. Lack of centromere-specific DNA sequence motifs or repetitive elements suggests an epigenetic specification of centromere function in M. oryzae. PacBio genome assemblies and synteny analyses facilitated comparison of the centromeric/pericentromeric regions in distinct isolates of rice blast and wheat blast and in Magnaporthiopsis poae. Overall, this study revealed unusual centromere dynamics and precisely identified the centromere loci in the top model fungal pathogens that belong to Magnaporthales and cause severe losses in the global production of food crops and turf grasses.
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46
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Oka N, Kasamatsu A, Endo-Sakamoto Y, Eizuka K, Wagai S, Koide-Ishida N, Miyamoto I, Iyoda M, Tanzawa H, Uzawa K. Centromere Protein N Participates in Cellular Proliferation of Human Oral Cancer by Cell-Cycle Enhancement. J Cancer 2019; 10:3728-3734. [PMID: 31333790 PMCID: PMC6636300 DOI: 10.7150/jca.32281] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/11/2019] [Indexed: 12/25/2022] Open
Abstract
Centromere protein N (CENP-N), an important member of the centromere protein family, is essential for kinetochore assembly and chromosome segregation; however, the relevance of CENP-N in cancers remains unknown. The aim of this study was to investigate CENP-N expression and its functional mechanisms in oral squamous cell carcinoma (OSCC). CENP-N expression was up-regulated significantly in vitro and in vivo in OSCCs. Overexpressed CENP-N was closely (p < 0.05) correlated with tumor growth using quantitative reverse transcriptase-polymerase chain reaction, immunoblot analysis, and immunohistochemistry. CENP-N knockdown (shCENP-N) cells showed depressed cellular proliferation by cell-cycle arrest at the G1 phase with up-regulation of p21Cip1 and p27Kip1 and down-regulation of cyclin D1, CDK2, and CDK4. Interestingly, we newly discovered that calcitriol (1, 25-dihydroxyvitamin D3) controlled the CENP-N expression level, leading to inhibition of tumor growth similar to shCENP-N cells. These results suggested that CENP-N plays a critical role in determining proliferation of OSCCs and that calcitriol might be a novel therapeutic drug for OSCCs by regulating CENP-N.
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Affiliation(s)
- Noritoshi Oka
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kasamatsu
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Yosuke Endo-Sakamoto
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Keitaro Eizuka
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Sho Wagai
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Nao Koide-Ishida
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Isao Miyamoto
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Manabu Iyoda
- Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Hideki Tanzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
| | - Katsuhiro Uzawa
- Department of Oral Science, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Dentistry and Oral-Maxillofacial Surgery, Chiba University Hospital, Chiba, Japan
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47
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French BT, Straight AF. The Power of Xenopus Egg Extract for Reconstitution of Centromere and Kinetochore Function. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:59-84. [PMID: 28840233 DOI: 10.1007/978-3-319-58592-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Faithful transmission of genetic information during cell division requires attachment of chromosomes to the mitotic spindle via the kinetochore. In vitro reconstitution studies are beginning to uncover how the kinetochore is assembled upon the underlying centromere, how the kinetochore couples chromosome movement to microtubule dynamics, and how cells ensure the site of kinetochore assembly is maintained from one generation to the next. Here we give special emphasis to advances made in Xenopus egg extract, which provides a unique, biochemically tractable in vitro system that affords the complexity of cytoplasm and nucleoplasm to permit reconstitution of the dynamic, cell cycle-regulated functions of the centromere and kinetochore.
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Affiliation(s)
- Bradley T French
- Department of Biochemistry, Stanford University, 279 Campus Drive, Beckman 409, Stanford, CA, 94305, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, 279 Campus Drive, Beckman 409, Stanford, CA, 94305, USA.
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48
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Centromeric non-coding RNA as a hidden epigenetic factor of the point centromere. Curr Genet 2019; 65:1165-1171. [PMID: 31073666 DOI: 10.1007/s00294-019-00988-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/19/2022]
Abstract
To ensure proper chromosome segregation during cell division, the centromere in many organisms is transcribed to produce a low level of long non-coding RNA to regulate the activity of the kinetochore. In the budding yeast point centromere, our recent work has shown that the level of centromeric RNAs (cenRNAs) is tightly regulated and repressed by the kinetochore protein Cbf1 and histone H2A variant H2A.ZHtz1, and de-repressed during S phase of the cell cycle. Too little or too much cenRNAs will disrupt centromere activity. Here, we discuss the current advance in the understanding of the action and regulation of cenRNAs at the point centromere of Saccharomyces cerevisiae. We further show that budding yeast cenRNAs are cryptic unstable transcripts (CUTs) that can be degraded by the nuclear RNA decay pathway. CenRNA provides an example that even CUTs, when present at the right time with the right level, can serve important cellular functions.
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49
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Abstract
Budding yeast harbors a simple point centromere, which is originally believed to be sequence dependent without much epigenetic regulation and is transcription incompatible, as inserting a strong promoter upstream inactivates the centromere completely. Here, we demonstrate that an optimal level centromeric noncoding RNA is required for budding yeast centromere activity. Centromeric transcription is induced in S phase, coinciding with the assembly of new centromeric proteins. Too much or too little centromeric noncoding RNA leads to centromere malfunction. Overexpression of centromeric noncoding RNA reduces the protein levels and chromatin localization of inner centromere and kinetochore proteins, such as CENP-A, CENP-C, and the chromosome passenger complex. This work shows that point centromere is epigenetically regulated by noncoding RNA. In budding yeast, which possesses simple point centromeres, we discovered that all of its centromeres express long noncoding RNAs (cenRNAs), especially in S phase. Induction of cenRNAs coincides with CENP-ACse4 loading time and is dependent on DNA replication. Centromeric transcription is repressed by centromere-binding factor Cbf1 and histone H2A variant H2A.ZHtz1. Deletion of CBF1 and H2A.ZHTZ1 results in an up-regulation of cenRNAs; an increased loss of a minichromosome; elevated aneuploidy; a down-regulation of the protein levels of centromeric proteins CENP-ACse4, CENP-A chaperone HJURPScm3, CENP-CMif2, SurvivinBir1, and INCENPSli15; and a reduced chromatin localization of CENP-ACse4, CENP-CMif2, and Aurora BIpl1. When the RNA interference system was introduced to knock down all cenRNAs from the endogenous chromosomes, but not the cenRNA from the circular minichromosome, an increase in minichromosome loss was still observed, suggesting that cenRNA functions in trans to regulate centromere activity. CenRNA knockdown partially alleviates minichromosome loss in cbf1Δ, htz1Δ, and cbf1Δ htz1Δ in a dose-dependent manner, demonstrating that cenRNA level is tightly regulated to epigenetically control point centromere function.
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50
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Magnaghi-Jaulin L, Eot-Houllier G, Gallaud E, Giet R. Aurora A Protein Kinase: To the Centrosome and Beyond. Biomolecules 2019; 9:biom9010028. [PMID: 30650622 PMCID: PMC6359016 DOI: 10.3390/biom9010028] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 12/25/2022] Open
Abstract
Accurate chromosome segregation requires the perfect spatiotemporal rearrangement of the cellular cytoskeleton. Isolated more than two decades ago from Drosophila, Aurora A is a widespread protein kinase that plays key roles during cell division. Numerous studies have described the localisation of Aurora A at centrosomes, the mitotic spindle, and, more recently, at mitotic centromeres. In this review, we will summarise the cytoskeletal rearrangements regulated by Aurora A during cell division. We will also discuss the recent discoveries showing that Aurora A also controls not only the dynamics of the cortical proteins but also regulates the centromeric proteins, revealing new roles for this kinase during cell division.
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Affiliation(s)
- Laura Magnaghi-Jaulin
- University of Rennes, CNRS UMR 6290, IGDR-Institute of Genetics and Development of Rennes, F-35000 Rennes, France.
| | - Grégory Eot-Houllier
- University of Rennes, CNRS UMR 6290, IGDR-Institute of Genetics and Development of Rennes, F-35000 Rennes, France.
| | - Emmanuel Gallaud
- University of Rennes, CNRS UMR 6290, IGDR-Institute of Genetics and Development of Rennes, F-35000 Rennes, France.
| | - Régis Giet
- University of Rennes, CNRS UMR 6290, IGDR-Institute of Genetics and Development of Rennes, F-35000 Rennes, France.
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