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Scelfo A, Fachinetti D. Centromere: A Trojan horse for genome stability. DNA Repair (Amst) 2023; 130:103569. [PMID: 37708591 DOI: 10.1016/j.dnarep.2023.103569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Abstract
Centromeres play a key role in the maintenance of genome stability to prevent carcinogenesis and diseases. They are specialized chromosome loci essential to ensure faithful transmission of genomic information across cell generations by mediating the interaction with spindle microtubules. Nonetheless, while fulfilling these essential roles, their distinct repetitive composition and susceptibility to mechanical stresses during cell division render them susceptible to breakage events. In this review, we delve into the present understanding of the underlying causes of centromere fragility, from the mechanisms governing its DNA replication and repair, to the pathways acting to counteract potential challenges. We propose that the centromere represents a "Trojan horse" exerting vital functions that, at the same time, potentially threatens whole genome stability.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
| | - Daniele Fachinetti
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
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2
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Smurova K, Damizia M, Irene C, Stancari S, Berto G, Perticari G, Iacovella MG, D'Ambrosio I, Giubettini M, Philippe R, Baggio C, Callegaro E, Casagranda A, Corsini A, Polese VG, Ricci A, Dassi E, De Wulf P. Rio1 downregulates centromeric RNA levels to promote the timely assembly of structurally fit kinetochores. Nat Commun 2023; 14:3172. [PMID: 37263996 DOI: 10.1038/s41467-023-38920-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/22/2023] [Indexed: 06/03/2023] Open
Abstract
Kinetochores assemble on centromeres via histone H3 variant CENP-A and low levels of centromere transcripts (cenRNAs). The latter are ensured by the downregulation of RNA polymerase II (RNAPII) activity, and cenRNA turnover by the nuclear exosome. Using S. cerevisiae, we now add protein kinase Rio1 to this scheme. Yeast cenRNAs are produced either as short (median lengths of 231 nt) or long (4458 nt) transcripts, in a 1:1 ratio. Rio1 limits their production by reducing RNAPII accessibility and promotes cenRNA degradation by the 5'-3'exoribonuclease Rat1. Rio1 similarly curtails the concentrations of noncoding pericenRNAs. These exist as short transcripts (225 nt) at levels that are minimally two orders of magnitude higher than the cenRNAs. In yeast depleted of Rio1, cen- and pericenRNAs accumulate, CEN nucleosomes and kinetochores misform, causing chromosome instability. The latter phenotypes are also observed with human cells lacking orthologue RioK1, suggesting that CEN regulation by Rio1/RioK1 is evolutionary conserved.
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Affiliation(s)
- Ksenia Smurova
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Michela Damizia
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Carmela Irene
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Stefania Stancari
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Giovanna Berto
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Giulia Perticari
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Maria Giuseppina Iacovella
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milano, Italy
| | - Ilaria D'Ambrosio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Maria Giubettini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Réginald Philippe
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Chiara Baggio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Elisabetta Callegaro
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Andrea Casagranda
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Alessandro Corsini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Vincenzo Gentile Polese
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Anna Ricci
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Peter De Wulf
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy.
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Di X, Xiang L, Jian Z. YAP-mediated mechanotransduction in urinary bladder remodeling: Based on RNA-seq and CUT&Tag. Front Genet 2023; 14:1106927. [PMID: 36741311 PMCID: PMC9895788 DOI: 10.3389/fgene.2023.1106927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
Yes-associated protein (YAP) is an important transcriptional coactivator binding to transcriptional factors that engage in many downstream gene transcription. Partial bladder outlet obstruction (pBOO) causes a massive burden to patients and finally leads to bladder fibrosis. Several cell types engage in the pBOO pathological process, including urothelial cells, smooth muscle cells, and fibroblasts. To clarify the function of YAP in bladder fibrosis, we performed the RNA-seq and CUT&Tag of the bladder smooth muscle cell to analyze the YAP ablation of human bladder smooth muscle cells (hBdSMCs) and immunoprecipitation of YAP. 141 differentially expressed genes (DEGs) were identified through RNA-seq between YAP-knockdown and nature control. After matching with the results of CUT&Tag, 36 genes were regulated directly by YAP. Then we identified the hub genes in the DEGs, including CDCA5, CENPA, DTL, NCAPH, and NEIL3, that contribute to cell proliferation. Thus, our study provides a regulatory network of YAP in smooth muscle proliferation. The possible effects of YAP on hBdSMC might be a vital target for pBOO-associated bladder fibrosis.
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Affiliation(s)
- Xingpeng Di
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liyuan Xiang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, China,Department of Clinical Research Management, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhongyu Jian
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, China,*Correspondence: Zhongyu Jian,
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Kan M, Huang T, Zhao P. Artificial chromosome technology and its potential application in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:970943. [PMID: 36186059 PMCID: PMC9519882 DOI: 10.3389/fpls.2022.970943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Plant genetic engineering and transgenic technology are powerful ways to study the function of genes and improve crop yield and quality in the past few years. However, only a few genes could be transformed by most available genetic engineering and transgenic technologies, so changes still need to be made to meet the demands for high throughput studies, such as investigating the whole genetic pathway of crop traits and avoiding undesirable genes simultaneously in the next generation. Plant artificial chromosome (PAC) technology provides a carrier which allows us to assemble multiple and specific genes to produce a variety of products by minichromosome. However, PAC technology also have limitations that may hinder its further development and application. In this review, we will introduce the current state of PACs technology from PACs formation, factors on PACs formation, problems and potential solutions of PACs and exogenous gene(s) integration.
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Affiliation(s)
- Manman Kan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
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Hofstatter PG, Thangavel G, Lux T, Neumann P, Vondrak T, Novak P, Zhang M, Costa L, Castellani M, Scott A, Toegelová H, Fuchs J, Mata-Sucre Y, Dias Y, Vanzela AL, Huettel B, Almeida CC, Šimková H, Souza G, Pedrosa-Harand A, Macas J, Mayer KF, Houben A, Marques A. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell 2022; 185:3153-3168.e18. [DOI: 10.1016/j.cell.2022.06.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 01/30/2023]
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Liu T, Ma L, Song L, Yan B, Zhang S, Wang B, Zuo N, Sun X, Deng Y, Ren Q, Li Y, Zhou J, Liu Q, Wei L. CENPM upregulation by E5 oncoprotein of human papillomavirus promotes radiosensitivity in head and neck squamous cell carcinoma. Oral Oncol 2022; 129:105858. [DOI: 10.1016/j.oraloncology.2022.105858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/10/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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Kim T. Epigenetic control of centromere: what can we learn from neocentromere? Genes Genomics 2021; 44:317-325. [PMID: 34843088 DOI: 10.1007/s13258-021-01193-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND The centromere is the special region on a chromosome, which serves as the site for assembly of kinetochore complex and is essential for maintaining genomic integrity. Neocentromeres are new centromeres that form on the non-centromeric regions of the chromosome when the natural centromere is disrupted or inactivated. Although neocentromeres lack the typical features found in centromeres, cells with neocentromeres divide normally during mitosis and meiosis. Neocentromeres not only arise naturally but their formation can also be induced experimentally. Therefore, neocentromeres are a great tool for studying functions and formation of centromeres. OBJECTIVE To study neocentromeres and use that knowledge to gain insights into the epigenetic regulation of canonical centromeres. DISCUSSION Here, we review the characteristics of naturally occurring centromeres and neocentromeres and those of experimentally induced neocentromeres. We also discuss the mechanism of centromere formation and epigenetic regulation of centromere function, which we learned from studying the neocentromeres. Although neocentromeres lack main features of centromeres, such as presence of repetitive ⍺-satellite DNA and pericentric heterochromatin, they behave quite similar to the canonical centromere, indicating the epigenetic nature of the centromere. Still, further investigation will help to understand the formation and maintenance of the centromere, and the correlation to human diseases. CONCLUSION Neocentromeres helped us to understand the formation of canonical centromeres. Also, since neocentromeres are associated with certain cancer types, knowledge about them could be helpful to treat cancer.
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Affiliation(s)
- Taekyung Kim
- Department of Biology Education, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Korea.
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Legoff L, D'Cruz SC, Bouchekhchoukha K, Monfort C, Jaulin C, Multigner L, Smagulova F. In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood. Life Sci Alliance 2021; 4:4/6/e202000944. [PMID: 33837044 PMCID: PMC8091598 DOI: 10.26508/lsa.202000944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 01/06/2023] Open
Abstract
In utero exposure to chlordecone affects chromatin and leads to activation of retroelements. This study shows the changes induced by chlordecone in human umbilical cord blood and blood-derived cell line. Environmental factors can induce detrimental consequences into adulthood life. In this study, we examined the epigenetic effects induced by in utero chlordecone (CD) exposure on human male cord blood as well as in blood-derived Ke-37 cell line. Genome-wide analysis of histone H3K4me3 distribution revealed that genes related to chromosome segregation, chromatin organization, and cell cycle have altered occupancy in their promoters. The affected regions were enriched in ESR1, SP family, and IKZF1 binding motifs. We also observed a global reduction in H3K9me3, markedly in repeated sequences of the genome. Decrease in H3K9me3 after CD exposure correlates with decreased methylation in LINE-1 promoters and telomere length extension. These observations on human cord blood were assessed in the Ke-37 human cell line. H3K4me3 and the expression of genes related to immune response, DNA repair, and chromatin organization, which were affected in human cord blood were also altered in CD-exposed Ke-37 cells. Our data suggest that developmental exposure to CD leads to profound changes in histone modification patterns and affects the processes controlled by them in human cord blood.
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Affiliation(s)
- Louis Legoff
- University of Rennes, EHESP, Inserm, Institut de Recherche en Santé, Environnement et Travail (Irset)-UMR_S 1085, Rennes, France
| | - Shereen Cynthia D'Cruz
- University of Rennes, EHESP, Inserm, Institut de Recherche en Santé, Environnement et Travail (Irset)-UMR_S 1085, Rennes, France
| | - Katia Bouchekhchoukha
- University of Rennes, EHESP, Inserm, Institut de Recherche en Santé, Environnement et Travail (Irset)-UMR_S 1085, Rennes, France
| | - Christine Monfort
- University of Rennes, EHESP, Inserm, Institut de Recherche en Santé, Environnement et Travail (Irset)-UMR_S 1085, Rennes, France
| | - Christian Jaulin
- Institut de Génétique et Développement de Rennes, Epigenetics and Cancer Group, UMR 6290 CNRS, Université Rennes 1, Rennes Cedex, France
| | - Luc Multigner
- University of Rennes, EHESP, Inserm, Institut de Recherche en Santé, Environnement et Travail (Irset)-UMR_S 1085, Rennes, France
| | - Fatima Smagulova
- University of Rennes, EHESP, Inserm, Institut de Recherche en Santé, Environnement et Travail (Irset)-UMR_S 1085, Rennes, France
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Nagpal H, Fierz B. The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity? J Mol Biol 2021; 433:166676. [PMID: 33065112 DOI: 10.1016/j.jmb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023]
Abstract
The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epigenetic mark defining the centromere. In this review, we discuss the role of CENP-A on the structure and dynamics of centromeric chromatin. We further discuss the impact of the CENP-A binding proteins CENP-C, CENP-N, and CENP-B on modulating centro-chromatin structure. Based on these findings we provide an overview of the higher order structure of the centromere.
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Affiliation(s)
- Harsh Nagpal
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Wear EE, Song J, Zynda GJ, Mickelson-Young L, LeBlanc C, Lee TJ, Deppong DO, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF. Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots. PLoS Genet 2020; 16:e1008623. [PMID: 33052904 PMCID: PMC7588055 DOI: 10.1371/journal.pgen.1008623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 10/26/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed. In traditional cell division, or mitosis, a cell’s genetic material is duplicated and then split between two daughter cells. In contrast, in some specialized cell types, the DNA is duplicated a second time without an intervening division step, resulting in cells that carry twice as much DNA. This phenomenon, which is called the endocycle, is common during plant development. At each step, DNA replication follows an ordered program in which highly compacted DNA is unraveled and replicated in sections at different times during the synthesis (S) phase. In plants, it is unclear whether traditional and endocycle programs are the same, especially since endocycling cells are typically in the process of differentiation. Using root tips of maize, we found that in comparison to replication in the mitotic cell cycle, there is a small portion of the genome whose replication in the endocycle is shifted in time, usually to later in S phase. Some of these regions are scattered around the genome and mostly coincide with active genes. However, the most prominent shifts occur in centromeres. The shift to later replication in centromeres is noteworthy because they orchestrate the process of separating duplicated chromosomes into daughter cells, a function that is not needed in the endocycle.
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Affiliation(s)
- Emily E. Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Gregory J. Zynda
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chantal LeBlanc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - George C. Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - William F. Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
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Leo L, Marchetti M, Giunta S, Fanti L. Epigenetics as an Evolutionary Tool for Centromere Flexibility. Genes (Basel) 2020; 11:genes11070809. [PMID: 32708654 PMCID: PMC7397245 DOI: 10.3390/genes11070809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022] Open
Abstract
Centromeres are the complex structures responsible for the proper segregation of chromosomes during cell division. Structural or functional alterations of the centromere cause aneuploidies and other chromosomal aberrations that can induce cell death with consequences on health and survival of the organism as a whole. Because of their essential function in the cell, centromeres have evolved high flexibility and mechanisms of tolerance to preserve their function following stress, whether it is originating from within or outside the cell. Here, we review the main epigenetic mechanisms of centromeres’ adaptability to preserve their functional stability, with particular reference to neocentromeres and holocentromeres. The centromere position can shift in response to altered chromosome structures, but how and why neocentromeres appear in a given chromosome region are still open questions. Models of neocentromere formation developed during the last few years will be hereby discussed. Moreover, we will discuss the evolutionary significance of diffuse centromeres (holocentromeres) in organisms such as nematodes. Despite the differences in DNA sequences, protein composition and centromere size, all of these diverse centromere structures promote efficient chromosome segregation, balancing genome stability and adaptability, and ensuring faithful genome inheritance at each cellular generation.
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Affiliation(s)
- Laura Leo
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Marcella Marchetti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Simona Giunta
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Laura Fanti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Correspondence:
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Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:2057-2068. [PMID: 32295767 PMCID: PMC7263675 DOI: 10.1534/g3.120.401131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The evolutionarily conserved centromeric histone H3 variant (Cse4 in budding yeast, CENP-A in humans) is essential for faithful chromosome segregation. Mislocalization of CENP-A to non-centromeric chromatin contributes to chromosomal instability (CIN) in yeast, fly, and human cells and CENP-A is highly expressed and mislocalized in cancers. Defining mechanisms that prevent mislocalization of CENP-A is an area of active investigation. Ubiquitin-mediated proteolysis of overexpressed Cse4 (GALCSE4) by E3 ubiquitin ligases such as Psh1 prevents mislocalization of Cse4, and psh1 Δ strains display synthetic dosage lethality (SDL) with GALCSE4 We previously performed a genome-wide screen and identified five alleles of CDC7 and DBF4 that encode the Dbf4-dependent kinase (DDK) complex, which regulates DNA replication initiation, among the top twelve hits that displayed SDL with GALCSE4 We determined that cdc7 -7 strains exhibit defects in ubiquitin-mediated proteolysis of Cse4 and show mislocalization of Cse4 Mutation of MCM5 (mcm5 -bob1) bypasses the requirement of Cdc7 for replication initiation and rescues replication defects in a cdc7 -7 strain. We determined that mcm5 -bob1 does not rescue the SDL and defects in proteolysis of GALCSE4 in a cdc7 -7 strain, suggesting a DNA replication-independent role for Cdc7 in Cse4 proteolysis. The SDL phenotype, defects in ubiquitin-mediated proteolysis, and the mislocalization pattern of Cse4 in a cdc7 -7 psh1 Δ strain were similar to that of cdc7 -7 and psh1 Δ strains, suggesting that Cdc7 regulates Cse4 in a pathway that overlaps with Psh1 Our results define a DNA replication initiation-independent role of DDK as a regulator of Psh1-mediated proteolysis of Cse4 to prevent mislocalization of Cse4.
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