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Estill M, Hauser R, Nassan FL, Moss A, Krawetz SA. The effects of di-butyl phthalate exposure from medications on human sperm RNA among men. Sci Rep 2019; 9:12397. [PMID: 31455814 PMCID: PMC6711971 DOI: 10.1038/s41598-019-48441-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/05/2019] [Indexed: 02/08/2023] Open
Abstract
Endocrine disruptors, such as phthalates, are suspected of affecting reproductive function. The Mesalamine and Reproductive Health Study (MARS) was designed to address the physiological effect of in vivo phthalate exposure on male reproduction in patients with Inflammatory Bowel Disease (IBD). As part of this effort, the effect on sperm RNAs to DBP exposure were longitudinally assessed using a cross-over cross-back binary design of high or background, exposures to DBP. As the DBP level was altered, numerous sperm RNA elements (REs) were differentially expressed, suggesting that exposure to or removal from high DBP produces effects that require longer than one spermatogenic cycle to resolve. In comparison, small RNAs were minimally affected by DBP exposure. While initial study medication (high or background) implicates different biological pathways, initiation on the high-DBP condition activated oxidative stress and DNA damage pathways. The negative correlation of REs with specific genomic repeats suggests a regulatory role. Using ejaculated sperm, this work provides insight into the male germline's response to phthalate exposure.
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Affiliation(s)
- Molly Estill
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Russ Hauser
- Vincent Memorial Obstetrics and Gynecology Service, Massachusetts General Hospital, Harvard Medical School, and Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Feiby L Nassan
- Departments of Environmental Health and Nutrition, Harvard T. H. Chan School of Public Health, MA, 02115, USA
| | - Alan Moss
- Department of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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Sharma AB, Dimitrov S, Hamiche A, Van Dyck E. Centromeric and ectopic assembly of CENP-A chromatin in health and cancer: old marks and new tracks. Nucleic Acids Res 2019; 47:1051-1069. [PMID: 30590707 PMCID: PMC6379705 DOI: 10.1093/nar/gky1298] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 12/20/2022] Open
Abstract
The histone H3 variant CENP-A confers epigenetic identity to the centromere and plays crucial roles in the assembly and function of the kinetochore, thus ensuring proper segregation of our chromosomes. CENP-A containing nucleosomes exhibit unique structural specificities and lack the complex profile of gene expression-associated histone posttranslational modifications found in canonical histone H3 and the H3.3 variant. CENP-A mislocalization into noncentromeric regions resulting from its overexpression leads to chromosomal segregation aberrations and genome instability. Overexpression of CENP-A is a feature of many cancers and is associated with malignant progression and poor outcome. The recent years have seen impressive progress in our understanding of the mechanisms that orchestrate CENP-A deposition at native centromeres and ectopic loci. They have witnessed the description of novel, heterotypic CENP-A/H3.3 nucleosome particles and the exploration of the phenotypes associated with the deregulation of CENP-A and its chaperones in tumor cells. Here, we review the structural specificities of CENP-A nucleosomes, the epigenetic features that characterize the centrochromatin and the mechanisms and factors that orchestrate CENP-A deposition at centromeres. We then review our knowledge of CENP-A ectopic distribution, highlighting experimental strategies that have enabled key discoveries. Finally, we discuss the implications of deregulated CENP-A in cancer.
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Affiliation(s)
- Abhishek Bharadwaj Sharma
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé-Allée des Alpes, 38700 La Tronche, France.,Izmir Biomedicine and Genome Center, İzmir, Turkey
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Eric Van Dyck
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
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Nishimura K, Cho Y, Tokunaga K, Nakao M, Tani T, Ideue T. DEAH box RNA helicase DHX38 associates with satellite I noncoding RNA involved in chromosome segregation. Genes Cells 2019; 24:585-590. [PMID: 31166646 DOI: 10.1111/gtc.12707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/29/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
Abstract
Noncoding (nc) RNA called satellite I is transcribed from the human centromere region. Depletion of this ncRNA results in abnormal nuclear morphology because of defects in chromosome segregation. Some protein factors interact with this ncRNA and function as a component of a nc ribonucleoprotein (RNP) complex in mitotic regulation. Here, we found that DHX38, a pre-mRNA splicing-related DEAH box RNA helicase, interacts with satellite I ncRNA. Depletion of DHX38 resulted in defective chromosome segregation similar to knockdown of satellite I ncRNA. Interaction between DHX38 and ncRNA was interphase-specific, but DHX38 depletion affected the function of Aurora B, which associated with satellite I ncRNA at mitotic phase. Based on these findings, we suggest that DHX38 has a role in mitotic regulation as a component of the satellite I ncRNP complex at interphase.
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Affiliation(s)
- Kanako Nishimura
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Yukiko Cho
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Kazuaki Tokunaga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto, Japan
| | - Tokio Tani
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Takashi Ideue
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
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Duda Z, Trusiak S, O'Neill R. Centromere Transcription: Means and Motive. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:257-281. [PMID: 28840241 DOI: 10.1007/978-3-319-58592-5_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The chromosome biology field at large has benefited from studies of the cell cycle components, protein cascades and genomic landscape that are required for centromere identity, assembly and stable transgenerational inheritance. Research over the past 20 years has challenged the classical descriptions of a centromere as a stable, unmutable, and transcriptionally silent chromosome component. Instead, based on studies from a broad range of eukaryotic species, including yeast, fungi, plants, and animals, the centromere has been redefined as one of the more dynamic areas of the eukaryotic genome, requiring coordination of protein complex assembly, chromatin assembly, and transcriptional activity in a cell cycle specific manner. What has emerged from more recent studies is the realization that the transcription of specific types of nucleic acids is a key process in defining centromere integrity and function. To illustrate the transcriptional landscape of centromeres across eukaryotes, we focus this review on how transcripts interact with centromere proteins, when in the cell cycle centromeric transcription occurs, and what types of sequences are being transcribed. Utilizing data from broadly different organisms, a picture emerges that places centromeric transcription as an integral component of centromere function.
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Affiliation(s)
- Zachary Duda
- Department of Molecular and Cell Biology, The Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | - Sarah Trusiak
- Department of Molecular and Cell Biology, The Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | - Rachel O'Neill
- Department of Molecular and Cell Biology, The Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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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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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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Smurova K, De Wulf P. Centromere and Pericentromere Transcription: Roles and Regulation … in Sickness and in Health. Front Genet 2018; 9:674. [PMID: 30627137 PMCID: PMC6309819 DOI: 10.3389/fgene.2018.00674] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/04/2018] [Indexed: 12/26/2022] Open
Abstract
The chromosomal loci known as centromeres (CEN) mediate the equal distribution of the duplicated genome between both daughter cells. Specifically, centromeres recruit a protein complex named the kinetochore, that bi-orients the replicated chromosome pairs to the mitotic or meiotic spindle structure. The paired chromosomes are then separated, and the individual chromosomes segregate in opposite direction along the regressing spindle into each daughter cell. Erroneous kinetochore assembly or activity produces aneuploid cells that contain an abnormal number of chromosomes. Aneuploidy may incite cell death, developmental defects (including genetic syndromes), and cancer (>90% of all cancer cells are aneuploid). While kinetochores and their activities have been preserved through evolution, the CEN DNA sequences have not. Hence, to be recognized as sites for kinetochore assembly, CEN display conserved structural themes. In addition, CEN nucleosomes enclose a CEN-exclusive variant of histone H3, named CENP-A, and carry distinct epigenetic labels on CENP-A and the other CEN histone proteins. Through the cell cycle, CEN are transcribed into non-coding RNAs. After subsequent processing, they become key components of the CEN chromatin by marking the CEN locus and by stably anchoring the CEN-binding kinetochore proteins. CEN transcription is tightly regulated, of low intensity, and essential for differentiation and development. Under- or overexpression of CEN transcripts, as documented for myriad cancers, provoke chromosome missegregation and aneuploidy. CEN are genetically stable and fully competent only when they are insulated from the surrounding, pericentromeric chromatin, which must be silenced. We will review CEN transcription and its contribution to faithful kinetochore function. We will further discuss how pericentromeric chromatin is silenced by RNA processing and transcriptionally repressive chromatin marks. We will report on the transcriptional misregulation of (peri)centromeres during stress, natural aging, and disease and reflect on whether their transcripts can serve as future diagnostic tools and anti-cancer targets in the clinic.
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Affiliation(s)
- Ksenia Smurova
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Peter De Wulf
- Centre for Integrative Biology, University of Trento, Trento, Italy
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Shukla M, Tong P, White SA, Singh PP, Reid AM, Catania S, Pidoux AL, Allshire RC. Centromere DNA Destabilizes H3 Nucleosomes to Promote CENP-A Deposition during the Cell Cycle. Curr Biol 2018; 28:3924-3936.e4. [PMID: 30503616 PMCID: PMC6303189 DOI: 10.1016/j.cub.2018.10.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 09/12/2018] [Accepted: 10/22/2018] [Indexed: 12/31/2022]
Abstract
Active centromeres are defined by the presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location, CENP-A chromatin and kinetochores are maintained at that location through a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication. Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences. Intrinsic properties of centromeric DNA may favor the assembly of CENP-A rather than H3 nucleosomes. Here we investigate histone dynamics on centromere DNA. We show that during S phase, histone H3 is deposited as a placeholder at fission yeast centromeres and is subsequently evicted in G2, when we detect deposition of the majority of new CENP-ACnp1. We also find that centromere DNA has an innate property of driving high rates of turnover of H3-containing nucleosomes, resulting in low nucleosome occupancy. When placed at an ectopic chromosomal location in the absence of any CENP-ACnp1 assembly, centromere DNA appears to retain its ability to impose S phase deposition and G2 eviction of H3, suggesting that features within centromere DNA program H3 dynamics. Because RNA polymerase II (RNAPII) occupancy on this centromere DNA coincides with H3 eviction in G2, we propose a model in which RNAPII-coupled chromatin remodeling promotes replacement of H3 with CENP-ACnp1 nucleosomes.
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Affiliation(s)
- Manu Shukla
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Pin Tong
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sharon A White
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Puneet P Singh
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Angus M Reid
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sandra Catania
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alison L Pidoux
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Robin C Allshire
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK.
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59
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The Behavior of the Maize B Chromosome and Centromere. Genes (Basel) 2018; 9:genes9100476. [PMID: 30275397 PMCID: PMC6210970 DOI: 10.3390/genes9100476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/16/2018] [Accepted: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
The maize B chromosome is a non-essential chromosome with an accumulation mechanism. The dispensable nature of the B chromosome facilitates many types of genetic studies in maize. Maize lines with B chromosomes have been widely used in studies of centromere functions. Here, we discuss the maize B chromosome alongside the latest progress of B centromere activities, including centromere misdivision, inactivation, reactivation, and de novo centromere formation. The meiotic features of the B centromere, related to mini-chromosomes and the control of the size of the maize centromere, are also discussed.
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60
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Abstract
Accurate chromosome segregation is a fundamental process in cell biology. During mitosis, chromosomes are segregated into daughter cells through interactions between centromeres and microtubules in the mitotic spindle. Centromere domains have evolved to nucleate formation of the kinetochore, which is essential for establishing connections between chromosomal DNA and microtubules during mitosis. Centromeres are typically formed on highly repetitive DNA that is not conserved in sequence or size among organisms and can differ substantially between individuals within the same organism. However, transcription of repetitive DNA has emerged as a highly conserved property of the centromere. Recent work has shown that both the topological effect of transcription on chromatin and the nascent noncoding RNAs contribute to multiple aspects of centromere function. In this review, we discuss the fundamental aspects of centromere transcription, i.e., its dual role in chromatin remodeling/CENP-A deposition and kinetochore assembly during mitosis, from a cell cycle perspective.
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Affiliation(s)
- Carlos Perea-Resa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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61
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Novais-Cruz M, Alba Abad M, van IJcken WFJ, Galjart N, Jeyaprakash AA, Maiato H, Ferrás C. Mitotic progression, arrest, exit or death relies on centromere structural integrity, rather than de novo transcription. eLife 2018; 7:36898. [PMID: 30080136 PMCID: PMC6128689 DOI: 10.7554/elife.36898] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/03/2018] [Indexed: 12/30/2022] Open
Abstract
Recent studies have challenged the prevailing dogma that transcription is repressed during mitosis. Transcription was also proposed to sustain a robust spindle assembly checkpoint (SAC) response. Here, we used live-cell imaging of human cells, RNA-seq and qPCR to investigate the requirement for de novo transcription during mitosis. Under conditions of persistently unattached kinetochores, transcription inhibition with actinomycin D, or treatment with other DNA-intercalating drugs, delocalized the chromosomal passenger complex (CPC) protein Aurora B from centromeres, compromising SAC signaling and cell fate. However, we were unable to detect significant changes in mitotic transcript levels. Moreover, inhibition of transcription independently of DNA intercalation had no effect on Aurora B centromeric localization, SAC response, mitotic progression, exit or death. Mechanistically, we show that DNA intercalating agents reduce the interaction of the CPC with nucleosomes. Thus, mitotic progression, arrest, exit or death is determined by centromere structural integrity, rather than de novo transcription.
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Affiliation(s)
- Marco Novais-Cruz
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
| | - Maria Alba Abad
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Niels Galjart
- Department of Cell BiologyErasmus Medical CenterRotterdamNetherlands
| | - A Arockia Jeyaprakash
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | - Helder Maiato
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
- Cell Division Group, Experimental Biology Unit, Department of Biomedicine, Faculdade de MedicinaUniversidade do PortoPortoPortugal
| | - Cristina Ferrás
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
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62
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Talbert PB, Henikoff S. Transcribing Centromeres: Noncoding RNAs and Kinetochore Assembly. Trends Genet 2018; 34:587-599. [DOI: 10.1016/j.tig.2018.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 12/20/2022]
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Cho Y, Ideue T, Nagayama M, Araki N, Tani T. RBMX is a component of the centromere noncoding RNP complex involved in cohesion regulation. Genes Cells 2018; 23:172-184. [PMID: 29383807 DOI: 10.1111/gtc.12562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/25/2017] [Indexed: 12/31/2022]
Abstract
Satellite I RNA, a noncoding (nc)RNA transcribed from repetitive regions in human centromeres, binds to Aurora kinase B and forms a ncRNP complex required for chromosome segregation. To examine its function in this process, we purified satellite I ncRNP complex from nuclear extracts prepared from asynchronized or mitotic (M) phase-arrested HeLa cells and then carried out LC/MS to identify proteins bound to satellite I RNA. RBMX (RNA-binding motif protein, X-linked), which was isolated from M phase-arrested cells, was selected for further characterization. We found that RBMX associates with satellite I RNA only during M phase. Knockdown of RBMX induced premature separation of sister chromatid cohesion and abnormal nuclear division. Likewise, knockdown of satellite I RNA also caused premature separation of sister chromatids during M phase. The amounts of RBMX and Sororin, a cohesion regulator, were reduced in satellite I RNA-depleted cells. These results suggest that satellite I RNA plays a role in stabilizing RBMX and Sororin in the ncRNP complex to maintain proper sister chromatid cohesion.
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Affiliation(s)
- Yukiko Cho
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Takashi Ideue
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Megumi Nagayama
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Norie Araki
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tokio Tani
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
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Vertii A, Kaufman PD, Hehnly H, Doxsey S. New dimensions of asymmetric division in vertebrates. Cytoskeleton (Hoboken) 2018; 75:87-102. [DOI: 10.1002/cm.21434] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/20/2017] [Accepted: 01/16/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Anastassiia Vertii
- Department of MolecularCell and Cancer Biology University of Massachusetts Medical SchoolWorcester Massachusetts
| | - Paul D. Kaufman
- Department of MolecularCell and Cancer Biology University of Massachusetts Medical SchoolWorcester Massachusetts
| | - Heidi Hehnly
- Department of Cell and Developmental BiologySUNY Upstate Medical UniversitySyracuse New York13210
| | - Stephen Doxsey
- Program in Molecular Medicine University of Massachusetts Medical SchoolWorcester Massachusetts
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65
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Saha P, Verma S, Pathak RU, Mishra RK. Long Noncoding RNAs in Mammalian Development and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:155-198. [PMID: 28815540 DOI: 10.1007/978-981-10-5203-3_6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively. These transcripts regulate epigenetic processes and constitute an important layer of regulatory information essential for organismal development and play a causative role in diseases. The noncoding RNA-directed regulatory circuit controls complex characteristics. Sequence variations in noncoding RNAs influence evolution, quantitative traits, and disease susceptibility. This chapter presents an account on a class of such noncoding transcripts that are longer than 200 nucleotides (long noncoding RNA-lncRNA) in mammalian development and diseases.
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Affiliation(s)
- Parna Saha
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Shreekant Verma
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Rashmi U Pathak
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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66
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Affiliation(s)
- Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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67
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Hindriksen S, Lens SMA, Hadders MA. The Ins and Outs of Aurora B Inner Centromere Localization. Front Cell Dev Biol 2017; 5:112. [PMID: 29312936 PMCID: PMC5743930 DOI: 10.3389/fcell.2017.00112] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/04/2017] [Indexed: 01/12/2023] Open
Abstract
Error-free chromosome segregation is essential for the maintenance of genomic integrity during cell division. Aurora B, the enzymatic subunit of the Chromosomal Passenger Complex (CPC), plays a crucial role in this process. In early mitosis Aurora B localizes predominantly to the inner centromere, a specialized region of chromatin that lies at the crossroads between the inter-kinetochore and inter-sister chromatid axes. Two evolutionarily conserved histone kinases, Haspin and Bub1, control the positioning of the CPC at the inner centromere and this location is thought to be crucial for the CPC to function. However, recent studies sketch a subtler picture, in which not all functions of the CPC require strict confinement to the inner centromere. In this review we discuss the molecular pathways that direct Aurora B to the inner centromere and deliberate if and why this specific localization is important for Aurora B function.
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Affiliation(s)
- Sanne Hindriksen
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Susanne M A Lens
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Michael A Hadders
- Oncode Institute, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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68
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McNulty SM, Sullivan LL, Sullivan BA. Human Centromeres Produce Chromosome-Specific and Array-Specific Alpha Satellite Transcripts that Are Complexed with CENP-A and CENP-C. Dev Cell 2017; 42:226-240.e6. [PMID: 28787590 DOI: 10.1016/j.devcel.2017.07.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/24/2017] [Accepted: 07/03/2017] [Indexed: 11/28/2022]
Abstract
Human centromeres are defined by alpha satellite DNA arrays that are distinct and chromosome specific. Most human chromosomes contain multiple alpha satellite arrays that are competent for centromere assembly. Here, we show that human centromeres are defined by chromosome-specific RNAs linked to underlying organization of distinct alpha satellite arrays. Active and inactive arrays on the same chromosome produce discrete sets of transcripts in cis. Non-coding RNAs produced from active arrays are complexed with CENP-A and CENP-C, while inactive-array transcripts associate with CENP-B and are generally less stable. Loss of CENP-A does not affect transcript abundance or stability. However, depletion of array-specific RNAs reduces CENP-A and CENP-C at the targeted centromere via faulty CENP-A loading, arresting cells before mitosis. This work shows that each human alpha satellite array produces a unique set of non-coding transcripts, and RNAs present at active centromeres are necessary for kinetochore assembly and cell-cycle progression.
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Affiliation(s)
- Shannon M McNulty
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lori L Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Division of Human Genetics, Duke University Medical Center, Durham, NC 27710, USA.
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69
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Garcia-Silva MR, Sollelis L, MacPherson CR, Stanojcic S, Kuk N, Crobu L, Bringaud F, Bastien P, Pagès M, Scherf A, Sterkers Y. Identification of the centromeres of Leishmania major: revealing the hidden pieces. EMBO Rep 2017; 18:1968-1977. [PMID: 28935715 DOI: 10.15252/embr.201744216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/15/2017] [Accepted: 08/28/2017] [Indexed: 01/16/2023] Open
Abstract
Leishmania affects millions of people worldwide. Its genome undergoes constitutive mosaic aneuploidy, a type of genomic plasticity that may serve as an adaptive strategy to survive distinct host environments. We previously found high rates of asymmetric chromosome allotments during mitosis that lead to the generation of such ploidy. However, the underlying molecular events remain elusive. Centromeres and kinetochores most likely play a key role in this process, yet their identification has failed using classical methods. Our analysis of the unconventional kinetochore complex recently discovered in Trypanosoma brucei (KKTs) leads to the identification of a Leishmania KKT gene candidate (LmKKT1). The GFP-tagged LmKKT1 displays "kinetochore-like" dynamics of intranuclear localization throughout the cell cycle. By ChIP-Seq assay, one major peak per chromosome is revealed, covering a region of 4 ±2 kb. We find two largely conserved motifs mapping to 14 of 36 chromosomes while a higher density of retroposons are observed in 27 of 36 centromeres. The identification of centromeres and of a kinetochore component of Leishmania chromosomes opens avenues to explore their role in mosaic aneuploidy.
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Affiliation(s)
- Maria-Rosa Garcia-Silva
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lauriane Sollelis
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Cameron Ross MacPherson
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Slavica Stanojcic
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Nada Kuk
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lucien Crobu
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), University of Bordeaux, Bordeaux, France.,CNRS, UMR 5234, Bordeaux, France
| | - Patrick Bastien
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
| | - Michel Pagès
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Artur Scherf
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Yvon Sterkers
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France .,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
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70
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Acharya S, Hartmann M, Erhardt S. Chromatin-associated noncoding RNAs in development and inheritance. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28840663 DOI: 10.1002/wrna.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs. Together, various ncRNAs establish many mitotically heritable epigenetic marks during development. Additionally, they participate in mechanisms that regulate maintenance of these epigenetic marks during the lifespan of the organism. Interestingly, some epigenetic traits are transmitted to the next generation(s) via paramutations or transgenerational inheritance mediated by sRNAs. In this review, we give an overview of the various functions and regulations of ncRNAs and the mechanisms they employ in the establishment and maintenance of epigenetic marks and multi-generational transmission of epigenetic traits. WIREs RNA 2017, 8:e1435. doi: 10.1002/wrna.1435 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sreemukta Acharya
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Mark Hartmann
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
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71
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Johnson WL, Yewdell WT, Bell JC, McNulty SM, Duda Z, O'Neill RJ, Sullivan BA, Straight AF. RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin. eLife 2017; 6. [PMID: 28760200 PMCID: PMC5538822 DOI: 10.7554/elife.25299] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 06/07/2017] [Indexed: 12/15/2022] Open
Abstract
Heterochromatin formed by the SUV39 histone methyltransferases represses transcription from repetitive DNA sequences and ensures genomic stability. How SUV39 enzymes localize to their target genomic loci remains unclear. Here, we demonstrate that chromatin-associated RNA contributes to the stable association of SUV39H1 with constitutive heterochromatin in human cells. We find that RNA associated with mitotic chromosomes is concentrated at pericentric heterochromatin, and is encoded, in part, by repetitive α-satellite sequences, which are retained in cis at their transcription sites. Purified SUV39H1 directly binds nucleic acids through its chromodomain; and in cells, SUV39H1 associates with α-satellite RNA transcripts. Furthermore, nucleic acid binding mutants destabilize the association of SUV39H1 with chromatin in mitotic and interphase cells – effects that can be recapitulated by RNase treatment or RNA polymerase inhibition – and cause defects in heterochromatin function. Collectively, our findings uncover a previously unrealized function for chromatin-associated RNA in regulating constitutive heterochromatin in human cells. DOI:http://dx.doi.org/10.7554/eLife.25299.001 Each cell in a human body contains the same DNA sequence, which serves as a set of instructions for how the body should develop and operate. However, only certain sections of DNA are “active” at any particular time and in any given type of cell. When a section of DNA is active, cells make many copies of it using a molecule called RNA. When a section of DNA in inactive, very little RNA is made. Some sections of DNA must always be kept inactive to avoid damaging the cell. DNA is packaged around proteins called histones, and enzymes that modify histones control which sections of DNA are switched on or off. One such modifying enzyme, called SUV39H1, is important for inactivating sections of DNA that could cause harm to the cell if they are active. Previous studies showed that the loss of SUV39H1 and related proteins cause abnormalities and cancer in mice. However, it is not clear how this enzyme identifies and inactivates the DNA it needs to target. Johnson, Yewdell et al. studied SUV39H1 in human cells. The experiments show that RNA binds to the SUV39H1 enzyme and controls how it interacts with DNA. Specifically, Johnson, Yewdell et al. found that sections of DNA that are inactive can still make a small amount of RNA, and that this RNA tethers SUV39H1 to the DNA to keep the DNA switched off. Mutant forms of SUV39H1 that are unable to interact with RNA fall off the DNA, which allows DNA sequences that are normally switched off to become active. The findings of Johnson, Yewdell et al. reveal a new role for RNAs in regulating whether DNA is switched on or off. The next step is to determine whether other enzymes that can also modify histones use the same mechanism to activate or inactivate DNA. Differences in how the activity of DNA is regulated between individuals plays a crucial role in generating the diversity we see in nature. Therefore, this work helps us to understand our basic biology and may provide new opportunities for treating disease. DOI:http://dx.doi.org/10.7554/eLife.25299.002
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Affiliation(s)
- Whitney L Johnson
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - William T Yewdell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Jason C Bell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Shannon M McNulty
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
| | - Zachary Duda
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute for Systems Genomics, University of Connecticut, Storrs, United States
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute for Systems Genomics, University of Connecticut, Storrs, United States
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, United States
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
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72
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Fukagawa T. Critical histone post-translational modifications for centromere function and propagation. Cell Cycle 2017; 16:1259-1265. [PMID: 28598241 DOI: 10.1080/15384101.2017.1325044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The centromere is a critical genomic region that enables faithful chromosome segregation during mitosis, and must be distinguishable from other genomic regions to facilitate establishment of the kinetochore. The centromere-specific histone H3-variant CENP-A forms a special nucleosome that functions as a marker for centromere specification. In addition to the CENP-A nucleosomes, there are additional H3 nucleosomes that have been identified in centromeres, both of which are predicted to exhibit specific features. It is likely that the composite organization of CENP-A and H3 nucleosomes contributes to the formation of centromere-specific chromatin, termed 'centrochromatin'. Recent studies suggest that centrochromatin has specific histone modifications that mediate centromere specification and kinetochore assembly. We use chicken non-repetitive centromeres as a model of centromeric activities to characterize functional features of centrochromatin. This review discusses our recent progress, and that of various other research groups, in elucidating the functional roles of histone modifications in centrochromatin.
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Affiliation(s)
- Tatsuo Fukagawa
- a Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka , Japan
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73
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Chen CC, Mellone BG. Chromatin assembly: Journey to the CENter of the chromosome. J Cell Biol 2017; 214:13-24. [PMID: 27377247 PMCID: PMC4932374 DOI: 10.1083/jcb.201605005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/14/2016] [Indexed: 11/22/2022] Open
Abstract
All eukaryotic genomes are packaged into basic units of DNA wrapped around histone proteins called nucleosomes. The ability of histones to specify a variety of epigenetic states at defined chromatin domains is essential for cell survival. The most distinctive type of chromatin is found at centromeres, which are marked by the centromere-specific histone H3 variant CENP-A. Many of the factors that regulate CENP-A chromatin have been identified; however, our understanding of the mechanisms of centromeric nucleosome assembly, maintenance, and reorganization remains limited. This review discusses recent insights into these processes and draws parallels between centromeric and noncentromeric chromatin assembly mechanisms.
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Affiliation(s)
- Chin-Chi Chen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
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74
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Cáceres-Gutiérrez R, Herrera LA. Centromeric Non-coding Transcription: Opening the Black Box of Chromosomal Instability? Curr Genomics 2017; 18:227-235. [PMID: 28603453 PMCID: PMC5439370 DOI: 10.2174/1389202917666161102095508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/01/2016] [Accepted: 10/27/2016] [Indexed: 02/05/2023] Open
Abstract
In eukaryotes, mitosis is tightly regulated to avoid the generation of numerical chromosome aberrations, or aneuploidies. The aneuploid phenotype is a consequence of chromosomal instability (CIN), i.e., an enhanced rate of chromosome segregation errors, which is frequently found in cancer cells and is associated with tumor aggressiveness and increased tumor cell survival potential. To avoid the generation of aneuploidies, cells rely on the spindle assembly checkpoint (SAC), a widely conserved mechanism that protects the genome against this type of error. This signaling pathway stops mitotic pro-gression before anaphase until all chromosomes are correctly attached to spindle microtubules. Howev-er, impairment of the SAC cannot account for the establishment of CIN because cells bearing this phe-notype have a functional SAC. Hence, in cells with CIN, anaphase is not triggered until all chromo-somes are correctly attached to spindle microtubules and congressed at the metaphase plate. Thus, an in-teresting question arises: What mechanisms actually mediate CIN in cancer cells? Recent research has shown that some pathways involved in chromosome segregation are closely associated to centromere-encoded non-coding RNA (cencRNA) and that these RNAs are deregulated in abnormal conditions, such as cancer. These mechanisms may provide new explanations for chromosome segregation errors. The present review discusses some of these findings and proposes novel mechanisms for the establish-ment of CIN based on regulation by cencRNA.
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Affiliation(s)
- Rodrigo Cáceres-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexicocity, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexicocity, Mexico
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75
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Abstract
Genomic variation is a source of functional diversity that is typically studied in genic and non-coding regulatory regions. However, the extent of variation within noncoding portions of the human genome, particularly highly repetitive regions, and the functional consequences are not well understood. Satellite DNA, including α satellite DNA found at human centromeres, comprises up to 10% of the genome, but is difficult to study because its repetitive nature hinders contiguous sequence assemblies. We recently described variation within α satellite DNA that affects centromere function. On human chromosome 17 (HSA17), we showed that size and sequence polymorphisms within primary array D17Z1 are associated with chromosome aneuploidy and defective centromere architecture. However, HSA17 can counteract this instability by assembling the centromere at a second, "backup" array lacking variation. Here, we discuss our findings in a broader context of human centromere assembly, and highlight areas of future study to uncover links between genomic and epigenetic features of human centromeres.
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Affiliation(s)
- Lori L Sullivan
- a Department of Molecular Genetics and Microbiology , Duke University Medical Center , Durham , NC , USA
| | - Kimberline Chew
- a Department of Molecular Genetics and Microbiology , Duke University Medical Center , Durham , NC , USA
| | - Beth A Sullivan
- a Department of Molecular Genetics and Microbiology , Duke University Medical Center , Durham , NC , USA
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76
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CENP-A chromatin disassembly in stressed and senescent murine cells. Sci Rep 2017; 7:42520. [PMID: 28186195 PMCID: PMC5301216 DOI: 10.1038/srep42520] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/11/2017] [Indexed: 12/25/2022] Open
Abstract
Centromeres are chromosomal domains essential for genomic stability. We report here the remarkable transcriptional and epigenetic perturbations at murine centromeres in genotoxic stress conditions. A strong and selective transcriptional activation of centromeric repeats is detected within hours. This is followed by disorganization of centromeres with striking delocalization of nucleosomal CENP-A, the key determinant of centromere identity and function, in a mechanism requiring active transcription of centromeric repeats, the DNA Damage Response (DDR) effector ATM and chromatin remodelers/histone chaperones. In the absence of p53 checkpoint, activated transcription of centromeric repeats and CENP-A delocalization do not occur and cells accumulate micronuclei indicative of genomic instability. In addition, activated transcription and loss of centromeres identity are features of permanently arrested senescent cells with persistent DDR activation. Together, these findings bring out cooperation between DDR effectors and loss of centromere integrity as a safeguard mechanism to prevent genomic instability in context of persistent DNA damage signalling.
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77
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García Del Arco A, Erhardt S. Post-translational Modifications of Centromeric Chromatin. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:213-231. [PMID: 28840239 DOI: 10.1007/978-3-319-58592-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Regulation of chromatin structures is important for the control of DNA processes such as gene expression, and misregulation of chromatin is implicated in diverse diseases. Covalent post-translational modifications of histones are a prominent way to regulate chromatin structure and different chromatin regions bear their specific signature of histone modifications. The composition of centromeric chromatin is significantly different from other chromatin structures and mainly defined by the presence of the histone H3-variant CENP-A. Here we summarize the composition of centromeric chromatin and what we know about its differential regulation by post-translational modifications.
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Affiliation(s)
- Ana García Del Arco
- Center for Molecular Biology of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
- Cell Networks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
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78
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Long Noncoding RNA: Genome Organization and Mechanism of Action. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:47-74. [PMID: 28815536 DOI: 10.1007/978-981-10-5203-3_2] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For the last four decades, we have known that noncoding RNAs maintain critical housekeeping functions such as transcription, RNA processing, and translation. However, in the late 1990s and early 2000s, the advent of high-throughput sequencing technologies and computational tools to analyze these large sequencing datasets facilitated the discovery of thousands of small and long noncoding RNAs (lncRNAs) and their functional role in diverse biological functions. For example, lncRNAs have been shown to regulate dosage compensation, genomic imprinting, pluripotency, cell differentiation and development, immune response, etc. Here we review how lncRNAs bring about such copious functions by employing diverse mechanisms such as translational inhibition, mRNA degradation, RNA decoys, facilitating recruitment of chromatin modifiers, regulation of protein activity, regulating the availability of miRNAs by sponging mechanism, etc. In addition, we provide a detailed account of different mechanisms as well as general principles by which lncRNAs organize functionally different nuclear sub-compartments and their impact on nuclear architecture.
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79
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Jarroux J, Morillon A, Pinskaya M. History, Discovery, and Classification of lncRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:1-46. [PMID: 28815535 DOI: 10.1007/978-981-10-5203-3_1] [Citation(s) in RCA: 562] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s. Thirty years later, the first regulatory non-coding RNAs (ncRNAs) were initially identified in bacteria and then in most eukaryotic organisms. A few long ncRNAs (lncRNAs) such as H19 and Xist were characterized in the pre-genomic era but remained exceptions until the early 2000s. Indeed, when the sequence of the human genome was published in 2001, studies showed that only about 1.2% encodes proteins, the rest being deemed "non-coding." It was later shown that the genome is pervasively transcribed into many ncRNAs, but their functionality remained controversial. Since then, regulatory lncRNAs have been characterized in many species and were shown to be involved in processes such as development and pathologies, revealing a new layer of regulation in eukaryotic cells. This newly found focus on lncRNAs, together with the advent of high-throughput sequencing, was accompanied by the rapid discovery of many novel transcripts which were further characterized and classified according to specific transcript traits.In this review, we will discuss the many discoveries that led to the study of lncRNAs, from Friedrich Miescher's "nuclein" in 1869 to the elucidation of the human genome and transcriptome in the early 2000s. We will then focus on the biological relevance during lncRNA evolution and describe their basic features as genes and transcripts. Finally, we will present a non-exhaustive catalogue of lncRNA classes, thus illustrating the vast complexity of eukaryotic transcriptomes.
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Affiliation(s)
- Julien Jarroux
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France.
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
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80
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Radford SJ, Nguyen AL, Schindler K, McKim KS. The chromosomal basis of meiotic acentrosomal spindle assembly and function in oocytes. Chromosoma 2016; 126:351-364. [PMID: 27837282 DOI: 10.1007/s00412-016-0618-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 12/20/2022]
Abstract
Several aspects of meiosis are impacted by the absence of centrosomes in oocytes. Here, we review four aspects of meiosis I that are significantly affected by the absence of centrosomes in oocyte spindles. One, microtubules tend to assemble around the chromosomes. Two, the organization of these microtubules into a bipolar spindle is directed by the chromosomes. Three, chromosome bi-orientation and attachment to microtubules from the correct pole require modification of the mechanisms used in mitotic cells. Four, chromosome movement to the poles at anaphase cannot rely on polar anchoring of spindle microtubules by centrosomes. Overall, the chromosomes are more active participants during acentrosomal spindle assembly in oocytes, compared to mitotic and male meiotic divisions where centrosomes are present. The chromosomes are endowed with information that can direct the meiotic divisions and dictate their own behavior in oocytes. Processes beyond those known from mitosis appear to be required for their bi-orientation at meiosis I. As mitosis occurs without centrosomes in many systems other than oocytes, including all plants, the concepts discussed here may not be limited to oocytes. The study of meiosis in oocytes has revealed mechanisms that are operating in mitosis and will probably continue to do so.
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Affiliation(s)
- Sarah J Radford
- Waksman Institute, 190 Frelinghuysen Rd, Piscataway, NJ, 08854, USA
| | | | - Karen Schindler
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Kim S McKim
- Waksman Institute, 190 Frelinghuysen Rd, Piscataway, NJ, 08854, USA.
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA.
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81
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Oestergaard VH, Lisby M. Transcription-replication conflicts at chromosomal fragile sites-consequences in M phase and beyond. Chromosoma 2016; 126:213-222. [PMID: 27796495 DOI: 10.1007/s00412-016-0617-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 12/29/2022]
Abstract
Collision between the molecular machineries responsible for transcription and replication is an important source of genome instability. Certain transcribed regions known as chromosomal fragile sites are particularly prone to recombine and mutate in a manner that correlates with specific transcription and replication patterns. At the same time, these chromosomal fragile sites engage in aberrant DNA structures in mitosis. Here, we discuss the mechanistic details of transcription-replication conflicts including putative scenarios for R-loop-induced replication inhibition to understand how transcription-replication conflicts transition from S phase into various aberrant DNA structures in mitosis.
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Affiliation(s)
- Vibe H Oestergaard
- Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200, Copenhagen N, Denmark.
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200, Copenhagen N, Denmark.
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82
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Grenfell AW, Heald R, Strzelecka M. Mitotic noncoding RNA processing promotes kinetochore and spindle assembly in Xenopus. J Cell Biol 2016; 214:133-41. [PMID: 27402954 PMCID: PMC4949451 DOI: 10.1083/jcb.201604029] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/22/2016] [Indexed: 12/26/2022] Open
Abstract
Grenfell et al. show that transcription and RNA processing occur in metaphase-arrested egg extracts and that noncoding RNA biogenesis is important for centromere, kinetochore, and mitotic spindle assembly. Transcription at the centromere of chromosomes plays an important role in kinetochore assembly in many eukaryotes, and noncoding RNAs contribute to activation of the mitotic kinase Aurora B. However, little is known about how mitotic RNA processing contributes to spindle assembly. We found that inhibition of transcription initiation or RNA splicing, but not translation, leads to spindle defects in Xenopus egg extracts. Spliceosome inhibition resulted in the accumulation of high molecular weight centromeric transcripts, concomitant with decreased recruitment of the centromere and kinetochore proteins CENP-A, CENP-C, and NDC80 to mitotic chromosomes. In addition, blocking transcript synthesis or processing during mitosis caused accumulation of MCAK, a microtubule depolymerase, on the spindle, indicating misregulation of Aurora B. These findings suggest that co-transcriptional recruitment of the RNA processing machinery to nascent mitotic transcripts is an important step in kinetochore and spindle assembly and challenge the idea that RNA processing is globally repressed during mitosis.
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Affiliation(s)
- Andrew W Grenfell
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Magdalena Strzelecka
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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