251
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Groth A. Replicating chromatin: a tale of histonesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2009; 87:51-63. [DOI: 10.1139/o08-102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures reassembly on nascent DNA strands. The aim of this review is to discuss how histones — new and old — are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms.
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Affiliation(s)
- Anja Groth
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark (e-mail: )
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252
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Abstract
We are in the midst of a revolution in the genomic sciences that will forever change the way we view biology and medicine, particularly with respect to brain form, function, development, evolution, plasticity, neurological disease pathogenesis and neural regenerative potential. The application of epigenetic principles has already begun to identify and characterize previously unrecognized molecular signatures of disease latency, onset and progression, mechanisms underlying disease pathogenesis, and responses to new and evolving therapeutic modalities. Moreover, epigenomic medicine promises to usher in a new era of neurological therapeutics designed to promote disease prevention and recovery of seemingly lost neurological function via reprogramming of stem cells, redirecting cell fate decisions and dynamically modulating neural network plasticity and connectivity.
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Affiliation(s)
- Mark F Mehler
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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253
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Histone modification patterns and epigenetic codes. Biochim Biophys Acta Gen Subj 2009; 1790:863-8. [PMID: 19168116 DOI: 10.1016/j.bbagen.2008.12.006] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 12/22/2008] [Accepted: 12/29/2008] [Indexed: 01/19/2023]
Abstract
The eukaryotic DNA is wrapped around histone octamers, which consist of four different histones, H2A, H2B, H3 and H4. The N-terminal tail of each histone is post-transcriptionally modified. The modification patterns constitute codes that regulate chromatin organisation and DNA utilization processes, including transcription. Recent progress in technology development has made it possible to perform systematic genome-wide studies of histone modifications. This helps immensely in deciphering the histone codes and their biological influence. In this review, we discuss the histone modification patterns found in genome-wide studies in different biological models and how they influence cell differentiation and carcinogenesis.
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254
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Abstract
Heterochromatin, once thought to be the useless junk of chromosomes, is now known to play significant roles in biology. Underlying much of this newfound fame are links between the repressive chromatin structure and cohesin, the protein complex that mediates sister chromatid cohesion. Heterochromatin-mediated recruitment and retention of cohesin to domains flanking centromeres promotes proper attachment of chromosomes to the mitotic and meiotic spindles. Heterochromatin assembled periodically between convergently transcribed genes also recruits cohesin, which promotes a novel form of transcription termination. Heterochromatin-like structures in budding yeast also recruit cohesin. Here the complex appears to regulate transcriptional silencing and recombination between repeated DNA sequences. The link between heterochromatin and cohesin is particularly relevant to human health. In Roberts-SC phocomelia syndrome, heterochromatic cohesion is selectively lost due to mutation of the acetyltransferase responsible for cohesin activation. In this review I discuss recent work that relates to these relationships between heterochromatin and cohesin.
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Affiliation(s)
- Marc Gartenberg
- Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA.
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255
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Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF. RNA regulation of epigenetic processes. Bioessays 2009; 31:51-9. [DOI: 10.1002/bies.080099] [Citation(s) in RCA: 259] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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256
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Ugarković DI. Centromere-competent DNA: structure and evolution. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 48:53-76. [PMID: 19521812 DOI: 10.1007/978-3-642-00182-6_3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although extant data favour centromere being an epigenetic structure, it is also clear that centromere formation is based on DNA, in particular, tandemly repeated satellite DNA and its transcripts. Presence of conserved structural motifs within satellite DNAs such as periodically distributed AT tracts, protein binding sites, or promoter elements indicate that despite sequence flexibility, there are structural determinants that are prerequisite for centromere function. In addition, existence of functional centromeric DNA transcripts indicates possible importance of structural elements at the level of RNA secondary or tertiary structure. Rapid centromere evolution is explained by homologous recombination followed by extrachromosomal rolling circle replication. This could lead to amplification of different satellite sequences within a genome. However, only those satellites that have inherent centromere-competence in the form of structural requirements necessary for centromere function are after amplification fixed in a population as a new centromere.
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Affiliation(s)
- Durd Ica Ugarković
- Department of Molecular Biology, Rud er Bosković Institute, Bijenicka 54, HR-10002, Zagreb, Croatia.
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257
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Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nat Rev Genet 2008; 9:923-37. [PMID: 19002142 DOI: 10.1038/nrg2466] [Citation(s) in RCA: 440] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The assembly of just a single kinetochore at the centromere of each sister chromatid is essential for accurate chromosome segregation during cell division. Surprisingly, despite their vital function, centromeres show considerable plasticity with respect to their chromosomal locations and activity. The establishment and maintenance of centromeric chromatin, and therefore the location of kinetochores, is epigenetically regulated. The histone H3 variant CENP-A is the key determinant of centromere identity and kinetochore assembly. Recent studies have identified many factors that affect CENP-A localization, but their precise roles in this process are unknown. We build on these advances and on new information about the timing of CENP-A assembly during the cell cycle to propose new models for how centromeric chromatin is established and propagated.
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258
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Epigenetic Silencing of Pericentromeric Heterochromatin by RNA Interference in Schizosaccharomyces pombe. Epigenomics 2008. [DOI: 10.1007/978-1-4020-9187-2_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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259
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Utani KI, Shimizu N. How transcription proceeds in a large artificial heterochromatin in human cells. Nucleic Acids Res 2008; 37:393-404. [PMID: 19043073 PMCID: PMC2632932 DOI: 10.1093/nar/gkn970] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Heterochromatin is critical for genome integrity, and recent studies have suggested the importance of transcription in heterochromatin for maintaining its silent state. We previously developed a method to generate a large homogeneously staining region (HSR) composed of tandem plasmid sequences in human cells that showed typical heterochromatin characteristics. In this study, we examined transcription in the HSR. We found that transcription of genes downstream to no-inducible SRα promoter was restricted to a few specific points inside the large HSR domain. Furthermore, the HSR localized to either to the surface or to the interior of the nucleolus, where it was more actively transcribed. The perinucleolar or intranucleolar locations were biased to late or early S-phase, and the location depended on either RNA polymerase II/III or I transcription, respectively. Strong activation of the inducible TRE promoter resulted in the reversible loosening of the HSR domain and the appearance of transcripts downstream of not only the TRE promoters, but also the SRα promoters. During this process, detection of HP1α or H3K9Me3 suggested that transcription was activated at many specific points dispersed inside large heterochromatin. The transcriptional rules obtained from studying artificial heterochromatin should be useful for understanding natural heterochromatin.
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Affiliation(s)
- Koh-ichi Utani
- Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-hiroshima, 739-8521, Japan
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260
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Frescas D, Guardavaccaro D, Kuchay SM, Kato H, Poleshko A, Basrur V, Elenitoba-Johnson KS, Katz RA, Pagano M. KDM2A represses transcription of centromeric satellite repeats and maintains the heterochromatic state. Cell Cycle 2008; 7:3539-47. [PMID: 19001877 PMCID: PMC2636745 DOI: 10.4161/cc.7.22.7062] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin plays an essential role in the preservation of epigenetic information, the transcriptional repression of repetitive DNA elements and inactive genes, and the proper segregation of chromosomes during mitosis. Here we identify KDM2A, a JmjC-domain containing histone demethylase, as a heterochromatin-associated and HP1-interacting protein that promotes HP1 localization to chromatin. We show that KDM2A is required to maintain the heterochromatic state, as determined using a candidate-based approach coupled to an in vivo epigenetic reporter system. Remarkably, a parallel and independent siRNA screen also detected a role for KDM2A in epigenetic silencing. Moreover, we demonstrate that KDM2A associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Dissecting the relationship between heterochromatin and centromeric RNA transcription is the basis of ongoing studies. We demonstrate that forced expression of these satellite RNA transcripts compromise the heterochromatic state and HP1 localization to chromatin. Finally, we show that KDM2A is required to sustain centromeric integrity and genomic stability, particularly during mitosis. Since the disruption of epigenetic control mechanisms contributes to cellular transformation, these results, together with the low levels of KDM2A found in prostate carcinomas, suggest a role for KDM2A in cancer development.
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Affiliation(s)
- David Frescas
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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261
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Bühler M. RNA turnover and chromatin-dependent gene silencing. Chromosoma 2008; 118:141-51. [DOI: 10.1007/s00412-008-0195-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 12/31/2022]
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262
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Pebernard S, Schaffer L, Campbell D, Head SR, Boddy MN. Localization of Smc5/6 to centromeres and telomeres requires heterochromatin and SUMO, respectively. EMBO J 2008; 27:3011-23. [PMID: 18923417 DOI: 10.1038/emboj.2008.220] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 09/22/2008] [Indexed: 01/19/2023] Open
Abstract
The Smc5/6 holocomplex executes key functions in genome maintenance that include ensuring the faithful segregation of chromosomes at mitosis and facilitating critical DNA repair pathways. Smc5/6 is essential for viability and therefore, dissecting its chromosome segregation and DNA repair roles has been challenging. We have identified distinct epigenetic and post-translational modifications that delineate roles for fission yeast Smc5/6 in centromere function, versus replication fork-associated DNA repair. We monitored Smc5/6 subnuclear and genomic localization in response to different replicative stresses, using fluorescence microscopy and chromatin immunoprecipitation (ChIP)-on-chip methods. Following hydroxyurea treatment, and during an unperturbed S phase, Smc5/6 is transiently enriched at the heterochromatic outer repeats of centromeres in an H3-K9 methylation-dependent manner. In contrast, methyl methanesulphonate treatment induces the accumulation of Smc5/6 at subtelomeres, in an Nse2 SUMO ligase-dependent, but H3-K9 methylation-independent manner. Finally, we determine that Smc5/6 loads at all genomic tDNAs, a phenomenon that requires intact consensus TFIIIC-binding sites in the tDNAs.
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Affiliation(s)
- Stephanie Pebernard
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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263
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Guil S, Esteller M. DNA methylomes, histone codes and miRNAs: tying it all together. Int J Biochem Cell Biol 2008; 41:87-95. [PMID: 18834952 DOI: 10.1016/j.biocel.2008.09.005] [Citation(s) in RCA: 236] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 12/12/2022]
Abstract
Our current knowledge of the deregulation that occurs during the onset and progression of cancer and other diseases leads us to recognize both genetic and epigenetic alterations as being at the core of the pathological state. The epigenetic landscape includes a variety of covalent modifications that affect the methylation status of DNA but also the post-translational modifications of histones, and determines the structural features of chromatin that ultimately control the transcriptional outcome of the cell to accommodate developmental, proliferative or environmental requirements. MicroRNAs are small non-coding RNAs that regulate the expression of complementary messenger RNAs and function as key controllers in a myriad of cellular processes, including proliferation, differentiation and apoptosis. In the last few years, increasing evidence has indicated that a substantial number of microRNA genes are subjected to epigenetic alterations, resulting in aberrant patterns of expression upon the occurrence of cancer. In this review we discuss microRNA genes that are epigenetically modified in cancer cells, and the role that microRNAs themselves can have as chromatin modifiers.
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Affiliation(s)
- Sònia Guil
- Institut d'Investigacio Biomedica de Bellvitge, 08907 L'Hospitalet, Barcelona, Catalonia, Spain
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264
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Bühler M, Spies N, Bartel DP, Moazed D. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 2008; 15:1015-23. [PMID: 18776903 PMCID: PMC3240669 DOI: 10.1038/nsmb.1481] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 07/24/2008] [Indexed: 12/27/2022]
Abstract
In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) machinery is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic gene silencing. Efficient silencing also requires the TRAMP complex, which contains the noncanonical Cid14 poly(A) polymerase and targets aberrant RNAs for degradation. Here we use high-throughput sequencing to analyze Argonaute-associated small RNAs (sRNAs) in both the presence and absence of Cid14. Most sRNAs in fission yeast start with a 5′ uracil, and we argue these are loaded most efficiently into Argonaute. In wild-type cells most sRNAs match to repeated regions of the genome, whereas in cid14Δ cells the sRNA profile changes to include major new classes of sRNAs originating from ribosomal RNAs and a tRNA. Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets.
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Affiliation(s)
- Marc Bühler
- Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115 USA
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265
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Kloc A, Martienssen R. RNAi, heterochromatin and the cell cycle. Trends Genet 2008; 24:511-7. [PMID: 18778867 DOI: 10.1016/j.tig.2008.08.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/04/2008] [Accepted: 08/05/2008] [Indexed: 01/15/2023]
Abstract
For many decades after its initial characterization, heterochromatin was considered to be transcriptionally inert, but newer work indicates that this highly condensed chromosomal material is transcribed, and rapidly silenced, by an orchestrated sequence of events directed by RNA interference (RNAi). Recent studies shed light on the timely assembly and inheritance of heterochromatin within a short period during the cell cycle, thereby providing an explanation for how 'silent' heterochromatin can be transcribed during the S phase of the cell cycle. Together, these findings suggest a model of RNAi-directed epigenetic inheritance.
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Affiliation(s)
- Anna Kloc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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266
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Dohke K, Miyazaki S, Tanaka K, Urano T, Grewal SIS, Murakami Y. Fission yeast chromatin assembly factor 1 assists in the replication-coupled maintenance of heterochromatin. Genes Cells 2008; 13:1027-43. [PMID: 18761674 DOI: 10.1111/j.1365-2443.2008.01225.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chromatin assembly factor-1 (CAF1) is a well-conserved histone chaperone that loads the histone H3-H4 complex onto newly synthesized DNA in vitro through interaction with the replication factor PCNA. CAF1 is considered to be involved in heterochromatin maintenance in several organisms, but the evidence is circumstantial and functional details have not been established. We identified fission yeast CAF-1 (spCAF1), which interacts with PCNA in S phase. Depletion of spCAF1 caused defects in silencing at centromeric and mating locus heterochromatin, accompanied with a decrease in Swi6, the fission yeast HP1 homologue. Loss of spCAF1 destabilized both the silent and active states of chromatin at the meta-stable heterochromatic region, with a more pronounced effect on the silent state, indicating that spCAF1 is involved in the maintenance of heterochromatin. Swi6 dissociated from heterochromatin during G1/S phase appears to associate with spCAF1. In early S phase, spCAF1 localized to replicating heterochromatin as well as euchromatin and remained associated with Swi6, and Swi6 then bound to heterochromatin. Taken together, we propose that spCAF1 functions in heterochromatin maintenance by recruiting dislocated Swi6 during replication to replicated heterochromatin at the replication fork.
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Affiliation(s)
- Kohei Dohke
- Department of Cell Biology, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507 Japan
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267
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Small RNA-directed heterochromatin formation in the context of development: what flies might learn from fission yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:3-16. [PMID: 18789407 DOI: 10.1016/j.bbagrm.2008.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 08/03/2008] [Accepted: 08/07/2008] [Indexed: 11/21/2022]
Abstract
A link between the RNAi system and heterochromatin formation has been established in several model organisms including Schizosaccharomyces pombe and Arabidopsis thaliana. However, the data to support a role for small RNAs and the associated machinery in transcriptional gene silencing in animal systems is more tenuous. Using the S. pombe system as a model, we analyze the role of small RNA pathway components and associated small RNAs in regulating transposable elements and potentially directing heterochromatin formation at these elements in Drosophila melanogaster.
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268
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269
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Kloc A, Zaratiegui M, Nora E, Martienssen R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr Biol 2008; 18:490-5. [PMID: 18394897 DOI: 10.1016/j.cub.2008.03.016] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 03/03/2008] [Accepted: 03/03/2008] [Indexed: 12/29/2022]
Abstract
BACKGROUND Heterochromatin is chromosomal material that remains condensed throughout the cell division cycle and silences genes nearby. It is found in almost all eukaryotes, and although discovered (in plants) almost 100 years ago, the mechanism by which heterochromatin is inherited has remained obscure. Heterochromatic silencing and histone H3 lysine-9 methylation (H3K9me2) depend, paradoxically, on heterochromatic transcription and RNA interference (RNAi). RESULTS Here, we show that heterochromatin protein 1 in fission yeast (Swi6) is lost via phosphorylation of H3 serine 10 (H3S10) during mitosis, allowing heterochromatic transcripts to transiently accumulate in S phase. Rapid processing of these transcripts into small interfering RNA (siRNA) promotes restoration of H3K9me2 and Swi6 after replication when cohesin is recruited. We also show that RNAi in fission yeast is inhibited at high temperatures, providing a plausible mechanism for epigenetic phenomena that depend on replication and temperature, such as vernalization in plants and position effect variegation in animals. CONCLUSIONS These results explain how "silent" heterochromatin can be transcribed and lead to a model for epigenetic inheritance during replication.
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Affiliation(s)
- Anna Kloc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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270
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Abstract
Rb mutants exhibit aneuploidy and aberrant chromosome structure during mitosis. In this issue of Genes & Development, a new paper from Longworth and colleagues (1011-1024) describes both physical and functional interactions between Drosophila Rbf1 and the dCAP-D3 subunit of condensin II. This work directly implicates the Rb family proteins in mitotic chromosome condensation and suggests that a failure in targeting condensin II to chromatin underlies the aneuploidy in rbf1 mutants.
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Affiliation(s)
- Brigitte D Lavoie
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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271
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Abstract
Structural maintenance of chromosomes (SMC) proteins form the cohesin and condensin complexes and play important roles in sister chromatid pairing, chromosome segregation, and transcriptional regulation. Two papers in Nature Genetics now show that SMC-like proteins also participate in epigenetic processes such as X inactivation in mammals and RNA-directed DNA methylation in plants.
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Affiliation(s)
- Edith Heard
- CNRS UMR 218, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.
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272
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Affiliation(s)
- Ingela Djupedal
- Department of Biosciences and Medical Nutrition, Karolinska Institutet, Sweden/School of Life Sciences, University College Sodertorn, NOVUM, 141 57 Huddinge, Sweden
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273
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Abstract
Histone modifications tend to be lost during chromosome duplication. Several recent studies suggest that the RNA interference pathway becomes active during the weakened transcriptional repression occurring at centromeres in S phase, resulting in the re-establishment of histone modifications that direct the formation of heterochromatin.
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Affiliation(s)
- Geneviève Thon
- Department of Biology, University of Copenhagen, BioCenter, Copenhagen N, Denmark.
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274
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Lu J, Gilbert DM. Cell cycle regulated transcription of heterochromatin in mammals vs. fission yeast: functional conservation or coincidence? Cell Cycle 2008; 7:1907-10. [PMID: 18604169 DOI: 10.4161/cc.7.13.6206] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although it is tempting to speculate that the transcription-dependent heterochromatin assembly pathway found in fission yeast may operate in higher mammals, transcription of heterochromatin has been difficult to substantiate in mammalian cells. We recently demonstrated that transcription from the mouse pericentric heterochromatin major (gamma) satellite repeats is under cell cycle control, being sharply downregulated at the metaphase to anaphase transition and resuming in late G(1)-phase dependent upon passage through the restriction point. The highest rates of transcription were in early S-phase and again in mitosis with different RNA products detected at each of these times.(1) Importantly, differences in the percentage of cells in G(1)-phase can account for past discrepancies in the detection of major satellite transcripts and suggest that pericentric heterochromatin transcription takes place in all proliferating mammalian cells. A similar cell cycle regulation of heterochromatin transcription has now been shown in fission yeast,(2,3) providing further support for a conserved mechanism. However, there are still fundamental differences between these two systems that preclude the identification of a functional or mechanistic link.
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Affiliation(s)
- Junjie Lu
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
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275
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Abstract
The past few years have revealed that the genomes of all studied eukaryotes are almost entirely transcribed, generating an enormous number of non-protein-coding RNAs (ncRNAs). In parallel, it is increasingly evident that many of these RNAs have regulatory functions. Here, we highlight recent advances that illustrate the diversity of ncRNA control of genome dynamics, cell biology, and developmental programming.
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Affiliation(s)
- Paulo P Amaral
- Institute for Molecular Bioscience, University of Queensland, St. Lucia QLD 4072, Australia
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276
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Gullerova M, Proudfoot NJ. Cohesin complex promotes transcriptional termination between convergent genes in S. pombe. Cell 2008; 132:983-95. [PMID: 18358811 DOI: 10.1016/j.cell.2008.02.040] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 11/21/2007] [Accepted: 02/05/2008] [Indexed: 01/02/2023]
Abstract
Transcription analyses reported in these studies reveal that convergent genes in S. pombe generate overlapping transcripts in the G1 phase of the cell cycle. We show that this double-strand (ds) RNA induces localized RNAi (Dicer and RITS) dependent transient heterochromatin structures including histone H3 lysine 9 trimethylation marks and Swi6 association. Consequently cohesin is recruited to these chromosomal positions through interaction with Swi6. In G2, localized cohesin is further concentrated into the intergenic regions of the convergent genes tested. This results in a block to further dsRNA formation by promoting gene-proximal transcription termination between the convergent genes. Cohesin release at mitosis leads to a new G1 phase with repeated dsRNA formation, transient heterochromatin, and cohesin recruitment. Our results uncover a hitherto unanticipated role for cohesin and further suggest a widespread role for the selective formation of dsRNA, heterochromatin, and subsequent cohesin recruitment in regulated transcriptional termination.
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Affiliation(s)
- Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Rd, Oxford OX1 3RE, UK
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277
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Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat Struct Mol Biol 2008; 15:381-8. [DOI: 10.1038/nsmb.1406] [Citation(s) in RCA: 289] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/22/2008] [Indexed: 11/09/2022]
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