51
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Replication of the Plant Genome. Mol Biol 2014. [DOI: 10.1007/978-1-4614-7570-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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52
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Takebayashi SI, Lei I, Ryba T, Sasaki T, Dileep V, Battaglia D, Gao X, Fang P, Fan Y, Esteban MA, Tang J, Crabtree GR, Wang Z, Gilbert DM. Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains. Epigenetics Chromatin 2013; 6:42. [PMID: 24330833 PMCID: PMC3895691 DOI: 10.1186/1756-8935-6-42] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 12/02/2013] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Cellular differentiation and reprogramming are accompanied by changes in replication timing and 3D organization of large-scale (400 to 800 Kb) chromosomal domains ('replication domains'), but few gene products have been identified whose disruption affects these properties. RESULTS Here we show that deletion of esBAF chromatin-remodeling complex components BAF250a and Brg1, but not BAF53a, disrupts replication timing at specific replication domains. Also, BAF250a-deficient fibroblasts reprogrammed to a pluripotency-like state failed to reprogram replication timing in many of these same domains. About half of the replication domains affected by Brg1 loss were also affected by BAF250a loss, but a much larger set of domains was affected by BAF250a loss. esBAF binding in the affected replication domains was dependent upon BAF250a but, most affected domains did not contain genes whose transcription was affected by loss of esBAF. CONCLUSIONS Loss of specific esBAF complex subunits alters replication timing of select replication domains in pluripotent cells.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Gilbert
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA.
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53
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Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster. Chromosoma 2013; 123:253-64. [DOI: 10.1007/s00412-013-0445-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 08/09/2013] [Accepted: 11/18/2013] [Indexed: 12/30/2022]
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54
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Rosenberg M, Fan AX, Lin IJ, Liang SY, Bungert J. Cell-cycle specific association of transcription factors and RNA polymerase ii with the human β-globin gene locus. J Cell Biochem 2013; 114:1997-2006. [PMID: 23519692 DOI: 10.1002/jcb.24542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 03/05/2013] [Indexed: 12/28/2022]
Abstract
The human β-globin genes are regulated by a locus control region (LCR) and are expressed at extremely high levels in erythroid cells. How transcriptional fidelity of highly expressed genes is regulated and maintained during the cell cycle is not completely understood. Here, we analyzed the association of transcription factor USF, the co-activator CBP, topoisomerase I (Topo I), basal transcription factor TFIIB, and RNA polymerase II (Pol II) with the β-globin gene locus at specific cell-cycle stages. The data demonstrate that while association of Pol II with globin locus associated chromatin decreased in mitotically arrested cells, it remained bound at lower levels at the γ-globin gene promoter. During early S-phase, association of CBP, USF, and Pol II with the globin gene locus decreased. The re-association of CBP and USF2 with the LCR preceded re-association of Pol II, suggesting that these proteins together mediate recruitment of Pol II to the β-globin gene locus during S-phase. Finally, we analyzed the association of Topo I with the globin gene locus during late S-phase. In general, Topo I association correlated with the binding of Pol II. Inhibition of Topo I activity reduced Pol II binding at the LCR and intergenic regions but not at the γ-globin gene promoter. The data demonstrate dynamic associations of transcription factors with the globin gene locus during the cell cycle and support previous results showing that specific components of transcription complexes remain associated with highly transcribed genes during mitosis.
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Affiliation(s)
- Michael Rosenberg
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Alex Xiucheng Fan
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - I-Ju Lin
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Shermi Y Liang
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, Florida, 32610
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55
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Julienne H, Zoufir A, Audit B, Arneodo A. Human genome replication proceeds through four chromatin states. PLoS Comput Biol 2013; 9:e1003233. [PMID: 24130466 PMCID: PMC3794905 DOI: 10.1371/journal.pcbi.1003233] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/06/2013] [Indexed: 12/26/2022] Open
Abstract
Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a framework for further studies in different cell types, in both health and disease. Previous studies revealed spatially coherent and biological-meaningful chromatin mark combinations in human cells. Here, we analyze thirteen epigenetic mark maps in the human cell line K562 at 100 kb resolution of MRT data. The complexity of epigenetic data is reduced to four chromatin states that display remarkable similarities with those reported in fly, worm and plants. These states have different MRT: (C1) is transcriptionally active, early replicating, enriched in CTCF; (C2) is Polycomb repressed, mid-S replicating; (C3) lacks of marks and replicates late and (C4) is a late-replicating gene-poor HP1 repressed heterochromatin state. When mapping these states inside the 876 replication U-domains of K562, the replication fork polarity gradient observed in these U-domains comes along with a remarkable epigenetic organization from C1 at U-domain borders to C2, C3 and ultimately C4 at centers. The remaining genome half displays early replicating, gene rich and high GC domains of intermingled C1 and C2 states segregating from late replicating, gene poor and low GC domains of concatenated C3 and/or C4 states. This constitutes the first evidence of epigenetic compartmentalization of the human genome into replication domains likely corresponding to autonomous units in the 3D chromatin architecture.
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Affiliation(s)
- Hanna Julienne
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Azedine Zoufir
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Benjamin Audit
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
| | - Alain Arneodo
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
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56
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Yoshida K, Poveda A, Pasero P. Time to be versatile: regulation of the replication timing program in budding yeast. J Mol Biol 2013; 425:4696-705. [PMID: 24076190 DOI: 10.1016/j.jmb.2013.09.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/24/2023]
Abstract
Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells coordinate replication at hundreds of origins distributed on the chromosomes. In this review, we discuss recent advances shedding new light on how this complex process is regulated in the budding yeast Saccharomyces cerevisiae. The picture that emerges from these studies is that replication timing is regulated in cis by mechanisms modulating the chromatin structure and the subnuclear organization of origins. These mechanisms do not affect the licensing of replication origins but determine their ability to compete for limiting initiation factors, which are recycled from early to late origins throughout the length of the S phase.
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Affiliation(s)
- Kazumasa Yoshida
- Institute of Human Genetics, CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer, 34396 Montpellier cedex 5, France; Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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57
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Abstract
In eukaryotic cells, genomic DNA replicates in a defined temporal order. The inactive X chromosome (Xi), the most extensive instance of facultative heterochromatin in mammals, replicates later than the active X chromosome (Xa), but the replication dynamics of inactive chromatin are not known. By profiling human DNA replication in an allele-specific, chromosomally phased manner, we determined for the first time the replication timing along the active and inactive chromosomes (Xa and Xi) separately. Replication of the Xi was different from that of the Xa, varied among individuals, and resembled a random, unstructured process. The Xi replicated rapidly and at a time largely separable from that of the euchromatic genome. Late-replicating, transcriptionally inactive regions on the autosomes also replicated in an unstructured manner, similar to the Xi. We conclude that DNA replication follows two strategies: slow, ordered replication associated with transcriptional activity, and rapid, random replication of silent chromatin. The two strategies coexist in the same cell, yet are segregated in space and time.
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Affiliation(s)
- Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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58
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Belan E. LINEs of evidence: noncanonical DNA replication as an epigenetic determinant. Biol Direct 2013; 8:22. [PMID: 24034780 PMCID: PMC3868326 DOI: 10.1186/1745-6150-8-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/06/2013] [Indexed: 12/17/2022] Open
Abstract
LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are
capable of synthesizing DNA on their own RNA templates by harnessing reverse
transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their
RT are found to globally influence gene expression profiles, differentiation state,
and proliferation capacity of early embryos and many types of cancer, albeit by yet
unknown mechanisms. They are essential for the progression of early development and
the establishment of a cancer-related undifferentiated state. This raises important
questions regarding the functional significance of L1 RT in these cell systems.
Massive nuclear L1-linked reverse transcription has been shown to occur in mouse
zygotes and two-cell embryos, and this phenomenon is purported to be DNA replication
independent. This review argues against this claim with the goal of understanding the
nature of this phenomenon and the role of L1 RT in early embryos and cancers.
Available L1 data are revisited and integrated with relevant findings accumulated in
the fields of replication timing, chromatin organization, and epigenetics, bringing
together evidence that strongly supports two new concepts. First, noncanonical
replication of a portion of genomic full-length L1s by means of L1 RNP-driven reverse
transcription is proposed to co-exist with DNA polymerase-dependent replication of
the rest of the genome during the same round of DNA replication in embryonic and
cancer cell systems. Second, the role of this mechanism is thought to be epigenetic;
it might promote transcriptional competence of neighboring genes linked to
undifferentiated states through the prevention of tethering of involved L1s to the
nuclear periphery. From the standpoint of these concepts, several hitherto
inexplicable phenomena can be explained. Testing methods for the model are
proposed.
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Affiliation(s)
- Ekaterina Belan
- Genetics Laboratory, Royal University Hospital, Saskatoon, SK S7N 0W8, Canada.
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59
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Replication timing regulation of eukaryotic replicons: Rif1 as a global regulator of replication timing. Trends Genet 2013; 29:449-60. [DOI: 10.1016/j.tig.2013.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/27/2013] [Accepted: 05/01/2013] [Indexed: 12/13/2022]
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Abstract
Little is known about the molecular machinery that contributes to site-specific copy number variations or how CNVs fit into the chronology of tumor progression. Black et al. (2013) now demonstrate that the overexpression of a histone demethylase induces transient copy gain of specific genomic loci known to harbor proto-oncogenes.
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Affiliation(s)
- Ryan Rickels
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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61
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Abstract
Patterns of replication within eukaryotic genomes correlate with gene expression, chromatin structure, and genome evolution. Recent advances in genome-scale mapping of replication kinetics have allowed these correlations to be explored in many species, cell types, and growth conditions, and these large data sets have allowed quantitative and computational analyses. One striking new correlation to emerge from these analyses is between replication timing and the three-dimensional structure of chromosomes. This correlation, which is significantly stronger than with any single histone modification or chromosome-binding protein, suggests that replication timing is controlled at the level of chromosomal domains. This conclusion dovetails with parallel work on the heterogeneity of origin firing and the competition between origins for limiting activators to suggest a model in which the stochastic probability of individual origin firing is modulated by chromosomal domain structure to produce patterns of replication. Whether these patterns have inherent biological functions or simply reflect higher-order genome structure is an open question.
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Affiliation(s)
- Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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62
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Abstract
Although distinct chromatin types have been long known to replicate at different timepoints of S phase, fine replication control has only recently become considered as an epigenetic phenomenon. It is now clear that in course of differentiation significant changes in genome replication timing occur, and these changes are intimately linked with the changes in transcriptional activity and nuclear architecture. Temporally coordinate replication is organized spatially into discrete units having specific chromosomal organization and function. Even though the functional aspects of such tight control of replication timing remain to be explored, one can confidently consider the replication program as yet another fundamental feature characteristic of the given differentiation state. The present review touches upon the molecular mechanisms of spatial and temporal control of replication timing, involving individual replication origins as well as large chromatin domains.
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63
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Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol 2013; 20:412-8. [PMID: 23552296 DOI: 10.1038/nsmb.2543] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 02/07/2013] [Indexed: 12/16/2022]
Abstract
To ensure accurate duplication of genetic material, the replication fork must overcome numerous natural obstacles on its way, including transcription complexes engaged along the same template. Here we review the various levels of interdependence between transcription and replication processes and how different types of encounters between RNA- and DNA-polymerase complexes may result in clashes of those machineries on the DNA template and thus increase genomic instability. In addition, we summarize strategies evolved in bacteria and eukaryotes to minimize the consequences of collisions, including R-loop formation and topological stresses.
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64
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Gaggioli V, Le Viet B, Germe T, Hyrien O. DNA topoisomerase IIα controls replication origin cluster licensing and firing time in Xenopus egg extracts. Nucleic Acids Res 2013; 41:7313-31. [PMID: 23757188 PMCID: PMC3753627 DOI: 10.1093/nar/gkt494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sperm chromatin incubated in Xenopus egg extracts undergoes origin licensing and nuclear assembly before DNA replication. We found that depletion of DNA topoisomerase IIα (topo IIα), the sole topo II isozyme of eggs and its inhibition by ICRF-193, which clamps topo IIα around DNA have opposite effects on these processes. ICRF-193 slowed down replication origin cluster activation and fork progression in a checkpoint-independent manner, without altering replicon size. In contrast, topo IIα depletion accelerated origin cluster activation, and topo IIα add-back negated overinitiation. Therefore, topo IIα is not required for DNA replication, but topo IIα clamps slow replication, probably by forming roadblocks. ICRF-193 had no effect on DNA synthesis when added after nuclear assembly, confirming that topo IIα activity is dispensable for replication and revealing that topo IIα clamps formed on replicating DNA do not block replication, presumably because topo IIα acts behind and not in front of forks. Topo IIα depletion increased, and topo IIα addition reduced, chromatin loading of MCM2-7 replicative helicase, whereas ICRF-193 did not affect MCM2-7 loading. Therefore, topo IIα restrains MCM2-7 loading in an ICRF-193-resistant manner during origin licensing, suggesting a model for establishing the sequential firing of origin clusters.
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Affiliation(s)
- Vincent Gaggioli
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), S2-Génomique Fonctionnelle, CNRS UMR8197, Inserm U1024, 46 rue d'Ulm, 75005 Paris, France
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65
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Evertts AG, Coller HA. Back to the origin: reconsidering replication, transcription, epigenetics, and cell cycle control. Genes Cancer 2013; 3:678-96. [PMID: 23634256 DOI: 10.1177/1947601912474891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and transcription. In metazoans, the organization of replication is more enigmatic. The lack of a specific sequence that defines origins of replication has, until recently, severely limited our ability to define the organizing principles of DNA replication. This question is of particular importance as emerging data suggest that replication stress is an important contributor to inherited genetic damage and the genomic instability in tumors. We consider here the replication program in several different organisms including recent genome-wide analyses of replication origins in humans. We review recent studies on the role of cytosine methylation in replication origins, the role of transcriptional looping and gene gating in DNA replication, and the role of chromatin's 3-dimensional structure in DNA replication. We use these new findings to consider several questions surrounding DNA replication in metazoans: How are origins selected? What is the relationship between replication and transcription? How do checkpoints inhibit origin firing? Why are there early and late firing origins? We then discuss whether oncogenes promote cancer through a role in DNA replication and whether errors in DNA replication are important contributors to the genomic alterations and gene fusion events observed in cancer. We conclude with some important areas for future experimentation.
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66
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Asynchronous replication, mono-allelic expression, and long range Cis-effects of ASAR6. PLoS Genet 2013; 9:e1003423. [PMID: 23593023 PMCID: PMC3617217 DOI: 10.1371/journal.pgen.1003423] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 02/14/2013] [Indexed: 11/19/2022] Open
Abstract
Mammalian chromosomes initiate DNA replication at multiple sites along their length during each S phase following a temporal replication program. The majority of genes on homologous chromosomes replicate synchronously. However, mono-allelically expressed genes such as imprinted genes, allelically excluded genes, and genes on female X chromosomes replicate asynchronously. We have identified a cis-acting locus on human chromosome 6 that controls this replication-timing program. This locus encodes a large intergenic non-coding RNA gene named Asynchronous replication and Autosomal RNA on chromosome 6, or ASAR6. Disruption of ASAR6 results in delayed replication, delayed mitotic chromosome condensation, and activation of the previously silent alleles of mono-allelic genes on chromosome 6. The ASAR6 gene resides within an ∼1.2 megabase domain of asynchronously replicating DNA that is coordinated with other random asynchronously replicating loci along chromosome 6. In contrast to other nearby mono-allelic genes, ASAR6 RNA is expressed from the later-replicating allele. ASAR6 RNA is synthesized by RNA Polymerase II, is not polyadenlyated, is restricted to the nucleus, and is subject to random mono-allelic expression. Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6. Finally, ectopic integration of cloned genomic DNA containing ASAR6 causes delayed replication of entire mouse chromosomes. Mammalian chromosomes are duplicated every cell cycle during a precise temporal DNA replication program. Thus, every chromosome contains regions that are replicated early and other regions that are replicated late during each S phase. Most of the genes, present in two copies on homologous chromosomes, replicate synchronously during each S phase. Exceptions to this rule are genes located on X chromosomes, genetically imprinted genes, and genes subject to allelic exclusion. Thus, all mono-allelically expressed genes are subject to asynchronous replication, where one allele replicates before the other. Perhaps the best-studied example of asynchronous replication in mammals occurs during X inactivation in female cells. A large non-coding RNA gene called XIST, located within the X inactivation center, controls the transcriptional silencing and late replication of the inactive X chromosome. We have identified a locus on human chromosome 6 that shares many characteristics with XIST. This chromosome 6 locus encodes a large intergenic non-coding RNA gene, ASAR6, which displays random mono-allelic expression, asynchronous replication, and controls the mono-allelic expression of other genes on chromosome 6. Our work supports a model in which all mammalian chromosomes contain similar cis-acting loci that function to ensure proper chromosome replication, mitotic condensation, mono-allelic expression, and stability of individual chromosomes.
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67
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Cavalli G, Misteli T. Functional implications of genome topology. Nat Struct Mol Biol 2013; 20:290-9. [PMID: 23463314 PMCID: PMC6320674 DOI: 10.1038/nsmb.2474] [Citation(s) in RCA: 299] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/20/2012] [Indexed: 01/21/2023]
Abstract
Although genomes are defined by their sequence, the linear arrangement of nucleotides is only their most basic feature. A fundamental property of genomes is their topological organization in three-dimensional space in the intact cell nucleus. The application of imaging methods and genome-wide biochemical approaches, combined with functional data, is revealing the precise nature of genome topology and its regulatory functions in gene expression and genome maintenance. The emerging picture is one of extensive self-enforcing feedback between activity and spatial organization of the genome, suggestive of a self-organizing and self-perpetuating system that uses epigenetic dynamics to regulate genome function in response to regulatory cues and to propagate cell-fate memory.
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Affiliation(s)
- Giacomo Cavalli
- Institut de Génétique Humaine, UPR 1142, Centre National de la Recherche Scientifique, Montpellier, France.
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68
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Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V. PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C. PLoS Genet 2013; 9:e1003283. [PMID: 23437006 PMCID: PMC3578750 DOI: 10.1371/journal.pgen.1003283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 12/14/2012] [Indexed: 12/03/2022] Open
Abstract
Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time. DNA replication is a tightly orchestrated process that precisely duplicates the entire genome during cell division to ensure that daughter cells inherit the same genetic information. The genome is replicated following a specific temporal program, where different segments replicate in distinct moments of the S phase correlating with active (early) and repressed (late) transcriptional state of resident genes. Moreover, replicating chromosomal domains are organized in the nuclear space, perhaps to guarantee the conservation of the same topological order in daughter cells. Epigenetic mechanisms, acting via chromatin organization, determine transcriptional states and must be maintained through cell division. Here, we analyzed in detail the link between Polycomb Group (PcG) proteins, higher-order chromatin structure, and replication timing in Drosophila. By using bioinformatic analyses combined with functional experiments, we show that Polycomb Repressive Complex 1 (PRC1), PRC2, and PhoRC differently correlate with replication timing of their targets and that transcription per se does not determine replication timing. Strikingly, by analyzing the PcG-regulated Bithorax Complex, where PRC1, PRC2, and PhoRC complexes are bound to repressed targets, we provide evidence for a synergistic role of PcG proteins in the modulation and maintenance of replication timing through the definition of specific, topologically distinct genomic domains.
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Affiliation(s)
- Federica Lo Sardo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Chiara Lanzuolo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
| | - Marco De Bardi
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Valerio Orlando
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
- * E-mail:
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69
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Donley N, Thayer MJ. DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability. Semin Cancer Biol 2013; 23:80-9. [PMID: 23327985 DOI: 10.1016/j.semcancer.2013.01.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/04/2013] [Indexed: 11/30/2022]
Abstract
Normal cellular division requires that the genome be faithfully replicated to ensure that unaltered genomic information is passed from one generation to the next. DNA replication initiates from thousands of origins scattered throughout the genome every cell cycle; however, not all origins initiate replication at the same time. A vast amount of work over the years indicates that different origins along each eukaryotic chromosome are activated in early, middle or late S phase. This temporal control of DNA replication is referred to as the replication-timing program. The replication-timing program represents a very stable epigenetic feature of chromosomes. Recent evidence has indicated that the replication-timing program can influence the spatial distribution of mutagenic events such that certain regions of the genome experience increased spontaneous mutagenesis compared to surrounding regions. This influence has helped shape the genomes of humans and other multicellular organisms and can affect the distribution of mutations in somatic cells. It is also becoming clear that the replication-timing program is deregulated in many disease states, including cancer. Aberrant DNA replication timing is associated with changes in gene expression, changes in epigenetic modifications and an increased frequency of structural rearrangements. Furthermore, certain replication timing changes can directly lead to overt genomic instability and may explain unique mutational signatures that are present in cells that have undergone the recently described processes of "chromothripsis" and "kataegis". In this review, we will discuss how the normal replication timing program, as well as how alterations to this program, can contribute to the evolution of the genomic landscape in normal and cancerous cells.
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Affiliation(s)
- Nathan Donley
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Knight Cancer Institute, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239, USA
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70
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Abstract
It is almost ten years since senescence associated heterochromatic foci (SAHFs) were first described in human diploid fibroblasts (HDFs). Since then, a number of factors have been identified that affect SAHF formation, including HMGA proteins, structural components of SAHFs. However, the involvement of epigenetic marks in SAHF formation remains unclear. Our recent study, combining microscopy and ChIP-seq approaches, revealed that SAHFs are formed through spatial repositioning of the genome. This occurs according to certain chromatin features that are correlated with, but do not require, the repressive marks histone H3 trimethylated on lysine 9 (H3K9me3) and H3K27me3. These repressive marks are segregated from each other within SAHFs, forming layered high-order chromatin structures (HOCS). During the dynamic change in HOCS as SAHFs form, the linear epigenomic profiles of these repressive marks are highly static. This is in marked contrast to the spreading of repressive marks occurring during embryonic cell differentiation. Thus the layered HOCS of SAHFs is likely achieved mainly through the spatial rearrangement of pre-existing heterochromatin, rather than spreading of heterochromatin. Evidence for the co-association of similar types of chromatin is emerging and SAHFs may provide a unique model system to study the correlation between HOCS and chromatin types, which are readily visible and regulable.
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Affiliation(s)
- Tamir Chandra
- Epigenetics and Nuclear Dynamics; The Babraham Institute; Cambridge, UK
| | - Masashi Narita
- Cancer Research UK; Cambridge Research Institute; Cambridge, UK
- Department of Oncology; University of Cambridge; Cambridge, UK
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71
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Nucleus and Genome: DNA Replication. Mol Biol 2013. [DOI: 10.1007/978-1-4939-0263-7_1-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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72
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Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet 2012. [PMID: 23176822 DOI: 10.1016/j.ajhg.2012.10.018] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human genetic variation is distributed nonrandomly across the genome, though the principles governing its distribution are only partially known. DNA replication creates opportunities for mutation, and the timing of DNA replication correlates with the density of SNPs across the human genome. To enable deeper investigation of how DNA replication timing relates to human mutation and variation, we generated a high-resolution map of the human genome's replication timing program and analyzed its relationship to point mutations, copy number variations, and the meiotic recombination hotspots utilized by males and females. DNA replication timing associated with point mutations far more strongly than predicted from earlier analyses and showed a stronger relationship to transversion than transition mutations. Structural mutations arising from recombination-based mechanisms and recombination hotspots used more extensively by females were enriched in early-replicating parts of the genome, though these relationships appeared to relate more strongly to the genomic distribution of causative sequence features. These results indicate differential and sex-specific relationship of DNA replication timing to different forms of mutation and recombination.
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Affiliation(s)
- Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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73
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Sanchez MDLP, Costas C, Sequeira-Mendes J, Gutierrez C. Regulating DNA replication in plants. Cold Spring Harb Perspect Biol 2012; 4:a010140. [PMID: 23209151 PMCID: PMC3504439 DOI: 10.1101/cshperspect.a010140] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chromosomal DNA replication in plants has requirements and constraints similar to those in other eukaryotes. However, some aspects are plant-specific. Studies of DNA replication control in plants, which have unique developmental strategies, can offer unparalleled opportunities of comparing regulatory processes with yeast and, particularly, metazoa to identify common trends and basic rules. In addition to the comparative molecular and biochemical studies, genomic studies in plants that started with Arabidopsis thaliana in the year 2000 have now expanded to several dozens of species. This, together with the applicability of genomic approaches and the availability of a large collection of mutants, underscores the enormous potential to study DNA replication control in a whole developing organism. Recent advances in this field with particular focus on the DNA replication proteins, the nature of replication origins and their epigenetic landscape, and the control of endoreplication will be reviewed.
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Affiliation(s)
- Maria de la Paz Sanchez
- Centro de Biologia Molecular "Severo Ochoa," CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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74
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Kolesnikova TD, Posukh OV, Andreyeva EN, Bebyakina DS, Ivankin AV, Zhimulev IF. Drosophila SUUR protein associates with PCNA and binds chromatin in a cell cycle-dependent manner. Chromosoma 2012; 122:55-66. [DOI: 10.1007/s00412-012-0390-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/25/2012] [Accepted: 10/22/2012] [Indexed: 01/06/2023]
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75
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Meuleman W, Peric-Hupkes D, Kind J, Beaudry JB, Pagie L, Kellis M, Reinders M, Wessels L, van Steensel B. Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence. Genome Res 2012; 23:270-80. [PMID: 23124521 PMCID: PMC3561868 DOI: 10.1101/gr.141028.112] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In metazoans, the nuclear lamina is thought to play an important role in the spatial organization of interphase chromosomes, by providing anchoring sites for large genomic segments named lamina-associated domains (LADs). Some of these LADs are cell-type specific, while many others appear constitutively associated with the lamina. Constitutive LADs (cLADs) may contribute to a basal chromosome architecture. By comparison of mouse and human lamina interaction maps, we find that the sizes and genomic positions of cLADs are strongly conserved. Moreover, cLADs are depleted of synteny breakpoints, pointing to evolutionary selective pressure to keep cLADs intact. Paradoxically, the overall sequence conservation is low for cLADs. Instead, cLADs are universally characterized by long stretches of DNA of high A/T content. Cell-type specific LADs also tend to adhere to this “A/T rule” in embryonic stem cells, but not in differentiated cells. This suggests that the A/T rule represents a default positioning mechanism that is locally overruled during lineage commitment. Analysis of paralogs suggests that during evolution changes in A/T content have driven the relocation of genes to and from the nuclear lamina, in tight association with changes in expression level. Taken together, these results reveal that the spatial organization of mammalian genomes is highly conserved and tightly linked to local nucleotide composition.
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Affiliation(s)
- Wouter Meuleman
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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76
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Takebayashi SI, Ryba T, Gilbert DM. Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding. Nucleus 2012; 3:500-7. [PMID: 23023599 PMCID: PMC3515532 DOI: 10.4161/nucl.22318] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We recently identified a set of chromosome domains that are early replicating uniquely in pluripotent cells. Their switch from early to late replication occurs just prior to germ layer commitment, associated with a stable form of gene silencing that is difficult to reverse. Here, we discuss results demonstrating that these domains are among the least sensitive regions in the genome to global digestion by either MNase or restriction enzymes. This inaccessible chromatin state persists whether these regions are in their physically distended early replicating or compact late replicating configuration, despite dramatic changes in 3D chromatin folding and long-range chromatin interactions, and despite large changes in transcriptional activity. This contrasts with the strong correlation between early replication, accessibility, transcriptional activity and open chromatin configuration that is observed genome-wide. We put these results in context with findings from other studies indicating that many structural (DNA sequence) and functional (density and activity of replication origins) properties of developmentally regulated replication timing ("switching") domains resemble properties of constitutively late replicating domains. This suggests that switching domains are a type of late replicating domain within which both replication timing and transcription are subject to unique or additional layers of control not experienced by the bulk of the genome. We predict that understanding the unusual structure of these domains will reveal a novel principle of chromosome folding.
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Affiliation(s)
| | - Tyrone Ryba
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - David M. Gilbert
- Department of Biological Science; Florida State University; Tallahassee, FL USA
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77
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Abstract
In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription.
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78
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Ryba T, Battaglia D, Chang BH, Shirley JW, Buckley Q, Pope BD, Devidas M, Druker BJ, Gilbert DM. Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res 2012; 22:1833-44. [PMID: 22628462 PMCID: PMC3460179 DOI: 10.1101/gr.138511.112] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/22/2012] [Indexed: 02/03/2023]
Abstract
Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication-timing profiles for pediatric leukemias from 17 patients and three cell lines, as well as normal B and T cells. Nonleukemic EBV-transformed lymphoblastoid cell lines displayed highly stable replication-timing profiles that were more similar to normal T cells than to leukemias. Leukemias were more similar to each other than to B and T cells but were considerably more heterogeneous than nonleukemic controls. Some differences were patient specific, while others were found in all leukemic samples, potentially representing early epigenetic events. Differences encompassed large segments of chromosomes and included genes implicated in other types of cancer. Remarkably, differences that distinguished leukemias aligned in register to the boundaries of developmentally regulated replication-timing domains that distinguish normal cell types. Most changes did not coincide with copy-number variation or translocations. However, many of the changes that were associated with translocations in some leukemias were also shared between all leukemic samples independent of the genetic lesion, suggesting that they precede and possibly predispose chromosomes to the translocation. Altogether, our results identify sites of abnormal developmental control of DNA replication in cancer that reveal the significance of replication-timing boundaries to chromosome structure and function and support the replication domain model of replication-timing regulation. They also open new avenues of investigation into the chromosomal basis of cancer and provide a potential novel source of epigenetic cancer biomarkers.
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Affiliation(s)
- Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Dana Battaglia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Bill H. Chang
- Division of Hematology and Oncology, Department of Pediatrics, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - James W. Shirley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Quinton Buckley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Meenakshi Devidas
- COG and Department of Biostatistics, College of Medicine, University of Florida, Gainesville, Florida 32601, USA
| | - Brian J. Druker
- Division of Hematology and Medical Oncology, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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79
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Rizzardi LF, Dorn ES, Strahl BD, Cook JG. DNA replication origin function is promoted by H3K4 di-methylation in Saccharomyces cerevisiae. Genetics 2012; 192:371-84. [PMID: 22851644 PMCID: PMC3454870 DOI: 10.1534/genetics.112.142349] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/18/2012] [Indexed: 12/18/2022] Open
Abstract
DNA replication is a highly regulated process that is initiated from replication origins, but the elements of chromatin structure that contribute to origin activity have not been fully elucidated. To identify histone post-translational modifications important for DNA replication, we initiated a genetic screen to identify interactions between genes encoding chromatin-modifying enzymes and those encoding proteins required for origin function in the budding yeast Saccharomyces cerevisiae. We found that enzymes required for histone H3K4 methylation, both the histone methyltransferase Set1 and the E3 ubiquitin ligase Bre1, are required for robust growth of several hypomorphic replication mutants, including cdc6-1. Consistent with a role for these enzymes in DNA replication, we found that both Set1 and Bre1 are required for efficient minichromosome maintenance. These phenotypes are recapitulated in yeast strains bearing mutations in the histone substrates (H3K4 and H2BK123). Set1 functions as part of the COMPASS complex to mono-, di-, and tri-methylate H3K4. By analyzing strains lacking specific COMPASS complex members or containing H2B mutations that differentially affect H3K4 methylation states, we determined that these replication defects were due to loss of H3K4 di-methylation. Furthermore, histone H3K4 di-methylation is enriched at chromosomal origins. These data suggest that H3K4 di-methylation is necessary and sufficient for normal origin function. We propose that histone H3K4 di-methylation functions in concert with other histone post-translational modifications to support robust genome duplication.
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Affiliation(s)
- Lindsay F. Rizzardi
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Elizabeth S. Dorn
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Brian D. Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, and
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, and
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
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80
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81
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Regulation of timing of replication. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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82
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Yamazaki S, Ishii A, Kanoh Y, Oda M, Nishito Y, Masai H. Rif1 regulates the replication timing domains on the human genome. EMBO J 2012; 31:3667-77. [PMID: 22850674 DOI: 10.1038/emboj.2012.180] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 06/13/2012] [Indexed: 11/09/2022] Open
Abstract
DNA replication is spatially and temporally regulated during S-phase. DNA replication timing is established in early-G1-phase at a point referred to as timing decision point. However, how the genome-wide replication timing domains are established is unknown. Here, we show that Rif1 (Rap1-interacting-factor-1), originally identified as a telomere-binding factor in yeast, is a critical determinant of the replication timing programme in human cells. Depletion of Rif1 results in specific loss of mid-S replication foci profiles, stimulation of initiation events in early-S-phase and changes in long-range replication timing domain structures. Analyses of replication timing show replication of sequences normally replicating early is delayed, whereas that normally replicating late is advanced, suggesting that replication timing regulation is abrogated in the absence of Rif1. Rif1 tightly binds to nuclear-insoluble structures at late-M-to-early-G1 and regulates chromatin-loop sizes. Furthermore, Rif1 colocalizes specifically with the mid-S replication foci. Thus, Rif1 establishes the mid-S replication domains that are restrained from being activated at early-S-phase. Our results indicate that Rif1 plays crucial roles in determining the replication timing domain structures in human cells through regulating higher-order chromatin architecture.
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Affiliation(s)
- Satoshi Yamazaki
- Genome Dynamics Project, Department of Genome Medicine, Tokyo, Japan
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83
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Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells. EMBO J 2012; 31:3678-90. [PMID: 22850673 DOI: 10.1038/emboj.2012.214] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 07/13/2012] [Indexed: 12/25/2022] Open
Abstract
The eukaryotic genome is replicated according to a specific spatio-temporal programme. However, little is known about both its molecular control and biological significance. Here, we identify mouse Rif1 as a key player in the regulation of DNA replication timing. We show that Rif1 deficiency in primary cells results in an unprecedented global alteration of the temporal order of replication. This effect takes place already in the first S-phase after Rif1 deletion and is neither accompanied by alterations in the transcriptional landscape nor by major changes in the biochemical identity of constitutive heterochromatin. In addition, Rif1 deficiency leads to both defective G1/S transition and chromatin re-organization after DNA replication. Together, these data offer a novel insight into the global regulation and biological significance of the replication-timing programme in mammalian cells.
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84
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Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell 2012; 47:203-14. [PMID: 22795131 PMCID: PMC3701408 DOI: 10.1016/j.molcel.2012.06.010] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 04/17/2012] [Accepted: 06/06/2012] [Indexed: 01/02/2023]
Abstract
The expansion of repressive epigenetic marks has been implicated in heterochromatin formation during embryonic development, but the general applicability of this mechanism is unclear. Here we show that nuclear rearrangement of repressive histone marks H3K9me3 and H3K27me3 into nonoverlapping structural layers characterizes senescence-associated heterochromatic foci (SAHF) formation in human fibroblasts. However, the global landscape of these repressive marks remains unchanged upon SAHF formation, suggesting that in somatic cells, heterochromatin can be formed through the spatial repositioning of pre-existing repressively marked histones. This model is reinforced by the correlation of presenescent replication timing with both the subsequent layered structure of SAHFs and the global landscape of the repressive marks, allowing us to integrate microscopic and genomic information. Furthermore, modulation of SAHF structure does not affect the occupancy of these repressive marks, nor vice versa. These experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events.
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Affiliation(s)
- Tamir Chandra
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
| | - Kristina Kirschner
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | | | - Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Scott Newman
- Department of Pathology and Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Kashif Ahmed
- The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Shamith A. Samarajiwa
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
| | - Rafik Salama
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Thomas Carroll
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Rory Stark
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Rekin’s Janky
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Masako Narita
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Lixiang Xue
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Agustin Chicas
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sabrina Nũnez
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | | | - Michael D. Wilson
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
- The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Aileen Marshall
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Hepatobiliary Unit, Addenbrooke’s Hospital, Cambridge CB2 2QQ, UK
| | - Duncan T. Odom
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Simon Tavaré
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
| | - Paul A.W. Edwards
- Department of Pathology and Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Masashi Narita
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
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85
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Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat Struct Mol Biol 2012; 19:837-44. [PMID: 22751019 DOI: 10.1038/nsmb.2339] [Citation(s) in RCA: 295] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/01/2012] [Indexed: 11/08/2022]
Abstract
DNA replication is highly regulated, ensuring faithful inheritance of genetic information through each cell cycle. In metazoans, this process is initiated at many thousands of DNA replication origins whose cell type-specific distribution and usage are poorly understood. We exhaustively mapped the genome-wide location of replication origins in human cells using deep sequencing of short nascent strands and identified ten times more origin positions than we expected; most of these positions were conserved in four different human cell lines. Furthermore, we identified a consensus G-quadruplex-forming DNA motif that can predict the position of DNA replication origins in human cells, accounting for their distribution, usage efficiency and timing. Finally, we discovered a cell type-specific reprogrammable signature of cell identity that was revealed by specific efficiencies of conserved origin positions and not by the selection of cell type-specific subsets of origins.
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86
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Thayer MJ. Mammalian chromosomes contain cis-acting elements that control replication timing, mitotic condensation, and stability of entire chromosomes. Bioessays 2012; 34:760-70. [PMID: 22706734 DOI: 10.1002/bies.201200035] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent studies indicate that mammalian chromosomes contain discrete cis-acting loci that control replication timing, mitotic condensation, and stability of entire chromosomes. Disruption of the large non-coding RNA gene ASAR6 results in late replication, an under-condensed appearance during mitosis, and structural instability of human chromosome 6. Similarly, disruption of the mouse Xist gene in adult somatic cells results in a late replication and instability phenotype on the X chromosome. ASAR6 shares many characteristics with Xist, including random mono-allelic expression and asynchronous replication timing. Additional "chromosome engineering" studies indicate that certain chromosome rearrangements affecting many different chromosomes display this abnormal replication and instability phenotype. These observations suggest that all mammalian chromosomes contain "inactivation/stability centers" that control proper replication, condensation, and stability of individual chromosomes. Therefore, mammalian chromosomes contain four types of cis-acting elements, origins, telomeres, centromeres, and "inactivation/stability centers", all functioning to ensure proper replication, condensation, segregation, and stability of individual chromosomes.
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Affiliation(s)
- Mathew J Thayer
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Knight Cancer Institute, Portland, OR, USA.
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87
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Bianco JN, Poli J, Saksouk J, Bacal J, Silva MJ, Yoshida K, Lin YL, Tourrière H, Lengronne A, Pasero P. Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing. Methods 2012; 57:149-57. [PMID: 22579803 DOI: 10.1016/j.ymeth.2012.04.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 04/11/2012] [Accepted: 04/14/2012] [Indexed: 11/17/2022] Open
Abstract
DNA combing is a powerful method developed by Bensimon and colleagues to stretch DNA molecules on silanized glass coverslips. This technique provides a unique way to monitor the activation of replication origins and the progression of replication forks at the level of single DNA molecules, after incorporation of thymidine analogs, such as 5-bromo-2'-deoxyuridine (BrdU), 5-iodo-2'-deoxyuridine (IdU) and 5-chloro-2'-deoxyuridine (CldU) in newly-synthesized DNA. Unlike microarray-based approaches, this assay gives access to the variability of replication profiles in individual cells. It can also be used to monitor the effect of DNA lesions on fork progression, arrest and restart. In this review, we propose standard DNA combing methods to analyze DNA replication in budding yeast and in human cells. We also show that 5-ethynyl-2'-deoxyuridine (EdU) can be used as a good alternative to BrdU for DNA combing analysis, as unlike halogenated nucleotides, it can be detected without prior denaturation of DNA.
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Affiliation(s)
- Julien N Bianco
- Institute of Human Genetics, CNRS UPR 1142, Montpellier F-34396, France
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88
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Bechhoefer J, Rhind N. Replication timing and its emergence from stochastic processes. Trends Genet 2012; 28:374-81. [PMID: 22520729 DOI: 10.1016/j.tig.2012.03.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 03/21/2012] [Accepted: 03/22/2012] [Indexed: 01/28/2023]
Abstract
The temporal organization of DNA replication has puzzled cell biologists since before the mechanism of replication was understood. The realization that replication timing correlates with important features, such as transcription, chromatin structure and genome evolution, and is misregulated in cancer and aging has only deepened the fascination. Many ideas about replication timing have been proposed, but most have been short on mechanistic detail. However, recent work has begun to elucidate basic principles of replication timing. In particular, mathematical modeling of replication kinetics in several systems has shown that the reproducible replication timing patterns seen in population studies can be explained by stochastic origin firing at the single-cell level. This work suggests that replication timing need not be controlled by a hierarchical mechanism that imposes replication timing from a central regulator, but instead results from simple rules that affect individual origins.
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Affiliation(s)
- John Bechhoefer
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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89
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Abstract
The duration of S phase in early embryos is often short, and then increases as development proceeds because of the appearance of late-replicating regions of the genome. In the April 1, 2012, issue of Genes & Development, Farrell and colleagues (pp. 714-725) demonstrate that the down-regulation of cyclin-dependent kinase 1 (Cdk1) activity triggers the onset of late-replicating DNA and an increase in S-phase length in Drosophila embryos, revealing an unexpected role for Cdk1 in replication control during development.
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Affiliation(s)
- Robert J Duronio
- Department of Biology, Department of Genetics, Lineberger Comprehensive Cancer Center, Program in Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, NC 27599, USA.
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90
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Knott SRV, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM. Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell 2012; 148:99-111. [PMID: 22265405 DOI: 10.1016/j.cell.2011.12.012] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 10/11/2011] [Accepted: 12/09/2011] [Indexed: 12/28/2022]
Abstract
The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function. The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure. Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing. Forkhead regulation of origin timing is independent of local levels or changes of transcription. Instead, we show that Fkh1 and Fkh2 are required for the clustering of early origins and their association with the key initiation factor Cdc45 in G1 phase, suggesting that Fkh1 and Fkh2 selectively recruit origins to emergent replication factories. Fkh1 and Fkh2 bind Fkh-activated origins, and interact physically with ORC, providing a plausible mechanism to cluster origins. These findings add a new dimension to our understanding of the epigenetic basis for differential origin regulation and its connection to chromosomal domain organization.
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Affiliation(s)
- Simon R V Knott
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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91
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Hassan-Zadeh V, Chilaka S, Cadoret JC, Ma MKW, Boggetto N, West AG, Prioleau MN. USF binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator. PLoS Biol 2012; 10:e1001277. [PMID: 22412349 PMCID: PMC3295818 DOI: 10.1371/journal.pbio.1001277] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 01/25/2012] [Indexed: 11/18/2022] Open
Abstract
The nuclear genomes of vertebrates show a highly organized program of DNA replication where GC-rich isochores are replicated early in S-phase, while AT-rich isochores are late replicating. GC-rich regions are gene dense and are enriched for active transcription, suggesting a connection between gene regulation and replication timing. Insulator elements can organize independent domains of gene transcription and are suitable candidates for being key regulators of replication timing. We have tested the impact of inserting a strong replication origin flanked by the β-globin HS4 insulator on the replication timing of naturally late replicating regions in two different avian cell types, DT40 (lymphoid) and 6C2 (erythroid). We find that the HS4 insulator has the capacity to impose a shift to earlier replication. This shift requires the presence of HS4 on both sides of the replication origin and results in an advance of replication timing of the target locus from the second half of S-phase to the first half when a transcribed gene is positioned nearby. Moreover, we find that the USF transcription factor binding site is the key cis-element inside the HS4 insulator that controls replication timing. Taken together, our data identify a combination of cis-elements that might constitute the basic unit of multi-replicon megabase-sized early domains of DNA replication.
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Affiliation(s)
- Vahideh Hassan-Zadeh
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Sabarinadh Chilaka
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Jean-Charles Cadoret
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Meiji Kit-Wan Ma
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicole Boggetto
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
| | - Adam G. West
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Marie-Noëlle Prioleau
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, Paris, France
- * E-mail:
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92
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Xu D, Huang W, Li Y, Wang H, Huang H, Cui X. Elongator complex is critical for cell cycle progression and leaf patterning in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:792-808. [PMID: 22026817 DOI: 10.1111/j.1365-313x.2011.04831.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The mitotic cell cycle in higher eukaryotes is of pivotal importance for organ growth and development. Here, we report that Elongator, an evolutionarily conserved histone acetyltransferase complex, acts as an important regulator of mitotic cell cycle to promote leaf patterning in Arabidopsis. Mutations in genes encoding Elongator subunits resulted in aberrant cell cycle progression, and the altered cell division affects leaf polarity formation. The defective cell cycle progression is caused by aberrant DNA replication and increased DNA damage, which activate the DNA replication checkpoint to arrest the cell cycle. Elongator interacts with proliferating cell nuclear antigen (PCNA) and is required for efficient histone 3 (H3) and H4 acetylation coupled with DNA replication. Levels of chromatin-bound H3K56Ac and H4K5Ac known to associate with replicons during DNA replication were reduced in the mutants of both Elongator and chromatin assembly factor 1 (CAF-1), another protein complex that physically interacts with PCNA for DNA replication-coupled chromatin assembly. Disruptions of CAF-1 also led to severe leaf polarity defects, which indicated that Elongator and CAF-1 act, at least partially, in the same pathway to promote cell cycle progression. Collectively, our results demonstrate that Elongator is an important regulator of mitotic cell cycle, and the Elongator pathway plays critical roles in promoting leaf polarity formation.
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Affiliation(s)
- Deyang Xu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, China
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93
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Sarkies P, Sale JE. Propagation of histone marks and epigenetic memory during normal and interrupted DNA replication. Cell Mol Life Sci 2012; 69:697-716. [PMID: 21964926 PMCID: PMC11114753 DOI: 10.1007/s00018-011-0824-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 09/02/2011] [Accepted: 09/12/2011] [Indexed: 11/30/2022]
Abstract
Although all nucleated cells within a multicellular organism contain a complete copy of the genome, cell identity relies on the expression of a specific subset of genes. Therefore, when cells divide they must not only copy their genome to their daughters, but also ensure that the pattern of gene expression present before division is restored. While the carrier of this epigenetic memory has been a topic of much research and debate, post-translational modifications of histone proteins have emerged in the vanguard of candidates. In this paper we examine the mechanisms by which histone post-translational modifications are propagated through DNA replication and cell division, and we critically examine the evidence that they can also act as vectors of epigenetic memory. Finally, we consider ways in which epigenetic memory might be disrupted by interfering with the mechanisms of DNA replication.
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Affiliation(s)
- Peter Sarkies
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
| | - Julian E. Sale
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
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94
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The chromatin backdrop of DNA replication: lessons from genetics and genome-scale analyses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:794-801. [PMID: 22342530 DOI: 10.1016/j.bbagrm.2012.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/27/2012] [Accepted: 01/31/2012] [Indexed: 01/04/2023]
Abstract
The entire cellular genome must replicate during each cell cycle, but it is yet unclear how replication proceeds along with chromatin condensation and remodeling while ensuring the fidelity of the replicated genome. Mapping replication initiation sites can provide clues for the coordination of DNA replication and transcription on a whole-genome scale. Here we discuss recent insights obtained from genome-scale analyses of replication initiation sites and transcription in mammalian cells and ask how transcription and chromatin modifications affect the frequency of replication initiation events. We also discuss DNA sequences, such as insulators and replicators, which modulate replication and transcription of target genes, and use genome-wide maps of replication initiation sites to evaluate possible commonalities between replicators and chromatin insulators. This article is part of a Special Issue entitled: Chromatin in time and space.
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95
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Costas C, Sanchez MDLP, Sequeira-Mendes J, Gutierrez C. Progress in understanding DNA replication control. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:203-9. [PMID: 21763530 DOI: 10.1016/j.plantsci.2011.04.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/07/2011] [Accepted: 04/24/2011] [Indexed: 05/19/2023]
Abstract
Completion of genome duplication during the S-phase of the cell cycle is crucial for the maintenance of genomic integrity. In eukaryotes, chromosomal DNA replication is accomplished by the activity of multiple origins of DNA replication scattered across the genome. Origin specification, selection and activity as well as the availability of replication factors and the regulation of DNA replication licensing, have unique and common features among eukaryotes. Although the initial studies on the semiconservative nature of chromosome duplication were carried out in the mid 1950s in Vicia faba, since then plant DNA replication studies have been scarce. However, they have received an unprecedented drive in the last decade after the completion of sequencing the Arabidopsis thaliana genome, and more recently of other plant genomes. In particular, the past year has witnessed major advances with the use of genomic approaches to study chromosomal replication timing, DNA replication origins and licensing control mechanisms. In this minireview article we discuss these recent discoveries in plants in the context of what is known at the genomic level in other eukaryotes. These studies constitute the basis for addressing in the future key questions about replication origin specification and function that will be of relevance not only for plants but also for the rest of multicellular organisms.
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Affiliation(s)
- Celina Costas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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96
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Casas-Delucchi CS, Brero A, Rahn HP, Solovei I, Wutz A, Cremer T, Leonhardt H, Cardoso MC. Histone acetylation controls the inactive X chromosome replication dynamics. Nat Commun 2011; 2:222. [PMID: 21364561 PMCID: PMC3072080 DOI: 10.1038/ncomms1218] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/27/2011] [Indexed: 12/20/2022] Open
Abstract
In mammals, dosage compensation between male and female cells is achieved by inactivating one female X chromosome (Xi). Late replication of Xi was proposed to be involved in the maintenance of its silenced state. Here, we show a highly synchronous replication of the Xi within 1 to 2 h during early-mid S-phase by following DNA replication in living mammalian cells with green fluorescent protein-tagged replication proteins. The Xi was replicated before or concomitant with perinuclear or perinucleolar facultative heterochromatin and before constitutive heterochromatin. Ectopic expression of the X-inactive-specific transcript (Xist) gene from an autosome imposed the same synchronous replication pattern. We used mutations and chemical inhibition affecting different epigenetic marks as well as inducible Xist expression and we demonstrate that histone hypoacetylation has a key role in controlling Xi replication. The epigenetically controlled, highly coordinated replication of the Xi is reminiscent of embryonic genome replication in flies and frogs before genome activation and might be a common feature of transcriptionally silent chromatin.
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97
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Ectopic gene expression and organogenesis in Arabidopsis mutants missing BRU1 required for genome maintenance. Genetics 2011; 189:83-95. [PMID: 21705754 DOI: 10.1534/genetics.111.130062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chromatin reconstitution after DNA replication and repair is essential for the inheritance of epigenetic information, but mechanisms underlying such a process are still poorly understood. Previously, we proposed that Arabidopsis BRU1 functions to ensure the chromatin reconstitution. Loss-of-function mutants of BRU1 are hypersensitive to genotoxic stresses and cause release of transcriptional gene silencing of heterochromatic genes. In this study, we show that BRU1 also plays roles in gene regulation in euchromatic regions. bru1 mutations caused sporadic ectopic expression of genes, including those that encode master regulators of developmental programs such as stem cell maintenance and embryogenesis. bru1 mutants exhibited adventitious organogenesis, probably due to the misexpression of such developmental regulators. The key regulatory genes misregulated in bru1 alleles were often targets of PcG SET-domain proteins, although the overlap between the bru1-misregulated and PcG SET-domain-regulated genes was limited at a genome-wide level. Surprisingly, a considerable fraction of the genes activated in bru1 were located in several subchromosomal regions ranging from 174 to 944 kb in size. Our results suggest that BRU1 has a function related to the stability of subchromosomal gene regulation in the euchromatic regions, in addition to the maintenance of chromatin states coupled with heritable epigenetic marks.
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98
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Barberis M, Spiesser TW, Klipp E. Replication origins and timing of temporal replication in budding yeast: how to solve the conundrum? Curr Genomics 2011; 11:199-211. [PMID: 21037857 PMCID: PMC2878984 DOI: 10.2174/138920210791110942] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 01/08/2010] [Accepted: 01/14/2010] [Indexed: 11/22/2022] Open
Abstract
Similarly to metazoans, the budding yeast Saccharomyces cereviasiae replicates its genome with a defined timing. In this organism, well-defined, site-specific origins, are efficient and fire in almost every round of DNA replication. However, this strategy is neither conserved in the fission yeast Saccharomyces pombe, nor in Xenopus or Drosophila embryos, nor in higher eukaryotes, in which DNA replication initiates asynchronously throughout S phase at random sites. Temporal and spatial controls can contribute to the timing of replication such as Cdk activity, origin localization, epigenetic status or gene expression. However, a debate is going on to answer the question how individual origins are selected to fire in budding yeast. Two opposing theories were proposed: the "replicon paradigm" or "temporal program" vs. the "stochastic firing". Recent data support the temporal regulation of origin activation, clustering origins into temporal blocks of early and late replication. Contrarily, strong evidences suggest that stochastic processes acting on origins can generate the observed kinetics of replication without requiring a temporal order. In mammalian cells, a spatiotemporal model that accounts for a partially deterministic and partially stochastic order of DNA replication has been proposed. Is this strategy the solution to reconcile the conundrum of having both organized replication timing and stochastic origin firing also for budding yeast? In this review we discuss this possibility in the light of our recent study on the origin activation, suggesting that there might be a stochastic component in the temporal activation of the replication origins, especially under perturbed conditions.
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Affiliation(s)
- Matteo Barberis
- Institute for Biology, Theoretical Biophysics, Humboldt University Berlin, Invalidenstraβe 42, 10115 Berlin, Germany
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99
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Prevention of transcriptional silencing by a replicator-binding complex consisting of SWI/SNF, MeCP1, and hnRNP C1/C2. Mol Cell Biol 2011; 31:3472-84. [PMID: 21690294 DOI: 10.1128/mcb.05587-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional silencing selectively impedes gene expression. Silencing is often accompanied by replication delay and can be prevented by replicator sequences. Here we report a replicator-binding protein complex involved in the prevention of transcriptional silencing. The protein complex interacts with an essential asymmetric region within the human β-globin Rep-P replicator and includes hnRNP C1/C2, SWI/SNF complex, and MeCP1, which are members of the locus control region (LCR)-associated remodeling complex (LARC). Interaction between LARC and Rep-P prevented transcriptional silencing and replication delay. Transgenes that did not contain the asymmetric LARC-binding region of Rep-P replicated late and exhibited stable silencing that could not be affected by a DNA methylation inhibitor. In contrast, transgenes that contain a mutation of the asymmetric region of Rep-P that could not bind LARC exhibited a silent state that could transiently be reactivated by DNA demethylation. The effect of DNA demethylation was transient, and prolonged exposure to a methylation inhibitor induced distinct, stable, methylation-independent silencing. These observations suggest that the interaction of LARC complex with replicators plays a role in preventing gene silencing and provides support for a novel, epigenetic mechanism of resistance to methylation inhibitors.
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100
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Gilbert DM. Cell fate transitions and the replication timing decision point. J Cell Biol 2010; 191:899-903. [PMID: 21115801 PMCID: PMC2995162 DOI: 10.1083/jcb.201007125] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 11/03/2010] [Indexed: 12/11/2022] Open
Abstract
Recent findings suggest that large-scale remodeling of three dimensional (3D) chromatin architecture occurs during a brief period in early G1 phase termed the replication timing decision point (TDP). In this speculative article, I suggest that the TDP may represent an as yet unappreciated window of opportunity for extracellular cues to influence 3D architecture during stem cell fate decisions. I also describe several testable predictions of this hypothesis.
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Affiliation(s)
- David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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