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Posukh OV, Maksimov DA, Laktionov PP, Koryakov DE, Belyakin SN. Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile. Epigenetics Chromatin 2017; 10:56. [PMID: 29191233 PMCID: PMC5709859 DOI: 10.1186/s13072-017-0163-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 11/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In eukaryotes, heterochromatin replicates late in S phase of the cell cycle and contains specific covalent modifications of histones. SuUR mutation found in Drosophila makes heterochromatin replicate earlier than in wild type and reduces the level of repressive histone modifications. SUUR protein was shown to be associated with moving replication forks, apparently through the interaction with PCNA. The biological process underlying the effects of SUUR on replication and composition of heterochromatin remains unknown. RESULTS Here we performed a functional dissection of SUUR protein effects on H3K27me3 level. Using hidden Markow model-based algorithm we revealed SuUR-sensitive chromosomal regions that demonstrated unusual characteristics: They do not contain Polycomb and require SUUR function to sustain H3K27me3 level. We tested the role of SUUR protein in the mechanisms that could affect H3K27me3 histone levels in these regions. We found that SUUR does not affect the initial H3K27me3 pattern formation in embryogenesis or Polycomb distribution in the chromosomes. We also ruled out the possible effect of SUUR on histone genes expression and its involvement in DSB repair. CONCLUSIONS Obtained results support the idea that SUUR protein contributes to the heterochromatin maintenance during the chromosome replication. A model that explains major SUUR-associated phenotypes is proposed.
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Affiliation(s)
- Olga V Posukh
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090
| | - Daniil A Maksimov
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090
| | - Petr P Laktionov
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090
| | - Dmitry E Koryakov
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogov str. 2, Novosibirsk, Russia
| | - Stepan N Belyakin
- Genomics Lab, Institute of Molecular and Cellular Biology SB RAS, Lavrentyev ave. 8/2, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Pirogov str. 2, Novosibirsk, Russia.
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2
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Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AHG, Nishida K, Romashchenko AV, Postberg J, Lipps H, Berezikov E, Sibon OCM, Giepmans BNG, Lansdorp PM. Guanine quadruplex structures localize to heterochromatin. Nucleic Acids Res 2015; 44:152-63. [PMID: 26384414 PMCID: PMC4705689 DOI: 10.1093/nar/gkv900] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/21/2015] [Indexed: 12/27/2022] Open
Abstract
Increasing amounts of data support a role for guanine quadruplex (G4) DNA and RNA structures in various cellular processes. We stained different organisms with monoclonal antibody 1H6 specific for G4 DNA. Strikingly, immuno-electron microscopy showed exquisite specificity for heterochromatin. Polytene chromosomes from Drosophila salivary glands showed bands that co-localized with heterochromatin proteins HP1 and the SNF2 domain-containing protein SUUR. Staining was retained in SUUR knock-out mutants but lost upon overexpression of SUUR. Somatic cells in Macrostomum lignano were strongly labeled, but pluripotent stem cells labeled weakly. Similarly, germline stem cells in Drosophila ovaries were weakly labeled compared to most other cells. The unexpected presence of G4 structures in heterochromatin and the difference in G4 staining between somatic cells and stem cells with germline DNA in ciliates, flatworms, flies and mammals point to a conserved role for G4 structures in nuclear organization and cellular differentiation.
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Affiliation(s)
- Roland F Hoffmann
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Nicola A Grzeschik
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ruby D Kalicharan
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Kazuki Nishida
- Faculty of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Aleksander V Romashchenko
- Department of Biochemistry, Erasmus University Medical Center, Dr. Molewaterplein 50, NL-3015 GE Rotterdam, The Netherlands Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jan Postberg
- Helios Medical Centre Wuppertal, Paediatrics Centre, Witten/Herdecke University, Wuppertal, Germany
| | - Hans Lipps
- Institute of Cell Biology, Centre for Biomedical Education and Research, Witten/Herdecke University, Witten, Germany
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ody C M Sibon
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medicine, University of British Columbia Vancouver, BC, V5Z 1L3, Canada
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Follmer NE, Wani AH, Francis NJ. A polycomb group protein is retained at specific sites on chromatin in mitosis. PLoS Genet 2012; 8:e1003135. [PMID: 23284300 PMCID: PMC3527277 DOI: 10.1371/journal.pgen.1003135] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 10/16/2012] [Indexed: 11/18/2022] Open
Abstract
Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states, but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells. Genome-wide sequencing of chromatin immunoprecipitations (ChIP–SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) is not present at well-characterized PcG targets including Hox genes in mitosis, but does remain at a subset of interphase sites. Many of these persistent sites overlap with chromatin domain borders described by Sexton et al. (2012), which are genomic regions characterized by low levels of long range contacts. Persistent PSC binding sites flank both Hox gene clusters. We hypothesize that disruption of long-range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long-range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis. Gene expression profiles must be maintained through the cell cycle in many situations during development. How gene expression profiles are maintained through mitosis by transcriptional regulators like the Polycomb Group (PcG) proteins is not well understood. Here we find that PcG proteins remain associated with mitotic chromatin, and a small subset of PcG binding sites throughout the genome is maintained between interphase and mitosis. These persistent binding sites preferentially overlap borders of chromatin domains. These results suggest a model in which PcG proteins retained at border sites may nucleate re-binding of PcG protein within domains after mitosis.
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Affiliation(s)
- Nicole E. Follmer
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ajazul H. Wani
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nicole J. Francis
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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Late replication domains in polytene and non-polytene cells of Drosophila melanogaster. PLoS One 2012; 7:e30035. [PMID: 22253867 PMCID: PMC3254639 DOI: 10.1371/journal.pone.0030035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 12/08/2011] [Indexed: 12/20/2022] Open
Abstract
In D. melanogaster polytene chromosomes, intercalary heterochromatin (IH) appears as large dense bands scattered in euchromatin and comprises clusters of repressed genes. IH displays distinctly low gene density, indicative of their particular regulation. Genes embedded in IH replicate late in the S phase and become underreplicated. We asked whether localization and organization of these late-replicating domains is conserved in a distinct cell type. Using published comprehensive genome-wide chromatin annotation datasets (modENCODE and others), we compared IH organization in salivary gland cells and in a Kc cell line. We first established the borders of 60 IH regions on a molecular map, these regions containing underreplicated material and encompassing ∼12% of Drosophila genome. We showed that in Kc cells repressed chromatin constituted 97% of the sequences that corresponded to IH bands. This chromatin is depleted for ORC-2 binding and largely replicates late. Differences in replication timing between the cell types analyzed are local and affect only sub-regions but never whole IH bands. As a rule such differentially replicating sub-regions display open chromatin organization, which apparently results from cell-type specific gene expression of underlying genes. We conclude that repressed chromatin organization of IH is generally conserved in polytene and non-polytene cells. Yet, IH domains do not function as transcription- and replication-regulatory units, because differences in transcription and replication between cell types are not domain-wide, rather they are restricted to small “islands” embedded in these domains. IH regions can thus be defined as a special class of domains with low gene density, which have narrow temporal expression patterns, and so displaying relatively conserved organization.
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Tchurikov NA, Kretova OV, Sosin DV, Zykov IA, Zhimulev IF, Kravatsky YV. Genome-wide profiling of forum domains in Drosophila melanogaster. Nucleic Acids Res 2011; 39:3667-85. [PMID: 21247882 PMCID: PMC3089479 DOI: 10.1093/nar/gkq1353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Most forum domains are 50-200 kb in length. We mapped forum domain termini using FISH on polytene chromosomes and we performed genome-wide mapping using a Drosophila melanogaster genomic tiling microarray consisting of overlapping 3 kb fragments. We found that forum termini very often correspond to regions of intercalary heterochromatin and regions of late replication in polytene chromosomes. We found that forum domains contain clusters of several or many genes. The largest forum domains correspond to the main clusters of homeotic genes inside BX-C and ANTP-C, cluster of histone genes and clusters of piRNAs. PRE/TRE and transcription factor binding sites often reside inside domains and do not overlap with forum domain termini. We also found that about 20% of forum domain termini correspond to small chromosomal regions where Ago1, Ago2, small RNAs and repressive chromatin structures are detected. Our results indicate that forum domains correspond to big multi-gene chromosomal units, some of which could be coordinately expressed. The data on the global mapping of forum domains revealed a strong correlation between fragmentation sites in chromosomes, particular sets of mobile elements and regions of intercalary heterochromatin.
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Affiliation(s)
- Nickolai A Tchurikov
- Department of Genome Organization, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow 119991, Russia.
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Gene density profile reveals the marking of late replicated domains in the Drosophila melanogaster genome. Chromosoma 2010; 119:589-600. [PMID: 20602235 DOI: 10.1007/s00412-010-0280-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 06/04/2010] [Accepted: 06/07/2010] [Indexed: 10/19/2022]
Abstract
Regulation of replication timing has been a focus of many studies. It has been shown that numerous chromosomal regions switch their replication timing on cell differentiation in Drosophila and mice. However, it is not clear which features of these regions are essential for such regulation. In this study, we examined the organization of late underreplicated regions (URs) of the Drosophila melanogaster genome. When compared with their flanks, these regions showed decreased gene density. A detailed view revealed that these regions originate from unusual combination of short genes and long intergenic spacers. Furthermore, gene expression study showed that this pattern is mostly contributed by short testis-specific genes abundant in the URs. Based on these observations, we developed a genome scanning algorithm and identified 110 regions possessing similar gene density and transcriptional profiles. According to the published data, replication of these regions has been significantly shifted towards late S-phase in two Drosophila cell lines and in polytene chromosomes. Our results suggest that genomic organization of the underreplicated areas of Drosophila polytene chromosomes may be associated with the regulation of their replication timing.
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Conservation of domain structure in a fast-evolving heterochromatic SUUR protein in drosophilids. Genetics 2009; 183:119-29. [PMID: 19596903 DOI: 10.1534/genetics.109.104844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Different genomic regions replicate at a distinct time during S-phase. The SuUR mutation alters replication timing and the polytenization level of intercalary and pericentric heterochromatin in Drosophila melanogaster salivary gland polytene chromosomes. We analyzed SuUR in different insects, identified conserved regions in the protein, substituted conserved amino acid residues, and studied effects of the mutations on SUUR function. SuUR orthologs were identified in all sequenced drosophilids, and a highly divergent ortholog was found in the mosquito genome. We demonstrated that SUUR evolves at very high rate comparable with that of Transformer. Remarkably, upstream ORF within 5' UTR of the gene is more conserved than SUUR in drosophilids, but it is absent in the mosquito. The domain structure and charge of SUUR are maintained in drosophilids despite the high divergence of the proteins. The N-terminal part of SUUR with similarity to the SNF2/SWI2 proteins displays the highest level of conservation. Mutation of two conserved amino acid residues in this region impairs binding of SUUR to polytene chromosomes and reduces the ability of the protein to cause DNA underreplication. The least conserved middle part of SUUR interacting with HP1 retains positively and negatively charged clusters and nuclear localization signals. The C terminus contains interlacing conserved and variable motifs. Our results suggest that SUUR domains evolve with different rates and patterns but maintain their features.
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Francis NJ, Follmer NE, Simon MD, Aghia G, Butler JD. Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell 2009; 137:110-22. [PMID: 19303136 PMCID: PMC2667909 DOI: 10.1016/j.cell.2009.02.017] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Revised: 10/22/2008] [Accepted: 02/02/2009] [Indexed: 01/11/2023]
Abstract
The transcriptional status of a gene can be maintained through multiple rounds of cell division during development. This epigenetic effect is believed to reflect heritable changes in chromatin folding and histone modifications or variants at target genes, but little is known about how these chromatin features are inherited through cell division. A particular challenge for maintaining transcription states is DNA replication, which disrupts or dilutes chromatin-associated proteins and histone modifications. PRC1-class Polycomb group protein complexes are essential for development and are thought to heritably silence transcription by altering chromatin folding and histone modifications. It is not known whether these complexes and their effects are maintained during DNA replication or subsequently re-established. We find that when PRC1-class Polycomb complex-bound chromatin or DNA is replicated in vitro, Polycomb complexes remain bound to replicated templates. Retention of Polycomb proteins through DNA replication may contribute to maintenance of transcriptional silencing through cell division.
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Affiliation(s)
- Nicole J Francis
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
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9
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Kounatidis I, Papadopoulos N, Bourtzis K, Mavragani-Tsipidou P. Genetic and cytogenetic analysis of the fruit fly Rhagoletis cerasi (Diptera: Tephritidae). Genome 2008; 51:479-91. [PMID: 18545272 DOI: 10.1139/g08-032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The European cherry fruit fly, Rhagoletis cerasi, is a major agricultural pest for which biological, genetic, and cytogenetic information is limited. We report here a cytogenetic analysis of 4 natural Greek populations of R. cerasi, all of them infected with the endosymbiotic bacterium Wolbachia pipientis. The mitotic karyotype and detailed photographic maps of the salivary gland polytene chromosomes of this pest species are presented here. The mitotic metaphase complement consists of 6 pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement has shown a total of 5 long chromosomes (10 polytene arms) that correspond to the 5 autosomes of the mitotic nuclei and a heterochromatic mass corresponding to the sex chromosomes. The most prominent landmarks of each polytene chromosome, the "weak points", and the unusual asynapsis of homologous pairs of polytene chromosomes at certain regions of the polytene elements are also presented and discussed.
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Affiliation(s)
- Ilias Kounatidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
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Andreyeva EN, Kolesnikova TD, Belyaeva ES, Glaser RL, Zhimulev IF. Local DNA underreplication correlates with accumulation of phosphorylated H2Av in the Drosophila melanogaster polytene chromosomes. Chromosome Res 2008; 16:851-62. [PMID: 18704724 DOI: 10.1007/s10577-008-1244-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/05/2008] [Accepted: 06/05/2008] [Indexed: 12/29/2022]
Abstract
DNA in Drosophila melanogaster polytene chromosomes is known to be locally underreplicated in both pericentric and intercalary heterochromatin. When the SuUR gene is mutant, complete and partial suppression of underreplication are observed in intercalary and pericentric heterochromatin, respectively; in contrast, overexpression of SuUR results in stronger underreplication. Using antibodies against phosphorylated histone H2Av and flies with different levels of SuUR expression, we demonstrated a clear correlation between the extent of underreplication in specific chromosome regions and the accumulation of H2Av phosphorylated at S137 (gamma-H2AX) at the same sites. Phosphorylated H2Av is a well-established marker of DNA double-stranded breaks (DSB). Our data thus argue that DNA underreplication leads to DSBs and that DSBs accumulate as salivary gland cells progress throughout repeated endocycles. We speculate that ligation of free double-stranded DNA termini causes the formation of ectopic contacts between the underreplicated regions in heterochromatin.
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Affiliation(s)
- E N Andreyeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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11
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Mohan M, Bartkuhn M, Herold M, Philippen A, Heinl N, Bardenhagen I, Leers J, White RAH, Renkawitz-Pohl R, Saumweber H, Renkawitz R. The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning. EMBO J 2007; 26:4203-14. [PMID: 17805343 PMCID: PMC2230845 DOI: 10.1038/sj.emboj.7601851] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 08/15/2007] [Indexed: 01/08/2023] Open
Abstract
Insulator sequences guide the function of distantly located enhancer elements to the appropriate target genes by blocking inappropriate interactions. In Drosophila, five different insulator binding proteins have been identified, Zw5, BEAF-32, GAGA factor, Su(Hw) and dCTCF. Only dCTCF has a known conserved counterpart in vertebrates. Here we find that the structurally related factors dCTCF and Su(Hw) have distinct binding targets. In contrast, the Su(Hw) interacting factor CP190 largely overlapped with dCTCF binding sites and interacts with dCTCF. Binding of dCTCF to targets requires CP190 in many cases, whereas others are independent of CP190. Analysis of the bithorax complex revealed that six of the borders between the parasegment specific regulatory domains are bound by dCTCF and by CP190 in vivo. dCTCF null mutations affect expression of Abdominal-B, cause pharate lethality and a homeotic phenotype. A short pulse of dCTCF expression during larval development rescues the dCTCF loss of function phenotype. Overall, we demonstrate the importance of dCTCF in fly development and in the regulation of abdominal segmentation.
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Affiliation(s)
- Man Mohan
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Martin Herold
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Angela Philippen
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Nina Heinl
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Imke Bardenhagen
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Joerg Leers
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Robert A H White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Renate Renkawitz-Pohl
- Philipps-Universität Marburg, Fachbereich Biologie, Entwicklungsbiologie, Marburg, Germany
| | - Harald Saumweber
- Cytogenetics Division, Institute of Biology, Humboldt University, Berlin, Germany
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58-62, Giessen 35392, Germany. Tel.: +49 641 99 35460; Fax: +49 641 99 35469; E-mail:
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Agrawal UR, Tewari RR. Intercalary Heterochromatin in the Pupal Foot Pad Polytene Chromosomes of Flesh Fly Parasarcophaga ruficornis Fab. (Sarcophagidae: Diptera). CYTOLOGIA 2007. [DOI: 10.1508/cytologia.72.329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Wallace JA, Orr-Weaver TL. Replication of heterochromatin: insights into mechanisms of epigenetic inheritance. Chromosoma 2005; 114:389-402. [PMID: 16220346 DOI: 10.1007/s00412-005-0024-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Revised: 08/13/2005] [Accepted: 08/15/2005] [Indexed: 12/20/2022]
Abstract
Heterochromatin is composed of tightly condensed chromatin in which the histones are deacetylated and methylated, and specific nonhistone proteins are bound. Additionally, in vertebrates and plants, the DNA within heterochromatin is methylated. As the heterochromatic state is stably inherited, replication of heterochromatin requires not only duplication of the DNA but also a reinstallment of the appropriate protein and DNA modifications. Thus replication of heterochromatin provides a framework for understanding mechanisms of epigenetic inheritance. In recent studies, roles have been identified for replication factors in reinstating heterochromatin, particularly functions for origin recognition complex, proliferating cell nuclear antigen, and chromatin-assembly factor 1 in recruiting the heterochromatin binding protein HP1, a histone methyltransferase, a DNA methyltransferase, and a chromatin remodeling complex. Potential mechanistic links between these factors are discussed. In some cells, replication of the heterochromatin is blocked, and in Drosophila this inhibition is mediated by a chromatin binding protein SuUR.
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Belyakin SN, Christophides GK, Alekseyenko AA, Kriventseva EV, Belyaeva ES, Nanayev RA, Makunin IV, Kafatos FC, Zhimulev IF. Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proc Natl Acad Sci U S A 2005; 102:8269-74. [PMID: 15928082 PMCID: PMC1149430 DOI: 10.1073/pnas.0502702102] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In Drosophila polytene chromosomes, most late-replicating regions remain underreplicated. A loss-of-function mutant of the suppressor of underreplication [Su(UR)] gene suppresses underreplication (UR), whereas extra copies of this gene enhance the level and number of regions showing UR. By combining DNA microarray analysis with manipulation of the number of Su(UR) gene copies, we achieved genomic-scale molecular identification of 1,036 genes that are arranged in clusters located in 52 UR chromosomal regions. These regions overlap extensively (96%) but are not completely identical with late-replicating regions of mitotically dividing Kc cells in culture. Reanalysis of published gene expression profiles revealed that genomic regions defined by replication properties include clusters of coordinately expressed genes. Genomic regions that are UR in polytene chromosomes and late replicated in Kc cell chromosomes show a particularly common association with transcriptional territories that are expressed in testis/males but not ovary/females or embryos. An attractive hypothesis for future testing is that factors involved in replication control, such as SU(UR), may interact physically with those involved in epigenetic silencing of transcription territories.
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Affiliation(s)
- Stepan N Belyakin
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
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