1
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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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The Sound of Silence: How Silenced Chromatin Orchestrates the Repair of Double-Strand Breaks. Genes (Basel) 2021; 12:genes12091415. [PMID: 34573397 PMCID: PMC8467445 DOI: 10.3390/genes12091415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/29/2022] Open
Abstract
The eukaryotic nucleus is continuously being exposed to endogenous and exogenous sources that cause DNA breaks, whose faithful repair requires the activity of dedicated nuclear machineries. DNA is packaged into a variety of chromatin domains, each characterized by specific molecular properties that regulate gene expression and help maintain nuclear structure. These different chromatin environments each demand a tailored response to DNA damage. Silenced chromatin domains in particular present a major challenge to the cell’s DNA repair machinery due to their specific biophysical properties and distinct, often repetitive, DNA content. To this end, we here discuss the interplay between silenced chromatin domains and DNA damage repair, specifically double-strand breaks, and how these processes help maintain genome stability.
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3
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Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species. Genes (Basel) 2021; 12:genes12020175. [PMID: 33513919 PMCID: PMC7911463 DOI: 10.3390/genes12020175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/19/2022] Open
Abstract
Pericentromeric heterochromatin in Drosophila generally consists of repetitive DNA, forming the environment associated with gene silencing. Despite the expanding knowledge of the impact of transposable elements (TEs) on the host genome, little is known about the evolution of pericentromeric heterochromatin, its structural composition, and age. During the evolution of the Drosophilidae, hundreds of genes have become embedded within pericentromeric regions yet retained activity. We investigated a pericentromeric heterochromatin fragment found in D. virilis and related species, describing the evolution of genes in this region and the age of TE invasion. Regardless of the heterochromatic environment, the amino acid composition of the genes is under purifying selection. However, the selective pressure affects parts of genes in varying degrees, resulting in expansion of gene introns due to TEs invasion. According to the divergence of TEs, the pericentromeric heterochromatin of the species of virilis group began to form more than 20 million years ago by invasions of retroelements, miniature inverted repeat transposable elements (MITEs), and Helitrons. Importantly, invasions into the heterochromatin continue to occur by TEs that fall under the scope of piRNA silencing. Thus, the pericentromeric heterochromatin, in spite of its ability to induce silencing, has the means for being dynamic, incorporating the regions of active transcription.
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4
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Funikov SY, Rezvykh AP, Kulikova DA, Zelentsova ES, Protsenko LA, Chuvakova LN, Tyukmaeva VI, Arkhipova IR, Evgen'ev MB. Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins. Sci Rep 2020; 10:11893. [PMID: 32681087 PMCID: PMC7368049 DOI: 10.1038/s41598-020-68879-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/23/2020] [Indexed: 01/11/2023] Open
Abstract
Pericentromeric heterochromatin is generally composed of repetitive DNA forming a transcriptionally repressive environment. Dozens of genes were embedded into pericentromeric heterochromatin during evolution of Drosophilidae lineage while retaining activity. However, factors that contribute to insusceptibility of gene loci to transcriptional silencing remain unknown. Here, we find that the promoter region of genes that can be embedded in both euchromatin and heterochromatin exhibits a conserved structure throughout the Drosophila phylogeny and carries motifs for binding of certain chromatin remodeling factors, including insulator proteins. Using ChIP-seq data, we demonstrate that evolutionary gene relocation between euchromatin and pericentric heterochromatin occurred with preservation of sites of insulation of BEAF-32 in evolutionarily distant species, i.e. D. melanogaster and D. virilis. Moreover, promoters of virtually all protein-coding genes located in heterochromatin in D. melanogaster are enriched with insulator proteins BEAF-32, GAF and dCTCF. Applying RNA-seq of a BEAF-32 mutant, we show that the impairment of BEAF-32 function has a complex effect on gene expression in D. melanogaster, affecting even those genes that lack BEAF-32 association in their promoters. We propose that conserved intrinsic properties of genes, such as sites of insulation near the promoter regions, may contribute to adaptation of genes to the heterochromatic environment and, hence, facilitate the evolutionary relocation of genes loci between euchromatin and heterochromatin.
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Affiliation(s)
- Sergei Yu Funikov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexander P Rezvykh
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Dina A Kulikova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Elena S Zelentsova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia
| | - Lyudmila A Protsenko
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Lyubov N Chuvakova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia
| | - Venera I Tyukmaeva
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Michael B Evgen'ev
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russia.
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5
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Helleu Q, Levine MT. Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera. Mol Biol Evol 2019; 35:2375-2389. [PMID: 29924345 PMCID: PMC6188558 DOI: 10.1093/molbev/msy128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that interspecies hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of coevolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter. Here we describe many such candidates encoded by the Heterochromatin Protein 1 (HP1) gene family across Diptera, an insect Order that encompasses dramatic episodes of heterochromatic sequence turnover. Using BLAST, synteny analysis, and phylogenetic tree building across 64 Diptera genomes, we discovered a staggering 121 HP1 duplication events. In contrast, we observed virtually no gene duplication in gene families that share a common “chromodomain” with HP1s, including Polycomb and Su(var)3-9. The remarkably high number of Dipteran HP1 paralogs arises from distant clades undergoing convergent HP1 family amplifications. These independently derived, young HP1s span diverse ages, domain structures, and rates of molecular evolution, including episodes of positive selection. Moreover, independently derived HP1s exhibit convergent expression evolution. While ancient HP1 parent genes are transcribed ubiquitously, young HP1 paralogs are transcribed primarily in male germline tissue, a pattern typical of young genes. Pervasive gene youth, rapid evolution, and germline specialization implicate heterochromatin-encoded selfish elements driving recurrent HP1 gene family expansions. The 121 young genes offer valuable experimental traction for elucidating the germline processes shaped by Diptera’s many dramatic episodes of heterochromatin turnover.
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Affiliation(s)
- Quentin Helleu
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
| | - Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
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6
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Genetic and Molecular Analysis of Essential Genes in Centromeric Heterochromatin of the Left Arm of Chromosome 3 in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:1581-1595. [PMID: 30948422 PMCID: PMC6505167 DOI: 10.1534/g3.119.0003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A large portion of the Drosophila melanogaster genome is contained within heterochromatic regions of chromosomes, predominantly at centromeres and telomeres. The remaining euchromatic portions of the genome have been extensively characterized with respect to gene organization, function and regulation. However, it has been difficult to derive similar data for sequences within centromeric (centric) heterochromatin because these regions have not been as amenable to analysis by standard genetic and molecular tools. Here we present an updated genetic and molecular analysis of chromosome 3L centric heterochromatin (3L Het). We have generated and characterized a number of new, overlapping deficiencies (Dfs) which remove regions of 3L Het. These Dfs were critically important reagents in our subsequent genetic analysis for the isolation and characterization of lethal point mutations in the region. The assignment of these mutations to genetically-defined essential loci was followed by matching them to gene models derived from genome sequence data: this was done by using molecular mapping plus sequence analysis of mutant alleles, thereby aligning genetic and physical maps of the region. We also identified putative essential gene sequences in 3L Het by using RNA interference to target candidate gene sequences. We report that at least 25, or just under 2/3 of loci in 3L Het, are essential for viability and/or fertility. This work contributes to the functional annotation of centric heterochromatin in Drosophila, and the genetic and molecular tools generated should help to provide important insights into the organization and functions of gene sequences in 3L Het.
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7
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Wang H, Zhang XM, Tomiyoshi G, Nakamura R, Shinmen N, Kuroda H, Kimura R, Mine S, Kamitsukasa I, Wada T, Aotsuka A, Yoshida Y, Kobayashi E, Matsutani T, Iwadate Y, Sugimoto K, Mori M, Uzawa A, Muto M, Kuwabara S, Takemoto M, Kobayashi K, Kawamura H, Ishibashi R, Yokote K, Ohno M, Chen PM, Nishi E, Ono K, Kimura T, Machida T, Takizawa H, Kashiwado K, Shimada H, Ito M, Goto KI, Iwase K, Ashino H, Taira A, Arita E, Takiguchi M, Hiwasa T. Association of serum levels of antibodies against MMP1, CBX1, and CBX5 with transient ischemic attack and cerebral infarction. Oncotarget 2017; 9:5600-5613. [PMID: 29464021 PMCID: PMC5814161 DOI: 10.18632/oncotarget.23789] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/16/2017] [Indexed: 11/25/2022] Open
Abstract
Transient ischemic attack (TIA) is a predictor for cerebral infarction (CI), and early diagnosis of TIA is extremely important for the prevention of CI. We set out to identify novel antibody biomarkers for TIA and CI, and detected matrix metalloproteinase 1 (MMP1), chromobox homolog 1 (CBX1), and chromobox homolog 5 (CBX5) as candidate antigens using serological identification of antigens by recombinant cDNA expression cloning (SEREX) and Western blotting to confirm the presence of serum antibodies against the antigens. Amplified luminescent proximity homogeneous assay-linked immunosorbent assay (AlphaLISA) revealed that serum antibody levels were significantly higher in patients with TIA or acute-phase CI (aCI) compared with healthy donors (P < 0.01). Spearman’s correlation analysis and multivariate logistic regression analysis demonstrated that levels of anti-MMP1, anti-CBX1, and anti-CBX5 antibodies were associated with age, cigarette-smoking habits, and blood pressure. Thus, serum levels of antibodies against MMP1, CBX1, and CBX5 could potentially serve as useful tools for diagnosing TIA and predicting the onset of aCI.
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Affiliation(s)
- Hao Wang
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Anesthesia, The First Affiliated Hospital, Jinan University, Guangzhou, P. R. China
| | - Xiao-Meng Zhang
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Go Tomiyoshi
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan.,Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, Japan
| | - Rika Nakamura
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan.,Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, Japan
| | - Natsuko Shinmen
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan.,Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, Japan
| | - Hideyuki Kuroda
- Medical Project Division, Research Development Center, Fujikura Kasei Co., Saitama, Japan
| | - Risa Kimura
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Seiichiro Mine
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Neurological Surgery, Chiba Prefectural Sawara Hospital, Chiba, Japan.,Department of Neurosurgery, Chiba Cerebral and Cardiovascular Center, Chiba, Japan
| | - Ikuo Kamitsukasa
- Department of Neurology, Chiba Rosai Hospital, Chiba, Japan.,Department of Neurology, Chibaken Saiseikai Narashino Hospital, Chiba, Japan
| | - Takeshi Wada
- Department of Internal Medicine, Chiba Aoba Municipal Hospital, Chiba, Japan
| | - Akiyo Aotsuka
- Department of Internal Medicine, Chiba Aoba Municipal Hospital, Chiba, Japan
| | - Yoichi Yoshida
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Eiichi Kobayashi
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoo Matsutani
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yasuo Iwadate
- Department of Neurological Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuo Sugimoto
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masahiro Mori
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akiyuki Uzawa
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mayumi Muto
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Kuwabara
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Minoru Takemoto
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuki Kobayashi
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Harukiyo Kawamura
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ryoichi Ishibashi
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Koutaro Yokote
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mikiko Ohno
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Pharmacology, Shiga University of Medical Science, Shiga, Japan
| | - Po-Min Chen
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eiichiro Nishi
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Pharmacology, Shiga University of Medical Science, Shiga, Japan
| | - Koh Ono
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshio Machida
- Department of Neurosurgery, Chiba Cerebral and Cardiovascular Center, Chiba, Japan
| | - Hirotaka Takizawa
- Port Square Kashiwado Clinic, Kashiwado Memorial Foundation, Chiba, Japan
| | | | - Hideaki Shimada
- Department of Surgery, School of Medicine, Toho University, Tokyo, Japan
| | - Masaaki Ito
- Department of Surgery, School of Medicine, Toho University, Tokyo, Japan
| | - Ken-Ichiro Goto
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Katsuro Iwase
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiromi Ashino
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akiko Taira
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Emiko Arita
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Takiguchi
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takaki Hiwasa
- Department of Biochemistry and Genetics, Graduate School of Medicine, Chiba University, Chiba, Japan
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8
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Lee YCG, Karpen GH. Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. eLife 2017; 6. [PMID: 28695823 PMCID: PMC5505702 DOI: 10.7554/elife.25762] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are widespread genomic parasites, and their evolution has remained a critical question in evolutionary genomics. Here, we study the relatively unexplored epigenetic impacts of TEs and provide the first genome-wide quantification of such effects in D. melanogaster and D. simulans. Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend up to 20 kb. This results in differential epigenetic states of genic alleles and, in turn, selection against TEs. Interestingly, the lower TE content in D. simulans compared to D. melanogaster correlates with stronger epigenetic effects of TEs and higher levels of host genetic factors known to promote epigenetic silencing. Our study demonstrates that the epigenetic effects of euchromatic TEs, and host genetic factors modulating such effects, play a critical role in the evolution of TEs both within and between species. DOI:http://dx.doi.org/10.7554/eLife.25762.001 The DNA inside an organism encodes all the instructions needed for the organism to develop and work properly. Organisms carefully organize and maintain their DNA (collectively known as the genome) so that the genetic information remains intact and the cell can understand the instructions. However, there are some pieces of DNA that are capable of moving around the genome. For example, pieces known as transposable elements can make new copies of themselves and jump into new locations in the genome. Most transposons do not appear to have any important roles, and in fact they are usually harmful to organisms. Despite this, transposons are present in the genomes of almost all species. The number of transposons in a genome varies greatly between individuals and species, but it is not clear why this is the case. Organisms have evolved ways to limit the damage caused by transposons. For example, many cells package regions of DNA containing transposons into a tightly packed structure known as heterochromatin. However, this type of DNA packaging sometimes spreads to neighboring sections of DNA. This is a problem because cells are not usually able to read the information contained within heterochromatin. This means that transposons can prevent some instructions from being produced when they should be. Lee and Karpen used fruit flies to investigate to what extent transposons harm organisms by changing the way DNA is packaged, and whether this influences how transposons evolve. The experiments show that that more than half of the transposons in fruit flies cause neighboring sections of DNA to be packaged into heterochromatin. This can negatively impact up to 20% of genes in the genome. As a result, transposons that have harmful effects on DNA packaging are more likely to be lost from the fly population during evolution than transposons that do not have harmful effects. Fruit fly species containing transposons that tend to package more neighboring sections of DNA into heterochromatin generally have fewer transposons than genomes containing less harmful transposons. The findings of Lee and Karpen provide new insight as to why the numbers of transposons vary among organisms. The next challenge is to find out whether transposons that alter how DNA is packaged are also common in primates and other animals. DOI:http://dx.doi.org/10.7554/eLife.25762.002
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Affiliation(s)
- Yuh Chwen G Lee
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, United States
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9
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McCracken A, Locke J. Mutations in ash1 and trx enhance P-element-dependent silencing in Drosophila melanogaster. Genome 2016; 59:527-40. [PMID: 27373142 DOI: 10.1139/gen-2014-0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Drosophila melanogaster, the mini-w(+) transgene in Pci is normally expressed throughout the adult eye; however, when other P or KP elements are present, a variegated-eye phenotype results, indicating random w(+) silencing during development called P-element-dependent silencing (PDS). Mutant Su(var)205 and Su(var)3-7 alleles act as haplo-suppressors/triplo-enhancers of this variegated phenotype, indicating that these heterochromatic modifiers act dose dependently in PDS. Previously, we recovered a spontaneous mutation of P{lacW}ci(Dplac) called P{lacW}ci(DplacE1) (E1) that variegated in the absence of P elements, presumably due to the insertion of an adjacent gypsy element. From a screen for genetic modifiers of E1 variegation, we describe here the isolation of five mutations in ash1 and three in trx that enhance the E1 variegated phenotype in a dose-dependent and cumulative manner. These mutant alleles enhance PDS at E1, and in E1/P{lacW}ci(Dplac), but suppress position effect variegation (PEV) at In(1)w(m)(4). This opposite action is consistent with a model where ASH1 and TRX mark transcriptionally active chromatin domains. If ASH1 or TRX function is lost or reduced, heterochromatin can spread into these domains creating a sink that diverts heterochromatic proteins from other variegating locations, which then may express a suppressed phenotype.
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Affiliation(s)
- Allen McCracken
- Department of Biological Sciences, CW 405, Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada.,Department of Biological Sciences, CW 405, Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - John Locke
- Department of Biological Sciences, CW 405, Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada.,Department of Biological Sciences, CW 405, Biological Sciences Building, University of Alberta, Edmonton, AB T6G 2E9, Canada
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10
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Masson F, Zaidman-Rémy A, Heddi A. Antimicrobial peptides and cell processes tracking endosymbiont dynamics. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150298. [PMID: 27160600 PMCID: PMC4874395 DOI: 10.1098/rstb.2015.0298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2016] [Indexed: 11/12/2022] Open
Abstract
Many insects sustain long-term relationships with intracellular symbiotic bacteria that provide them with essential nutrients. Such endosymbiotic relationships likely emerged from ancestral infections of the host by free-living bacteria, the genomes of which experience drastic gene losses and rearrangements during the host-symbiont coevolution. While it is well documented that endosymbiont genome shrinkage results in the loss of bacterial virulence genes, whether and how the host immune system evolves towards the tolerance and control of bacterial partners remains elusive. Remarkably, many insects rely on a 'compartmentalization strategy' that consists in secluding endosymbionts within specialized host cells, the bacteriocytes, thus preventing direct symbiont contact with the host systemic immune system. In this review, we compile recent advances in the understanding of the bacteriocyte immune and cellular regulators involved in endosymbiont maintenance and control. We focus on the cereal weevils Sitophilus spp., in which bacteriocytes form bacteriome organs that strikingly evolve in structure and number according to insect development and physiological needs. We discuss how weevils track endosymbiont dynamics through at least two mechanisms: (i) a bacteriome local antimicrobial peptide synthesis that regulates endosymbiont cell cytokinesis and helps to maintain a homeostatic state within bacteriocytes and (ii) some cellular processes such as apoptosis and autophagy which adjust endosymbiont load to the host developmental requirements, hence ensuring a fine-tuned integration of symbiosis costs and benefits.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.
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Affiliation(s)
- Florent Masson
- Université de Lyon, INSA-Lyon, INRA, BF2I, UMR0203, 69621 Villeurbanne, France
| | - Anna Zaidman-Rémy
- Université de Lyon, INSA-Lyon, INRA, BF2I, UMR0203, 69621 Villeurbanne, France
| | - Abdelaziz Heddi
- Université de Lyon, INSA-Lyon, INRA, BF2I, UMR0203, 69621 Villeurbanne, France
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11
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Coulthard AB, Taylor-Kamall RW, Hallson G, Axentiev A, Sinclair DA, Honda BM, Hilliker AJ. Meiotic recombination is suppressed near the histone-defined border of euchromatin and heterochromatin on chromosome 2L of Drosophila melanogaster. Genome 2016; 59:289-94. [DOI: 10.1139/gen-2015-0171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Drosophila melanogaster, the borders between pericentric heterochromatin and euchromatin on the major chromosome arms have been defined in various ways, including chromatin-specific histone modifications, the binding patterns of heterochromatin-enriched chromosomal proteins, and various cytogenetic techniques. Elucidation of the genetic properties that independently define the different chromatin states associated with heterochromatin and euchromatin should help refine the boundary. Since meiotic recombination is present in euchromatin, but absent in heterochromatin, it constitutes a key genetic property that can be observed transitioning between chromatin states. Using P element insertion lines marked with a su(Hw) insulated mini-white gene, meiotic recombination was found to transition in a region consistent with the H3K9me2 transition observed in ovaries.
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Affiliation(s)
| | | | - Graham Hallson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Anna Axentiev
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Don A. Sinclair
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Barry M. Honda
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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12
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Fang C, Schmitz L, Ferree PM. An unusually simple HP1 gene set in Hymenopteran insects. Biochem Cell Biol 2015; 93:596-603. [PMID: 26419616 DOI: 10.1139/bcb-2015-0046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The heterochromatin protein 1 (HP1) gene family includes a set of paralogs in higher eukaryotes that serve fundamental roles in heterochromatin structure and maintenance, and other chromatin-related functions. At least 10 full and 16 partial HP1 genes exist among Drosophila species, with multiple gene gains, losses, and sub-functionalizations within this insect group. An important question is whether this diverse set of HP1 genes and their dynamic evolution represent the standard rule in eukaryotic groups. Here we have begun to address this question by bio-informatically identifying the HP1 family genes in representative species of the insect order Hymenoptera, which includes all ants, bees, wasps, and sawflies. Compared to Drosophila species, Hymenopterans have a much simpler set of HP1 genes, including one full and two partial HP1s. All 3 genes appear to have been present in the common ancestor of the Hymenopterans and they derive from a Drosophila HP1B-like gene. In ants, a partial HP1 gene containing only a chromoshadow domain harbors amino acid changes at highly conserved sites within the PxVxL recognition region, suggesting that this gene has undergone sub-functionalization. In the jewel wasp Nasonia vitripennis, the full HP1 and partial chromoshadow-only HP1 are expressed in both germ line and somatic tissues. However, the partial chromodomain-only HP1 is expressed exclusively in the ovary and testis, suggesting that it may have a specialized chromatin role during gametogenesis. Our findings demonstrate that the HP1 gene family is much simpler and evolutionarily less dynamic within the Hymenopterans compared to the much younger Drosophila group, a pattern that may reflect major differences in the range of chromatin-related functions present in these and perhaps other insect groups.
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Affiliation(s)
- C Fang
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - L Schmitz
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - P M Ferree
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA.,W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
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13
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Teif VB, Kepper N, Yserentant K, Wedemann G, Rippe K. Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arrays. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064110. [PMID: 25563825 DOI: 10.1088/0953-8984/27/6/064110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Heterochromatin protein 1 (HP1) participates in establishing and maintaining heterochromatin via its histone-modification-dependent chromatin interactions. In recent papers HP1 binding to nucleosomal arrays was measured in vitro and interpreted in terms of nearest-neighbour cooperative binding. This mode of chromatin interaction could lead to the spreading of HP1 along the nucleosome chain. Here, we reanalysed previous data by representing the nucleosome chain as a 1D binding lattice and showed how the experimental HP1 binding isotherms can be explained by a simpler model without cooperative interactions between neighboring HP1 dimers. Based on these calculations and spatial models of dinucleosomes and nucleosome chains, we propose that binding stoichiometry depends on the nucleosome repeat length (NRL) rather than protein interactions between HP1 dimers. According to our calculations, more open nucleosome arrays with long DNA linkers are characterized by a larger number of binding sites in comparison to chains with a short NRL. Furthermore, we demonstrate by Monte Carlo simulations that the NRL dependent folding of the nucleosome chain can induce allosteric changes of HP1 binding sites. Thus, HP1 chromatin interactions can be modulated by the change of binding stoichiometry and the type of binding to condensed (methylated) and non-condensed (unmethylated) nucleosome arrays in the absence of direct interactions between HP1 dimers.
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Affiliation(s)
- Vladimir B Teif
- Deutsches Krebsforschungszentrum & BioQuant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
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14
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Sak A, Kübler D, Bannik K, Groneberg M, Stuschke M. Dependence of radiation-induced H2AX phosphorylation on histone methylation: Evidence from the chromatin immunoprecipitation assay. Int J Radiat Biol 2015; 91:346-53. [DOI: 10.3109/09553002.2015.997895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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15
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Burgess RC, Burman B, Kruhlak MJ, Misteli T. Activation of DNA damage response signaling by condensed chromatin. Cell Rep 2014; 9:1703-1717. [PMID: 25464843 DOI: 10.1016/j.celrep.2014.10.060] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/11/2014] [Accepted: 10/25/2014] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) occurs in the context of chromatin, and architectural features of chromatin have been implicated in DNA damage signaling and repair. Whereas a role of chromatin decondensation in the DDR is well established, we show here that chromatin condensation is integral to DDR signaling. We find that, in response to DNA damage chromatin regions transiently expand before undergoing extensive compaction. Using a protein-chromatin-tethering system to create defined chromatin domains, we show that interference with chromatin condensation results in failure to fully activate DDR. Conversely, forced induction of local chromatin condensation promotes ataxia telangiectasia mutated (ATM)- and ATR-dependent activation of upstream DDR signaling in a break-independent manner. Whereas persistent chromatin compaction enhanced upstream DDR signaling from irradiation-induced breaks, it reduced recovery and survival after damage. Our results demonstrate that chromatin condensation is sufficient for activation of DDR signaling and is an integral part of physiological DDR signaling.
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Affiliation(s)
- Rebecca C Burgess
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bharat Burman
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Program in Cell, Molecular and Developmental Biology, Sackler School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Michael J Kruhlak
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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16
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Müller-Ott K, Erdel F, Matveeva A, Mallm JP, Rademacher A, Hahn M, Bauer C, Zhang Q, Kaltofen S, Schotta G, Höfer T, Rippe K. Specificity, propagation, and memory of pericentric heterochromatin. Mol Syst Biol 2014; 10:746. [PMID: 25134515 PMCID: PMC4299515 DOI: 10.15252/msb.20145377] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The cell establishes heritable patterns of active and silenced chromatin via interacting factors
that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we
have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts.
We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in
living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2
demarcate the PCH state. From the experimental data, we developed a predictive mathematical model
that explains how chromatin-bound SUV39H1/2 complexes act as nucleation sites and propagate a
spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin
dynamics. This “nucleation and looping” mechanism is particularly robust toward
transient perturbations and stably maintains the PCH state. These features make it an attractive
model for establishing functional epigenetic domains throughout the genome based on the localized
immobilization of chromatin-modifying enzymes.
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Affiliation(s)
- Katharina Müller-Ott
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Fabian Erdel
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anna Matveeva
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anne Rademacher
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Matthias Hahn
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Caroline Bauer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Qin Zhang
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Sabine Kaltofen
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Gunnar Schotta
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Thomas Höfer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
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17
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Jiang N, Du G, Tobias E, Wood JG, Whitaker R, Neretti N, Helfand SL. Dietary and genetic effects on age-related loss of gene silencing reveal epigenetic plasticity of chromatin repression during aging. Aging (Albany NY) 2014; 5:813-24. [PMID: 24243774 PMCID: PMC3868724 DOI: 10.18632/aging.100614] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
During aging, changes in chromatin state that alter gene transcription have been postulated to result in expression of genes that are normally silenced, leading to deleterious age-related effects on cellular physiology. Despite the prevalence of this hypothesis, it is primarily in yeast that loss of gene silencing with age has been well documented. We use a novel position effect variegation (PEV) reporter in Drosophila melanogaster to show that age-related loss of repressive heterochromatin is associated with loss of gene silencing in metazoans and is affected by Sir2, as it is in yeast. The life span-extending intervention, calorie restriction (CR), delays the age-related loss of gene silencing, indicating that loss of gene silencing is a component of normal aging. Diet switch experiments show that such flies undergo a rapid change in their level of gene silencing, demonstrating the epigenetic plasticity of chromatin during aging and highlighting the potential role of diet and metabolism in chromatin maintenance, Thus, diet and related interventions may be of therapeutic importance for age-related diseases, such as cancer.
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Affiliation(s)
- Nan Jiang
- Department of Molecular Biology, Cell Biology and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA
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18
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Xu N, Emelyanov AV, Fyodorov DV, Skoultchi AI. Drosophila linker histone H1 coordinates STAT-dependent organization of heterochromatin and suppresses tumorigenesis caused by hyperactive JAK-STAT signaling. Epigenetics Chromatin 2014; 7:16. [PMID: 25177369 PMCID: PMC4149798 DOI: 10.1186/1756-8935-7-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/08/2014] [Indexed: 02/06/2023] Open
Abstract
Background Within the nucleus of eukaryotic cells, chromatin is organized into compact, silent regions called heterochromatin and more loosely packaged regions of euchromatin where transcription is more active. Although the existence of heterochromatin has been known for many years, the cellular factors responsible for its formation have only recently been identified. Two key factors involved in heterochromatin formation in Drosophila are the H3 lysine 9 methyltransferase Su(var)3-9 and heterochromatin protein 1 (HP1). The linker histone H1 also plays a major role in heterochromatin formation in Drosophila by interacting with Su(var)3-9 and helping to recruit it to heterochromatin. Drosophila STAT (Signal transducer and activator of transcription) (STAT92E) has also been shown to be involved in the maintenance of heterochromatin, but its relationship to the H1-Su(var)3-9 heterochromatin pathway is unknown. STAT92E is also involved in tumor formation in flies. Hyperactive Janus kinase (JAK)-STAT signaling due to a mutation in Drosophila JAK (Hopscotch) causes hematopoietic tumors Results We show here that STAT92E is a second partner of H1 in the regulation of heterochromatin structure. H1 physically interacts with STAT92E and regulates its ectopic localization in the chromatin. Mis-localization of STAT92E due to its hyperphosphorylation or H1 depletion disrupts heterochromatin integrity. The contribution of the H1-STAT pathway to heterochromatin formation is mechanistically distinct from that of H1 and Su(var)3-9. The recruitment of STAT92E to chromatin by H1 also plays an important regulatory role in JAK-STAT induced tumors in flies. Depleting the linker histone H1 in flies carrying the oncogenic hopscotchTum-l allele enhances tumorigenesis, and H1 overexpression suppresses tumorigenesis. Conclusions Our results suggest the existence of two independent pathways for heterochromatin formation in Drosophila, one involving Su(var)3-9 and HP1 and the other involving STAT92E and HP1. The H1 linker histone directs both pathways through physical interactions with Su(var)3-9 and STAT92E, as well with HP1. The physical interaction of H1 and STAT92E confers a regulatory role on H1 in JAK-STAT signaling. H1 serves as a molecular reservoir for STAT92E in chromatin, enabling H1 to act as a tumor suppressor and oppose an oncogenic mutation in the JAK-STAT signaling pathway.
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Affiliation(s)
- Na Xu
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Alexander V Emelyanov
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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19
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Basquin D, Spierer A, Begeot F, Koryakov DE, Todeschini AL, Ronsseray S, Vieira C, Spierer P, Delattre M. The Drosophila Su(var)3-7 gene is required for oogenesis and female fertility, genetically interacts with piwi and aubergine, but impacts only weakly transposon silencing. PLoS One 2014; 9:e96802. [PMID: 24820312 PMCID: PMC4018442 DOI: 10.1371/journal.pone.0096802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/11/2014] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin is made of repetitive sequences, mainly transposable elements (TEs), the regulation of which is critical for genome stability. We have analyzed the role of the heterochromatin-associated Su(var)3-7 protein in Drosophila ovaries. We present evidences that Su(var)3-7 is required for correct oogenesis and female fertility. It accumulates in heterochromatic domains of ovarian germline and somatic cells nuclei, where it co-localizes with HP1. Homozygous mutant females display ovaries with frequent degenerating egg-chambers. Absence of Su(var)3-7 in embryos leads to defects in meiosis and first mitotic divisions due to chromatin fragmentation or chromosome loss, showing that Su(var)3-7 is required for genome integrity. Females homozygous for Su(var)3-7 mutations strongly impair repression of P-transposable element induced gonadal dysgenesis but have minor effects on other TEs. Su(var)3-7 mutations reduce piRNA cluster transcription and slightly impact ovarian piRNA production. However, this modest piRNA reduction does not correlate with transposon de-silencing, suggesting that the moderate effect of Su(var)3-7 on some TE repression is not linked to piRNA production. Strikingly, Su(var)3-7 genetically interacts with the piwi and aubergine genes, key components of the piRNA pathway, by strongly impacting female fertility without impairing transposon silencing. These results lead us to propose that the interaction between Su(var)3-7 and piwi or aubergine controls important developmental processes independently of transposon silencing.
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Affiliation(s)
- Denis Basquin
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Anne Spierer
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Flora Begeot
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Anne-Laure Todeschini
- Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, Paris, France
| | - Stéphane Ronsseray
- Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, Paris, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon1, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Pierre Spierer
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Marion Delattre
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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20
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Klenov MS, Lavrov SA, Korbut AP, Stolyarenko AD, Yakushev EY, Reuter M, Pillai RS, Gvozdev VA. Impact of nuclear Piwi elimination on chromatin state in Drosophila melanogaster ovaries. Nucleic Acids Res 2014; 42:6208-18. [PMID: 24782529 PMCID: PMC4041442 DOI: 10.1093/nar/gku268] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Piwi-interacting RNA (piRNA)-interacting Piwi protein is involved in transcriptional silencing of transposable elements in ovaries of Drosophila melanogaster. Here we characterized the genome-wide effect of nuclear Piwi elimination on the presence of the heterochromatic H3K9me3 mark and HP1a, as well as on the transcription-associated mark H3K4me2. Our results demonstrate that a significant increase in the H3K4me2 level upon nuclear Piwi loss is not accompanied by the alterations in H3K9me3 and HP1a levels for several germline-expressed transposons, suggesting that in this case Piwi prevents transcription by a mechanism distinct from H3K9 methylation. We found that the targets of Piwi-dependent chromatin repression are mainly related to the elements that display a higher level of H3K4me2 modification in the absence of silencing, i.e. most actively transcribed elements. We also show that Piwi-guided silencing does not significantly influence the chromatin state of dual-strand piRNA-producing clusters. In addition, host protein-coding gene expression is essentially not affected due to the nuclear Piwi elimination, but we noted an increase in small nuclear spliceosomal RNAs abundance and propose Piwi involvement in their post-transcriptional regulation. Our work reveals new aspects of transposon silencing in Drosophila, indicating that transcription of transposons can underpin their Piwi dependent silencing, while canonical heterochromatin marks are not obligatory for their repression.
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Affiliation(s)
- Mikhail S Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Sergey A Lavrov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Alina P Korbut
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | | | - Evgeny Y Yakushev
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Michael Reuter
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042 France Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042 France Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Vladimir A Gvozdev
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
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21
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Eissenberg JC, Elgin SCR. HP1a: a structural chromosomal protein regulating transcription. Trends Genet 2014; 30:103-10. [PMID: 24555990 DOI: 10.1016/j.tig.2014.01.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/17/2014] [Accepted: 01/17/2014] [Indexed: 01/16/2023]
Abstract
Heterochromatin protein 1 (HP1a in Drosophila) is a conserved eukaryotic chromosomal protein that is prominently associated with pericentric heterochromatin and mediates the concomitant gene silencing. Mechanistic studies implicate HP1 family proteins as 'hub proteins,' able to interact with a variety of chromosomal proteins through the chromo-shadow domain (CSD), as well as to recognize key histone modification sites [primarily histone H3 di/trimethyl Lys9 (H3K9me2/3)] through the chromodomain (CD). Consequently, HP1 has many important roles in chromatin architecture and impacts both gene expression and gene silencing, utilizing a variety of mechanisms. Clearly, HP1 function is altered by context, and potentially by post-translational modifications (PTMs). Here, we report on recent ideas as to how this versatile protein accomplishes its diverse functions.
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Affiliation(s)
- Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry & Molecular Biology, Saint Louis University School of Medicine, Doisy Research Center, 1100 South Grand Boulevard, St Louis, MO 63104, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, Campus Box 1037, One Brookings Drive, St Louis, MO 63130-4899, USA.
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22
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Gu T, Elgin SCR. Maternal depletion of Piwi, a component of the RNAi system, impacts heterochromatin formation in Drosophila. PLoS Genet 2013; 9:e1003780. [PMID: 24068954 PMCID: PMC3777992 DOI: 10.1371/journal.pgen.1003780] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 07/25/2013] [Indexed: 02/05/2023] Open
Abstract
A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains, and how that chromatin state is faithfully transmitted. Stable heterochromatin is necessary to silence transposable elements (TEs) and maintain genome integrity. Both the RNAi system and heterochromatin components HP1 (Swi6) and H3K9me2/3 are required for initial establishment of heterochromatin structures in S. pombe. Here we utilize both loss of function alleles and the newly developed Drosophila melanogaster transgenic shRNA lines to deplete proteins of interest at specific development stages to dissect their roles in heterochromatin assembly in early zygotes and in maintenance of the silencing chromatin state during development. Using reporters subject to Position Effect Variegation (PEV), we find that depletion of key proteins in the early embryo can lead to loss of silencing assayed at adult stages. The piRNA component Piwi is required in the early embryo for reporter silencing in non-gonadal somatic cells, but knock-down during larval stages has no impact. This implies that Piwi is involved in targeting HP1a when heterochromatin is established at the late blastoderm stage and possibly also during embryogenesis, but that the silent chromatin state created is transmitted through cell division independent of the piRNA system. In contrast, heterochromatin structural protein HP1a is required for both initial heterochromatin assembly and the following mitotic inheritance. HP1a profiles in piwi mutant animals confirm that Piwi depletion leads to decreased HP1a levels in pericentric heterochromatin, particularly in TEs. The results suggest that the major role of the piRNA system in assembly of heterochromatin in non-gonadal somatic cells occurs in the early embryo during heterochromatin formation, and further demonstrate that failure of heterochromatin formation in the early embryo impacts the phenotype of the adult.
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Affiliation(s)
- Tingting Gu
- Department of Biology, Washington University, Saint Louis, Missouri, United States of America
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23
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Erdel F, Müller-Ott K, Rippe K. Establishing epigenetic domains via chromatin-bound histone modifiers. Ann N Y Acad Sci 2013; 1305:29-43. [PMID: 24033539 DOI: 10.1111/nyas.12262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The eukaryotic nucleus harbors the DNA genome, which associates with histones and other chromosomal proteins into a complex referred to as chromatin. It provides an additional layer of so-called epigenetic information via histone modifications and DNA methylation on top of the DNA sequence that determines the cell's active gene expression program. The nucleus is devoid of internal organelles separated by membranes. Thus, free diffusive transport of proteins and RNA can occur throughout the space accessible for a given macromolecule. At the same time, chromatin is partitioned into different specialized structures such as nucleoli, chromosome territories, and heterochromatin domains that serve distinct functions. Here, we address the question of how the activity of chromatin-modifying enzymes is confined to chromatin subcompartments. We discuss mechanisms for establishing activity gradients of diffusive chromatin-modifying enzymes that could give rise to distinct chromatin domains within the cell nucleus. Interestingly, such gradients might directly result from immobilization of the enzymes on the flexible chromatin chain. Thus, locus-specific tethering of these enzymes to chromatin could have the potential to establish, maintain, or modulate epigenetic patterns of characteristic domain size.
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Affiliation(s)
- Fabian Erdel
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Im Neuenheimer Feld 280, Heidelberg, Germany
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24
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Elgin SCR, Reuter G. Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb Perspect Biol 2013; 5:a017780. [PMID: 23906716 DOI: 10.1101/cshperspect.a017780] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Position-effect variegation (PEV) results when a gene normally in euchromatin is juxtaposed with heterochromatin by rearrangement or transposition. When heterochromatin packaging spreads across the heterochromatin/euchromatin border, it causes transcriptional silencing in a stochastic pattern. PEV is intensely studied in Drosophila using the white gene. Screens for dominant mutations that suppress or enhance white variegation have identified many conserved epigenetic factors, including the histone H3 lysine 9 methyltransferase SU(VAR)3-9. Heterochromatin protein HP1a binds H3K9me2/3 and interacts with SU(VAR)3-9, creating a core memory system. Genetic, molecular, and biochemical analysis of PEV in Drosophila has contributed many key findings concerning establishment and maintenance of heterochromatin with concomitant gene silencing.
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Affiliation(s)
- Sarah C R Elgin
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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25
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Shatskikh AS, Gvozdev VA. Heterochromatin formation and transcription in relation to trans-inactivation of genes and their spatial organization in the nucleus. BIOCHEMISTRY (MOSCOW) 2013; 78:603-12. [DOI: 10.1134/s0006297913060060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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26
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Lu X, Wontakal SN, Kavi H, Kim BJ, Guzzardo PM, Emelyanov AV, Xu N, Hannon GJ, Zavadil J, Fyodorov DV, Skoultchi AI. Drosophila H1 regulates the genetic activity of heterochromatin by recruitment of Su(var)3-9. Science 2013; 340:78-81. [PMID: 23559249 DOI: 10.1126/science.1234654] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Eukaryotic genomes harbor transposable elements and other repetitive sequences that must be silenced. Small RNA interference pathways play a major role in their repression. Here, we reveal another mechanism for silencing these sequences in Drosophila. Depleting the linker histone H1 in vivo leads to strong activation of these elements. H1-mediated silencing occurs in combination with the heterochromatin-specific histone H3 lysine 9 methyltransferase Su(var)3-9. H1 physically interacts with Su(var)3-9 and recruits it to chromatin in vitro, which promotes H3 methylation. We propose that H1 plays a key role in silencing by tethering Su(var)3-9 to heterochromatin. The tethering function of H1 adds to its established role as a regulator of chromatin compaction and accessibility.
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Affiliation(s)
- Xingwu Lu
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Lundberg LE, Stenberg P, Larsson J. HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster. Nucleic Acids Res 2013; 41:4481-94. [PMID: 23476027 PMCID: PMC3632140 DOI: 10.1093/nar/gkt158] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Heterochromatin protein 1a (HP1a) is a chromatin-associated protein important for the formation and maintenance of heterochromatin. In Drosophila, the two histone methyltransferases SETDB1 and Su(var)3-9 mediate H3K9 methylation marks that initiates the establishment and spreading of HP1a-enriched chromatin. Although HP1a is generally regarded as a factor that represses gene transcription, several reports have linked HP1a binding to active genes, and in some cases, it has been shown to stimulate transcriptional activity. To clarify the function of HP1a in transcription regulation and its association with Su(var)3-9, SETDB1 and the chromosome 4-specific protein POF, we conducted genome-wide expression studies and combined the results with available binding data in Drosophila melanogaster. The results suggest that HP1a, SETDB1 and Su(var)3-9 repress genes on chromosome 4, where non-ubiquitously expressed genes are preferentially targeted, and stimulate genes in pericentromeric regions. Further, we showed that on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes. In addition, we found that transposons are repressed by HP1a and Su(var)3-9 and that the binding level and expression effects of HP1a are affected by gene length. Our results indicate that genes have adapted to be properly expressed in their local chromatin environment.
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Affiliation(s)
- Lina E Lundberg
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
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28
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Yankulov K. Dynamics and stability: epigenetic conversions in position effect variegation. Biochem Cell Biol 2013; 91:6-13. [DOI: 10.1139/bcb-2012-0048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Position effect variegation (PEV) refers to quasi-stable patterns of gene expression that are observed at specific loci throughout the genomes of eukaryotes. The genes subjected to PEV can be completely silenced or fully active. Stochastic conversions between these 2 states are responsible for the variegated phenotypes. Positional variegation is used by human pathogens (Trypanosoma, Plasmodium, and Candida) to evade the immune system or adapt to the host environment. In the yeasts Saccharomyces cerevisiae and S accharomyces pombe, telomeric PEV aids the adaptation to a changing environment. In metazoans, similar epigenetic conversions are likely to accompany cell differentiation and the setting of tissue-specific gene expression programs. Surprisingly, we know very little about the mechanisms of epigenetic conversions. In this article, earlier models on the nature of PEV are revisited and recent advances on the dynamic nature of chromatin are reviewed. The normal dynamic histone turnover during transcription and DNA replication and its perturbation at transcription and replication pause sites are discussed. It is proposed that such perturbations play key roles in epigenetic conversions and in PEV.
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Affiliation(s)
- Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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29
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Van Wynsberghe PM, Maine EM. Epigenetic control of germline development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:373-403. [PMID: 22872484 DOI: 10.1007/978-1-4614-4015-4_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Dynamic regulation of histone modifications and small noncoding RNAs is observed throughout the development of the C. elegans germ line. Histone modifications are differentially regulated in the mitotic vs meiotic germ line, on X chromosomes vs autosomes and on paired chromosomes vs unpaired chromosomes. Small RNAs function in transposon silencing and developmental gene regulation. Histone modifications and small RNAs produced in the germ line can be inherited and impact embryonic development. Disruption of histone-modifying enzymes or small RNA machinery in the germ line can result in sterility due to degeneration of the germ line and/or an inability to produce functional gametes.
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Figueiredo MLA, Philip P, Stenberg P, Larsson J. HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster. PLoS Genet 2012; 8:e1003061. [PMID: 23166515 PMCID: PMC3499360 DOI: 10.1371/journal.pgen.1003061] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 09/19/2012] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin protein 1 (HP1) proteins, recognized readers of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me), are important regulators of heterochromatin-mediated gene silencing and chromosome structure. In Drosophila melanogaster three histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9: Su(var)3-9, Setdb1, and G9a. To probe the dependence of HP1a binding on H3K9me, its dependence on these three HKMTs, and the division of labor between the HKMTs, we have examined correlations between HP1a binding and H3K9me patterns in wild type and null mutants of these HKMTs. We show here that Su(var)3-9 controls H3K9me-dependent binding of HP1a in pericentromeric regions, while Setdb1 controls it in cytological region 2L:31 and (together with POF) in chromosome 4. HP1a binds to the promoters and within bodies of active genes in these three regions. More importantly, however, HP1a binding at promoters of active genes is independent of H3K9me and POF. Rather, it is associated with heterochromatin protein 2 (HP2) and open chromatin. Our results support a hypothesis in which HP1a nucleates with high affinity independently of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites. HP1 is a key protein in heterochromatin and epigenetic silencing, a phenomenon involving chromatin condensation. It is generally accepted that HP1 forms a dimer that links two adjacent nucleosomes through interactions with histone 3 methylated at lysine 9 (H3K9me). Since HP1 also interacts with the histone lysine methyltransferases (HKMTs) generating this modification, histone H3 becomes methylated and HP1 spreading is propagated. Here, we show that HP1a in Drosophila binds to promoters of active genes on chromosome 4 and pericentromeric regions. In contrast to current dogma, this binding is independent of H3K9me. In the presence of the HKMTs and H3K9me, HP1a is also enriched within the bodies of the bound genes. These findings shed new light on the role of HP1a and the epigenetic nature of this chromatin mark. We propose that HP1a interacts independently of H3K9me with the nucleosome with high affinity, probably via the H3 histone-fold. This interaction is followed by a more transient interaction between HP1a and H3K9me, which results in spreading of the HP1a enrichment into gene bodies. Overall, the presented results and hypothesized model provide an explanation for this epigenetic mark and possibly more general insights into the relationships between chromo-domain proteins and methylated histones.
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Affiliation(s)
| | - Philge Philip
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Jan Larsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- * E-mail:
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31
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A forward genetic screen identifies eukaryotic translation initiation factor 3, subunit H (eIF3h), as an enhancer of variegation in the mouse. G3-GENES GENOMES GENETICS 2012; 2:1393-6. [PMID: 23173090 PMCID: PMC3484669 DOI: 10.1534/g3.112.004036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 09/10/2012] [Indexed: 12/25/2022]
Abstract
We have used a forward genetic screen to identify genes required for transgene silencing in the mouse. Previously these genes were found using candidate-based sequencing, a slow and labor-intensive process. Recently, whole-exome deep sequencing has accelerated our ability to find the causative point mutations, resulting in the discovery of novel and sometimes unexpected genes. Here we report the identification of translation initiation factor 3, subunit H (eIF3h) in two modifier of murine metastable epialleles (Mommes) lines. Mice carrying mutations in this gene have not been reported previously, and a possible involvement of eIF3h in transcription or epigenetic regulation has not been considered.
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33
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How can satellite DNA divergence cause reproductive isolation? Let us count the chromosomal ways. GENETICS RESEARCH INTERNATIONAL 2012; 2012:430136. [PMID: 22567387 PMCID: PMC3335601 DOI: 10.1155/2012/430136] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Accepted: 10/24/2011] [Indexed: 12/31/2022]
Abstract
Satellites are one of the most enigmatic parts of the eukaryotic genome. These highly repetitive, noncoding sequences make up as much as half or more of the genomic content and are known to play essential roles in chromosome segregation during meiosis and mitosis, yet they evolve rapidly between closely related species. Research over the last several decades has revealed that satellite divergence can serve as a formidable reproductive barrier between sibling species. Here we highlight several key studies on Drosophila and other model organisms demonstrating deleterious effects of satellites and their rapid evolution on the structure and function of chromosomes in interspecies hybrids. These studies demonstrate that satellites can impact chromosomes at a number of different developmental stages and through distinct cellular mechanisms, including heterochromatin formation. These findings have important implications for how loci that cause postzygotic reproductive isolation are viewed.
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34
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Dronamraju R, Mason JM. MU2 and HP1a regulate the recognition of double strand breaks in Drosophila melanogaster. PLoS One 2011; 6:e25439. [PMID: 21966530 PMCID: PMC3179522 DOI: 10.1371/journal.pone.0025439] [Citation(s) in RCA: 15] [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: 01/27/2011] [Accepted: 09/05/2011] [Indexed: 11/18/2022] Open
Abstract
Chromatin structure regulates the dynamics of the recognition and repair of DNA double strand breaks; open chromatin enhances the recruitment of DNA damage response factors, while compact chromatin is refractory to the assembly of radiation-induced repair foci. MU2, an orthologue of human MDC1, a scaffold for ionizing radiation-induced repair foci, is a widely distributed chromosomal protein in Drosophila melanogaster that moves to DNA repair foci after irradiation. Here we show using yeast 2 hybrid screens and co-immunoprecipitation that MU2 binds the chromoshadow domain of the heterochromatin protein HP1 in untreated cells. We asked what role HP1 plays in the formation of repair foci and cell cycle control in response to DNA damage. After irradiation repair foci form in heterochromatin but are shunted to the edge of heterochromatic regions an HP1-dependent manner, suggesting compartmentalized repair. Hydroxyurea-induced repair foci that form at collapsed replication forks, however, remain in the heterochromatic compartment. HP1a depletion in irradiated imaginal disc cells increases apoptosis and disrupts G2/M arrest. Further, cells irradiated in mitosis produced more and brighter repair foci than to cells irradiated during interphase. Thus, the interplay between MU2 and HP1a is dynamic and may be different in euchromatin and heterochromatin during DNA break recognition and repair.
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Affiliation(s)
- Raghuvar Dronamraju
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - James M. Mason
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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35
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Erdel F, Müller-Ott K, Baum M, Wachsmuth M, Rippe K. Dissecting chromatin interactions in living cells from protein mobility maps. Chromosome Res 2011; 19:99-115. [PMID: 20848178 DOI: 10.1007/s10577-010-9155-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The genome of eukaryotes is organized into a dynamic nucleoprotein complex referred to as chromatin, which can adopt different functional states. Both the DNA and the protein component of chromatin are subject to various post-translational modifications that define the cell's gene expression program. Their readout and establishment occurs in a spatio-temporally coordinated manner that is controlled by numerous chromatin-interacting proteins. Binding to chromatin in living cells can be measured by a spatially resolved analysis of protein mobility using fluorescence microscopy based approaches. Recent advancements in the acquisition of protein mobility data using fluorescence bleaching and correlation methods provide data sets on diffusion coefficients, binding kinetics, and cellular concentrations on different time and length scales. The combination of different techniques is needed to dissect the complex interplay of diffusive translocations, binding events, and mobility constraints of the chromatin environment. While bleaching techniques have their strength in the characterization of particles that are immobile on the second/minute time scale, a correlation analysis is advantageous to characterize transient binding events with millisecond residence time. The application and synergy effects of the different approaches to obtain protein mobility and interaction maps in the nucleus are illustrated for the analysis of heterochromatin protein 1.
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Affiliation(s)
- Fabian Erdel
- Deutsches Krebsforschungszentrum and BioQuant, Research Group Genome Organization and Function, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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36
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Margueron R, Reinberg D. Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 2011; 11:285-96. [PMID: 20300089 DOI: 10.1038/nrg2752] [Citation(s) in RCA: 506] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although it is widely accepted that the regulation of the chromatin landscape is pivotal to conveying the epigenetic program, it is still unclear how a defined chromatin domain is reproduced following DNA replication and transmitted from one cell generation to the next. Here, we review the multiple mechanisms that potentially affect the inheritance of epigenetic information in somatic cells. We consider models of how histones might be recycled following replication, and discuss the importance of positive-feedback loops, long-range gene interactions and the complex network of trans-acting factors in the transmission of chromatin states.
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Affiliation(s)
- Raphaël Margueron
- Howard Hughes Medical Institute, Department of Biochemistry, New York University School of Medicine, 522 First Avenue, New York, New York 10016, USA
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37
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Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 2011; 144:732-44. [PMID: 21353298 DOI: 10.1016/j.cell.2011.02.012] [Citation(s) in RCA: 396] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 12/15/2010] [Accepted: 02/07/2011] [Indexed: 01/07/2023]
Abstract
Double-strand breaks (DSBs) in heterochromatic repetitive DNAs pose significant threats to genome integrity, but information about how such lesions are processed and repaired is sparse. We observe dramatic expansion and dynamic protrusions of the heterochromatin domain in response to ionizing radiation (IR) in Drosophila cells. We also find that heterochromatic DSBs are repaired by homologous recombination (HR) but with striking differences from euchromatin. Proteins involved in early HR events (resection) are rapidly recruited to DSBs within heterochromatin. In contrast, Rad51, which mediates strand invasion, only associates with DSBs that relocalize outside of the domain. Heterochromatin expansion and relocalization of foci require checkpoint and resection proteins. Finally, the Smc5/6 complex is enriched in heterochromatin and is required to exclude Rad51 from the domain and prevent abnormal recombination. We propose that the spatial and temporal control of DSB repair in heterochromatin safeguards genome stability by preventing aberrant exchanges between repeats.
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38
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Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 2011; 21:147-63. [PMID: 21177972 PMCID: PMC3032919 DOI: 10.1101/gr.110098.110] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 12/08/2010] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the "silencing" marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin-heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin patterns reveals distinct profiles for euchromatin, pericentric heterochromatin, and the 4th chromosome. Both silent and active protein-coding genes in heterochromatin display complex patterns of chromosomal proteins and histone modifications; a majority of the active genes exhibit both "activation" marks (e.g., H3K4me3 and H3K36me3) and "silencing" marks (e.g., H3K9me2 and HP1a). The hallmark of active genes in heterochromatic domains appears to be a loss of H3K9 methylation at the transcription start site. We also observe complex epigenomic profiles of intergenic regions, repeated transposable element (TE) sequences, and genes in the heterochromatic extensions. An unexpectedly large fraction of sequences in the euchromatic chromosome arms exhibits a heterochromatic chromatin signature, which differs in size, position, and impact on gene expression among cell types. We conclude that patterns of heterochromatin/euchromatin packaging show greater complexity and plasticity than anticipated. This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin.
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Affiliation(s)
- Nicole C. Riddle
- Department of Biology, Washington University St. Louis, Missouri 63130, USA
| | - Aki Minoda
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Peter V. Kharchenko
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Artyom A. Alekseyenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yuri B. Schwartz
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
- Department of Molecular Biology, Umea University, 90187 Umea, Sweden
| | - Michael Y. Tolstorukov
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Andrey A. Gorchakov
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jacob D. Jaffe
- Proteomics Group, The Broad Institute, Cambridge, Massachusetts 02139, USA
| | - Cameron Kennedy
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Daniela Linder-Basso
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Sally E. Peach
- Proteomics Group, The Broad Institute, Cambridge, Massachusetts 02139, USA
| | - Gregory Shanower
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Resource, Center for Advanced Biotechnology and Medicine, University of Dentistry and Medicine of New Jersey, Piscataway, New Jersey 08854, USA
| | - Mitzi I. Kuroda
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vincenzo Pirrotta
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Peter J. Park
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Sarah C.R. Elgin
- Department of Biology, Washington University St. Louis, Missouri 63130, USA
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
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39
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Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SCR, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010; 330:1787-97. [PMID: 21177974 PMCID: PMC3192495 DOI: 10.1126/science.1198374] [Citation(s) in RCA: 911] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
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Affiliation(s)
| | - Sushmita Roy
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Jason Ernst
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Peter V. Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Nicolas Negre
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Matthew L. Eaton
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jane M. Landolin
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Christopher A. Bristow
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Michael F. Lin
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Stefan Washietl
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Bradley I. Arshinoff
- Department of Molecular Genetics, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1, Canada
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Ferhat Ay
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Patrick E. Meyer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Machine Learning Group, Université Libre de Bruxelles, CP212, Brussels 1050, Belgium
| | - Nicolas Robine
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | | | - Luisa Di Stefano
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Eugene Berezikov
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - Christopher D. Brown
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Rogerio Candeias
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Joseph W. Carlson
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Adrian Carr
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Daniel Marbach
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Rachel Sealfon
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Michael Y. Tolstorukov
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Sebastian Will
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Artyom A. Alekseyenko
- Department of Medicine and Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Carlo Artieri
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Benjamin W. Booth
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Angela N. Brooks
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Qi Dai
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - Carrie A. Davis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael O. Duff
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, 263 Farmington, CT 06030–6403, USA
| | - Xin Feng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Andrey A. Gorchakov
- Department of Medicine and Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tingting Gu
- Department of Biology CB-1137, Washington University, Saint Louis, MO 63130, USA
| | - Jorja G. Henikoff
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | | | - Renhua Li
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Heather K. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - John Malone
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Aki Minoda
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | | | - Katsutomo Okamura
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - Marc Perry
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Sara K. Powell
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicole C. Riddle
- Department of Biology CB-1137, Washington University, Saint Louis, MO 63130, USA
| | - Akiko Sakai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Anastasia Samsonova
- Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jeremy E. Sandler
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Yuri B. Schwartz
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Noa Sher
- White-head Institute, Cambridge, MA 02142, USA
| | - Rebecca Spokony
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - David Sturgill
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Marijke van Baren
- Center for Genome Sciences, Washington University, 4444 Forest Park Boulevard, Saint Louis, MO 63108, USA
| | - Kenneth H. Wan
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Li Yang
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, 263 Farmington, CT 06030–6403, USA
| | - Charles Yu
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Elise Feingold
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Peter Good
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Mark Guyer
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Rebecca Lowdon
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Kami Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Justen Andrews
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Michael R. Brent
- Center for Genome Sciences, Washington University, 4444 Forest Park Boulevard, Saint Louis, MO 63108, USA
| | - Lucy Cherbas
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
- Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - Sarah C. R. Elgin
- Department of Biology CB-1137, Washington University, Saint Louis, MO 63130, USA
| | - Thomas R. Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Affymetrix, Santa Clara, CA 95051, USA
| | - Robert Grossman
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Roger A. Hoskins
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Thomas C. Kaufman
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - William Kent
- Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute (HHMI), University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mitzi I. Kuroda
- Department of Medicine and Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Norbert Perrimon
- Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - James W. Posakony
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bing Ren
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Steven Russell
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Peter Cherbas
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
- Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - Brenton R. Graveley
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, 263 Farmington, CT 06030–6403, USA
| | - Suzanna Lewis
- Genome Sciences Division, LBNL, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Gos Micklem
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Peter J. Park
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Susan E. Celniker
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Gary H. Karpen
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Eric C. Lai
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - David M. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Kevin P. White
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
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40
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Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SCR, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 2010; 471:480-5. [PMID: 21179089 PMCID: PMC3109908 DOI: 10.1038/nature09725] [Citation(s) in RCA: 654] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 12/06/2010] [Indexed: 12/17/2022]
Abstract
Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.
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Affiliation(s)
- Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
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41
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Shermoen AW, McCleland ML, O'Farrell PH. Developmental control of late replication and S phase length. Curr Biol 2010; 20:2067-77. [PMID: 21074439 DOI: 10.1016/j.cub.2010.10.021] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 10/05/2010] [Accepted: 10/07/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND Fast, early embryonic cell cycles have correspondingly fast S phases. In early Drosophila embryos, forks starting from closely spaced origins replicate the whole genome in 3.4 min, ten times faster than in embryonic cycle 14 and a hundred times faster than in a wing disc. It is not known how S phase duration is regulated. Here we examined prolongation of embryonic S phases, its coupling to development, and its relationship to the appearance of heterochromatin. RESULTS Imaging of fluorescent nucleotide incorporation and GFP-PCNA gave exquisite time resolution of S phase events. In the early S phases, satellite sequences replicated rapidly despite a compact chromatin structure. In S phases 11-13, a delay in satellite replication emerged in sync with modest and progressive prolongation of S phase. In S phase 14, major and distinct delays ordered the replication of satellites into a sequence that occupied much of S phase. This onset of late replication required transcription. Satellites only accumulated abundant heterochromatin protein 1 (HP1) after replicating in S phase 14. By cycle 15, satellites clustered in a compact HP1-positive mass, but replication occurred at decondensed foci at the surface of this mass. CONCLUSIONS The slowing of S phase is an active process, not a titration of maternal replication machinery. Most sequences continue to replicate rapidly in successive cycles, but increasing delays in the replication of satellite sequences extend S phase. Although called constitutively heterochromatic, satellites acquire the distinctive features of heterochromatin, compaction, late replication, HP1 binding, and aggregation at the chromocenter, in successive steps coordinated with developmental progress.
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Affiliation(s)
- Antony W Shermoen
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143-2200, USA
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Abstract
Genetic screens in Drosophila have been instrumental in distinguishing approximately 390 loci involved in position effect variegation and heterochromatin stabilization. Most of the identified genes [so-called Su(var) and E(var) genes] are also conserved in mammals, where more than 50 of their gene products are known to localize to constitutive heterochromatin. From these proteins, approximately 12 core heterochromatin components can be inferred. In addition, there are approximately 30 additional Su(var) and 10 E(var) factors that can, under distinct developmental options, interchange with constitutive heterochromatin and participate in the partitioning of the genome into repressed and active chromatin domains. A significant fraction of the Su(var) and E(var) factors are enzymes that respond to environmental and metabolic signals, thereby allowing both the variation and propagation of epigenetic states to a dynamic chromatin template. Moreover, the misregulation of human SU(VAR) and E(VAR) function can advance cancer and many other human diseases including more complex disorders. As such, mammalian Su(var) and E(var) genes and their products provide a rich source of novel targets for diagnosis of and pharmaceutical intervention in many human diseases.
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Affiliation(s)
- Barna D Fodor
- Max-Planck Institute of Immunobiology, D-79108 Freiburg, Germany.
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43
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Tamaru H. Confining euchromatin/heterochromatin territory: jumonji crosses the line. Genes Dev 2010; 24:1465-78. [PMID: 20634313 DOI: 10.1101/gad.1941010] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Heterochromatin is typically highly condensed, gene-poor, and transcriptionally silent, whereas euchromatin is less condensed, gene-rich, and more accessible to transcription. Besides acting as a graveyard for selfish mobile DNA repeats, heterochromatin contributes to important biological functions, such as chromosome segregation during cell division. Multiple features of heterochromatin-including the presence or absence of specific histone modifications, DNA methylation, and small RNAs-have been implicated in distinguishing heterochromatin from euchromatin in various organisms. Cells malfunction if the genome fails to restrict repressive chromatin marks within heterochromatin domains. How euchromatin and heterochromatin territories are confined remains poorly understood. Recent studies from the fission yeast Schizosaccharomyces pombe, the flowering plant Arabidopsis thaliana, and the filamentous fungus Neurospora crassa have revealed a new role for Jumonji C (JmjC) domain-containing proteins in protecting euchromatin from heterochromatin marks.
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Affiliation(s)
- Hisashi Tamaru
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria.
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44
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Reo E, Seum C, Spierer P, Bontron S. Sumoylation of Drosophila SU(VAR)3-7 is required for its heterochromatic function. Nucleic Acids Res 2010; 38:4254-62. [PMID: 20299342 PMCID: PMC2910048 DOI: 10.1093/nar/gkq168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In Drosophila, SU(VAR)3-7 is an essential heterochromatin component. It is required for proper chromatin condensation, and changing its dose modifies position-effect variegation. Sumoylation is a post-translational modification shown to play a role in diverse biological processes. Here, we demonstrate that sumoylation is essential for proper heterochromatin function in Drosophila through modification of SU(VAR)3-7. Indeed, SU(VAR)3-7 is sumoylated at lysine K839; this modification is required for localization of SU(VAR)3-7 at pericentric heterochromatin, chromosome 4, and telomeres. In addition, sumoylation of SU(VAR)3-7 is a prerequisite for its ability to enhance position-effect variegation. Thus, these results show that the heterochromatic function of SU(VAR)3-7 depends on its own sumoylation, and unveil a role for sumoylation in Drosophila heterochromatin.
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Affiliation(s)
- Emanuela Reo
- Department of Zoology and Animal Biology, University of Geneva, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
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45
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Emelyanov AV, Konev AY, Vershilova E, Fyodorov DV. Protein complex of Drosophila ATRX/XNP and HP1a is required for the formation of pericentric beta-heterochromatin in vivo. J Biol Chem 2010; 285:15027-15037. [PMID: 20154359 DOI: 10.1074/jbc.m109.064790] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATRX belongs to the family of SWI2/SNF2-like ATP-dependent nucleosome remodeling molecular motor proteins. Mutations of the human ATRX gene result in a severe genetic disorder termed X-linked alpha-thalassemia mental retardation (ATR-X) syndrome. Here we perform biochemical and genetic analyses of the Drosophila melanogaster ortholog of ATRX. The loss of function allele of the Drosophila ATRX/XNP gene is semilethal. Drosophila ATRX is expressed throughout development in two isoforms, p185 and p125. ATRX185 and ATRX125 form distinct multisubunit complexes in fly embryo. The ATRX185 complex comprises p185 and heterochromatin protein HP1a. Consistently, ATRX185 but not ATRX125 is highly concentrated in pericentric beta-heterochromatin of the X chromosome in larval cells. HP1a strongly stimulates biochemical activities of ATRX185 in vitro. Conversely, ATRX185 is required for HP1a deposition in pericentric beta-heterochromatin of the X chromosome. The loss of function allele of the ATRX/XNP gene and mutant allele that does not express p185 are strong suppressors of position effect variegation. These results provide evidence for essential biological functions of Drosophila ATRX in vivo and establish ATRX as a major determinant of pericentric beta-heterochromatin identity.
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Affiliation(s)
- Alexander V Emelyanov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Alexander Y Konev
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Elena Vershilova
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461.
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46
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Vermaak D, Malik HS. Multiple roles for heterochromatin protein 1 genes in Drosophila. Annu Rev Genet 2009; 43:467-92. [PMID: 19919324 DOI: 10.1146/annurev-genet-102108-134802] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Heterochromatin is the gene-poor, transposon-rich, late-replicating chromatin compartment that was first cytologically defined more than 70 years ago. The identification of heterochromatin protein 1 (HP1) paved the way for a molecular dissection of this important component of complex eukaryotic genomes. Although initial studies revealed HP1's key role in heterochromatin maintenance and function, more recent studies have discovered a role for HP1 in numerous processes including, surprisingly, euchromatic gene expression. Drosophila genomes possess at least five HP1 paralogs that have significantly different roles, ranging from canonical heterochromatic function at pericentric and telomeric regions to exclusive localization and regulation of euchromatic genes. They also possess paralogs exclusively involved in defending the germline against mobile elements. Pursuing a survey of recent genetic and evolutionary findings, we highlight how Drosophila genomes represent the best opportunity to dissect the diversity and incredible versatility of HP1 proteins in organizing and protecting eukaryotic genomes.
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Affiliation(s)
- Danielle Vermaak
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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47
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Müller KP, Erdel F, Caudron-Herger M, Marth C, Fodor BD, Richter M, Scaranaro M, Beaudouin J, Wachsmuth M, Rippe K. Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy. Biophys J 2009; 97:2876-85. [PMID: 19948116 PMCID: PMC2784559 DOI: 10.1016/j.bpj.2009.08.057] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 08/17/2009] [Accepted: 08/27/2009] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin protein 1 (HP1) is a central factor in establishing and maintaining the repressive heterochromatin state. To elucidate its mobility and interactions, we conducted a comprehensive analysis on different time and length scales by fluorescence fluctuation microscopy in mouse cell lines. The local mobility of HP1alpha and HP1beta was investigated in densely packed pericentric heterochromatin foci and compared with other bona fide euchromatin regions of the nucleus by fluorescence bleaching and correlation methods. A quantitative description of HP1alpha/beta in terms of its concentration, diffusion coefficient, kinetic binding, and dissociation rate constants was derived. Three distinct classes of chromatin-binding sites with average residence times t(res)
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Affiliation(s)
- Katharina P Müller
- Deutsches Krebsforschungszentrum and BioQuant, Research Group Genome Organization and Function, Heidelberg, Germany
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48
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