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Zhang W, Cheng L, Li K, Xie L, Ji J, Lei X, Jiang A, Chen C, Li H, Li P, Sun Q. Evolutional heterochromatin condensation delineates chromocenter formation and retrotransposon silencing in plants. NATURE PLANTS 2024; 10:1215-1230. [PMID: 39014153 DOI: 10.1038/s41477-024-01746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/20/2024] [Indexed: 07/18/2024]
Abstract
Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. It is therefore puzzling that the presence of chromocenters is variable across plant species. Here we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter formation in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimaera of ADCP1 and HMGA, which remarkably enables formation of chromocenters. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and silencing retrotransposons.
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Affiliation(s)
- Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lingling Cheng
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Leiming Xie
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinyao Ji
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xue Lei
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Anjie Jiang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Chunlai Chen
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haitao Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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Gutiérrez J, Aleix-Mata G, Montiel EE, Cabral-de-Mello DC, Marchal JA, Sánchez A. Satellitome Analysis on Talpa aquitania Genome and Inferences about the satDNAs Evolution on Some Talpidae. Genes (Basel) 2022; 14:117. [PMID: 36672858 PMCID: PMC9859602 DOI: 10.3390/genes14010117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
In the genus Talpa a new species, named Talpa aquitania, has been recently described. Only cytogenetic data are available for the nuclear genome of this species. In this work, we characterize the satellitome of the T. aquitania genome that presents 16 different families, including telomeric sequences, and they represent 1.24% of the genome. The first satellite DNA family (TaquSat1-183) represents 0.558%, and six more abundant families, including TaquSat1-183, comprise 1.13%, while the remaining 11 sat-DNAs represent only 0.11%. The average A + T content of the SatDNA families was 50.43% and the median monomer length was 289.24 bp. The analysis of these SatDNAs indicated that they have different grades of clusterization, homogenization, and degeneration. Most of the satDNA families are present in the genomes of the other Talpa species analyzed, while in the genomes of other more distant species of Talpidae, only some of them are present, in accordance with the library hypothesis. Moreover, chromosomal localization by FISH revealed that some satDNAs are localized preferentially on centromeric and non-centromeric heterochromatin in T. aquitania and also in the sister species T. occidentalis karyotype. The differences observed between T. aquitania and the close relative T. occidentalis and T. europaea suggested that the satellitome is a very dynamic component of the genomes and that the satDNAs could be responsible for chromosomal differences between the species. Finally, in a broad context, these data contribute to the understanding of the evolution of satellitomes on mammals.
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Affiliation(s)
- Juana Gutiérrez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Eugenia E. Montiel
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Diogo C. Cabral-de-Mello
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP—Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
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3
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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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4
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Liu J, Ali M, Zhou Q. Establishment and evolution of heterochromatin. Ann N Y Acad Sci 2020; 1476:59-77. [PMID: 32017156 PMCID: PMC7586837 DOI: 10.1111/nyas.14303] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/31/2019] [Accepted: 01/02/2020] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome is packaged into transcriptionally active euchromatin and silent heterochromatin, with most studies focused on the former encompassing the majority of protein-coding genes. The recent development of various sequencing techniques has refined this classic dichromatic partition and has better illuminated the composition, establishment, and evolution of this genomic and epigenomic "dark matter" in the context of topologically associated domains and phase-separated droplets. Heterochromatin includes genomic regions that can be densely stained by chemical dyes, which have been shown to be enriched for repetitive elements and epigenetic marks, including H3K9me2/3 and H3K27me3. Heterochromatin is usually replicated late, concentrated at the nuclear periphery or around nucleoli, and usually lacks highly expressed genes; and now it is considered to be as neither genetically inert nor developmentally static. Heterochromatin guards genome integrity against transposon activities and exerts important regulatory functions by targeting beyond its contained genes. Both its nucleotide sequences and regulatory proteins exhibit rapid coevolution between species. In addition, there are dynamic transitions between euchromatin and heterochromatin during developmental and evolutionary processes. We summarize here the ever-changing characteristics of heterochromatin and propose models and principles for the evolutionary transitions of heterochromatin that have been mainly learned from studies of Drosophila and yeast. Finally, we highlight the role of sex chromosomes in studying heterochromatin evolution.
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Affiliation(s)
- Jing Liu
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Mujahid Ali
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
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Puppo IL, Saifitdinova AF, Tonyan ZN. The Role of Satellite DNA in Causing Structural Rearrangements in Human Karyotype. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419080155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Yadav R, Srivastava P. Establishment of resveratrol and its derivatives as neuroprotectant against monocrotophos-induced alteration in NIPBL and POU4F1 protein through molecular docking studies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:291-304. [PMID: 31786755 DOI: 10.1007/s11356-019-06806-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Monocrotophos (MCP) is a broad spectrum organophosphorus insecticide, which is widely used as foliar spray to the different important crops. MCP may reach the soil and the aquatic environment directly or indirectly during and after the application, which leads to the different environmental issues. MCP is found to be associated with neurotoxicity and its toxic effects have been monitored during different stages of neuronal development. Identification of gene expression in MCP-induced neurotoxicity during neuronal developmental stage is a major area of genomic research interest. In accordance with this identification, screening of potential neuroprotective, natural resources are also required as a preventive aspects by targeting the impaired genes. In this current course of work, microarray experiment has been used to identify genes that were expressed in monocrotophos (MCP)-induced mesenchymal stem cells (MSC) and also the neuroprotectant activity of RV on MCP-exposed MSCs. Microarray experiment data have been deposited in NCBI's Gene Expression Omnibus database and are accessible through GEO Series accession number GSE121261. In this paper, we have discussed two important genes NIPBL (nipped-B-like protein) and POU4F1 (POU domain, class 4, transcription factor 1). These genes were found to be significantly expressed in MCP-exposed MSC and show minimum expression in presence of RV. Homology modelling and docking study was done to identify the interaction and binding affinity of resveratrol and its derivatives with NIPBL and POU4F1 protein. Docking analysis shows that RV and its derivatives have strong interaction with NIPBL and POU4F1 protein hence proves the significance of resveratrol as potential neuroprotectant. This paper highlights the hazardous impact of MCP on neuronal development disorders and repairing potentiality of RV and its derivatives on altered genes involved in neuronal diseases. Graphical Abstract.
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Affiliation(s)
- Ruchi Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, U.P., India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, U.P., India.
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Mossman JA, Biancani LM, Rand DM. Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks. BMC Genomics 2019; 20:691. [PMID: 31477008 PMCID: PMC6719383 DOI: 10.1186/s12864-019-6061-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mitochondria perform many key roles in their eukaryotic hosts, from integrating signaling pathways through to modulating whole organism phenotypes. The > 1 billion years of nuclear and mitochondrial gene co-evolution has necessitated coordinated expression of gene products from both genomes that maintain mitochondrial, and more generally, eukaryotic cellular function. How mitochondrial DNA (mtDNA) variation modifies host fitness has proved a challenging question but has profound implications for evolutionary and medical genetics. In Drosophila, we have previously shown that recently diverged mtDNA haplotypes within-species can have more impact on organismal phenotypes than older, deeply diverged haplotypes from different species. Here, we tested the effects of mtDNA haplotype variation on gene expression in Drosophila under standardized conditions. Using the Drosophila Genetic Reference Panel (DGRP), we constructed a panel of mitonuclear genotypes that consists of factorial variation in nuclear and mtDNA genomes, with mtDNAs originating in D. melanogaster (2x haplotypes) and D. simulans (2x haplotypes). RESULTS We show that mtDNA haplotype variation unequivocally alters nuclear gene expression in both females and males, and mitonuclear interactions are pervasive modifying factors for gene expression. There was appreciable overlap between the sexes for mtDNA-sensitive genes, and considerable transcriptional variation attributed to particular mtDNA contrasts. These genes are generally found in low-connectivity gene co-expression networks, occur in gene clusters along chromosomes, are often flanked by non-coding RNA, and are under-represented among housekeeping genes. Finally, we identify the giant (gt) transcription factor motif as a putative regulatory sequence associated with mtDNA-sensitive genes. CONCLUSIONS There are predictive conditions for nuclear genes that are influenced by mtDNA variation.
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Affiliation(s)
- Jim A Mossman
- Department of Ecology and Evolutionary Biology, Box G, Brown University, Providence, RI, 02912, USA.
| | - Leann M Biancani
- Department of Ecology and Evolutionary Biology, Box G, Brown University, Providence, RI, 02912, USA
- Present Address: Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Box G, Brown University, Providence, RI, 02912, USA.
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Smail HO. The epigenetics of diabetes, obesity, overweight and cardiovascular disease. AIMS GENETICS 2019; 6:36-45. [PMID: 31663031 PMCID: PMC6803788 DOI: 10.3934/genet.2019.3.36] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023]
Abstract
The objectives of this review were once to understand the roles of the epigenetics mechanism in different types of diabetes, obesity, overweight, and cardiovascular disease. Epigenetics represents a phenomenon of change heritable phenotypic expression of genetic records taking place except changes in DNA sequence. Epigenetic modifications can have an impact on a whole of metabolic disease with the aid of specific alteration of candidate genes based totally on the change of the target genes. In this review, I summarized the new findings in DNA methylation, histone modifications in each type of diabetes (type 1 and type 2), obesity, overweight, and cardiovascular disease. The involvement of histone alterations and DNA methylation in the development of metabolic diseases is now widely accepted recently many novel genes have been demonstrated that has roles in diabetes pathway and it can be used for detection prediabetic; however Over the modern-day years, mass spectrometry-based proteomics techniques positioned and mapped one-of a kind range of histone modifications linking obesity and metabolic diseases. The main point of these changes is rapidly growing; however, their points and roles in obesity are no longer properly understood in obesity. Furthermore, epigenetic seen in cardiovascular treatment revealed a massive quantity of modifications affecting the improvement and development of cardiovascular disease. In addition, epigenetics are moreover involved in cardiovascular risk factors such as smoking. The aberrant epigenetic mechanisms that make a contribution to cardiovascular disease.
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Affiliation(s)
- Harem Othman Smail
- Department of Biology, Faculty of science and health, Koya University Koya KOY45, Kurdistan Region-F.R. Iraq
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A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster. Trends Genet 2019; 35:615-631. [PMID: 31320181 DOI: 10.1016/j.tig.2019.06.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/14/2022]
Abstract
Constitutive heterochromatin represents a significant portion of eukaryotic genomes, but its functions still need to be elucidated. Even in the most updated genetics and molecular biology textbooks, constitutive heterochromatin is portrayed mainly as the 'silent' component of eukaryotic genomes. However, there may be more complexity to the relationship between heterochromatin and gene expression. In the fruit fly Drosophila melanogaster, a model for heterochromatin studies, about one-third of the genome is heterochromatic and is concentrated in the centric, pericentric, and telomeric regions of the chromosomes. Recent findings indicate that hundreds of D. melanogaster genes can 'live and work' properly within constitutive heterochromatin. The genomic size of these genes is generally larger than that of euchromatic genes and together they account for a significant fraction of the entire constitutive heterochromatin. Thus, this peculiar genome component in spite its ability to induce silencing, has in fact the means for being quite dynamic. A major scope of this review is to revisit the 'dogma of silent heterochromatin'.
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Saha P, Sowpati DT, Mishra RK. Epigenomic and genomic landscape of Drosophila melanogaster heterochromatic genes. Genomics 2019; 111:177-185. [DOI: 10.1016/j.ygeno.2018.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 01/21/2018] [Accepted: 02/04/2018] [Indexed: 01/05/2023]
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Caizzi R, Moschetti R, Piacentini L, Fanti L, Marsano RM, Dimitri P. Comparative Genomic Analyses Provide New Insights into the Evolutionary Dynamics of Heterochromatin in Drosophila. PLoS Genet 2016; 12:e1006212. [PMID: 27513559 PMCID: PMC4981424 DOI: 10.1371/journal.pgen.1006212] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 07/02/2016] [Indexed: 12/21/2022] Open
Abstract
The term heterochromatin has been long considered synonymous with gene silencing, but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes. Several studies have addressed the epigenetic changes that enable the expression of genes in pericentric heterochromatin, yet little is known about the evolutionary processes through which this has occurred. By combining genome annotation analysis and high-resolution cytology, we have identified and mapped 53 orthologs of D. melanogaster heterochromatic genes in the genomes of two evolutionarily distant species, D. pseudoobscura and D. virilis. Our results show that the orthologs of the D. melanogaster heterochromatic genes are clustered at three main genomic regions in D. virilis and D. pseudoobscura. In D. virilis, the clusters lie in the middle of euchromatin, while those in D. pseudoobscura are located in the proximal portion of the chromosome arms. Some orthologs map to the corresponding Muller C element in D. pseudoobscura and D. virilis, while others localize on the Muller B element, suggesting that chromosomal rearrangements that have been instrumental in the fusion of two separate elements involved the progenitors of genes currently located in D. melanogaster heterochromatin. These results demonstrate an evolutionary repositioning of gene clusters from ancestral locations in euchromatin to the pericentromeric heterochromatin of descendent D. melanogaster chromosomes. Remarkably, in both D. virilis and D. pseudoobscura the gene clusters show a conserved association with the HP1a protein, one of the most highly evolutionarily conserved epigenetic marks. In light of these results, we suggest a new scenario whereby ancestral HP1-like proteins (and possibly other epigenetic marks) may have contributed to the evolutionary repositioning of gene clusters into heterochromatin.
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Affiliation(s)
- Ruggiero Caizzi
- Dipartimento di Biologia, Università degli Studi di Bari, Bari, Italy
- * E-mail: (RC); (PD)
| | - Roberta Moschetti
- Dipartimento di Biologia, Università degli Studi di Bari, Bari, Italy
| | - Lucia Piacentini
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Laura Fanti
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | | | - Patrizio Dimitri
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- * E-mail: (RC); (PD)
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Zhang Y, Máté G, Müller P, Hillebrandt S, Krufczik M, Bach M, Kaufmann R, Hausmann M, Heermann DW. Radiation induced chromatin conformation changes analysed by fluorescent localization microscopy, statistical physics, and graph theory. PLoS One 2015; 10:e0128555. [PMID: 26042422 PMCID: PMC4456097 DOI: 10.1371/journal.pone.0128555] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
It has been well established that the architecture of chromatin in cell nuclei is not random but functionally correlated. Chromatin damage caused by ionizing radiation raises complex repair machineries. This is accompanied by local chromatin rearrangements and structural changes which may for instance improve the accessibility of damaged sites for repair protein complexes. Using stably transfected HeLa cells expressing either green fluorescent protein (GFP) labelled histone H2B or yellow fluorescent protein (YFP) labelled histone H2A, we investigated the positioning of individual histone proteins in cell nuclei by means of high resolution localization microscopy (Spectral Position Determination Microscopy = SPDM). The cells were exposed to ionizing radiation of different doses and aliquots were fixed after different repair times for SPDM imaging. In addition to the repair dependent histone protein pattern, the positioning of antibodies specific for heterochromatin and euchromatin was separately recorded by SPDM. The present paper aims to provide a quantitative description of structural changes of chromatin after irradiation and during repair. It introduces a novel approach to analyse SPDM images by means of statistical physics and graph theory. The method is based on the calculation of the radial distribution functions as well as edge length distributions for graphs defined by a triangulation of the marker positions. The obtained results show that through the cell nucleus the different chromatin re-arrangements as detected by the fluorescent nucleosomal pattern average themselves. In contrast heterochromatic regions alone indicate a relaxation after radiation exposure and re-condensation during repair whereas euchromatin seemed to be unaffected or behave contrarily. SPDM in combination with the analysis techniques applied allows the systematic elucidation of chromatin re-arrangements after irradiation and during repair, if selected sub-regions of nuclei are investigated.
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Affiliation(s)
- Yang Zhang
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Gabriell Máté
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Patrick Müller
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Sabina Hillebrandt
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Matthias Krufczik
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Margund Bach
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Rainer Kaufmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Dieter W. Heermann
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
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Küçük H, Aydin Y, Erzurumluoglu E, Özdemir M, Hassa H, Artan S. The effects of a heterochromatin polymorphism in chromosome 6 on premature ovarian failure. ASIAN PACIFIC JOURNAL OF REPRODUCTION 2015. [DOI: 10.1016/s2305-0500(14)60056-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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15
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Zurano JP, Ojeda DS, Bidau CJ, Molina WF, Ledesma MA, Martinez PA. A comparison of heterochromatic regions in three species of neotropical canids. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2014.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Mehta GD, Kumar R, Srivastava S, Ghosh SK. Cohesin: functions beyond sister chromatid cohesion. FEBS Lett 2013; 587:2299-312. [PMID: 23831059 DOI: 10.1016/j.febslet.2013.06.035] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/23/2013] [Accepted: 06/24/2013] [Indexed: 11/22/2022]
Abstract
Faithful segregation of chromosomes during mitosis and meiosis is the cornerstone process of life. Cohesin, a multi-protein complex conserved from yeast to human, plays a crucial role in this process by keeping the sister chromatids together from S-phase to anaphase onset during mitosis and meiosis. Technological advancements have discovered myriad functions of cohesin beyond its role in sister chromatid cohesion (SCC), such as transcription regulation, DNA repair, chromosome condensation, homolog pairing, monoorientation of sister kinetochore, etc. Here, we have focused on such functions of cohesin that are either independent of or dependent on its canonical role of sister chromatid cohesion. At the end, human diseases associated with malfunctioning of cohesin, albeit with mostly unperturbed sister chromatid cohesion, have been discussed.
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Affiliation(s)
- Gunjan D Mehta
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai 400076, India
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Shyamasundar S, Jadhav SP, Bay BH, Tay SSW, Kumar SD, Rangasamy D, Dheen ST. Analysis of epigenetic factors in mouse embryonic neural stem cells exposed to hyperglycemia. PLoS One 2013; 8:e65945. [PMID: 23776576 PMCID: PMC3679101 DOI: 10.1371/journal.pone.0065945] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/30/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Maternal diabetes alters gene expression leading to neural tube defects (NTDs) in the developing brain. The mechanistic pathways that deregulate the gene expression remain unknown. It is hypothesized that exposure of neural stem cells (NSCs) to high glucose/hyperglycemia results in activation of epigenetic mechanisms which alter gene expression and cell fate during brain development. METHODS AND FINDINGS NSCs were isolated from normal pregnancy and streptozotocin induced-diabetic pregnancy and cultured in physiological glucose. In order to examine hyperglycemia induced epigenetic changes in NSCs, chromatin reorganization, global histone status at lysine 9 residue of histone H3 (acetylation and trimethylation) and global DNA methylation were examined and found to be altered by hyperglycemia. In NSCs, hyperglycemia increased the expression of Dcx (Doublecortin) and Pafah1b1 (Platelet activating factor acetyl hydrolase, isoform 1b, subunit 1) proteins concomitant with decreased expression of four microRNAs (mmu-miR-200a, mmu-miR-200b, mmu-miR-466a-3p and mmu-miR-466 d-3p) predicted to target these genes. Knockdown of specific microRNAs in NSCs resulted in increased expression of Dcx and Pafah1b1 proteins confirming target prediction and altered NSC fate by increasing the expression of neuronal and glial lineage markers. CONCLUSION/INTERPRETATION This study revealed that hyperglycemia alters the epigenetic mechanisms in NSCs, resulting in altered expression of some development control genes which may form the basis for the NTDs. Since epigenetic changes are reversible, they may be valuable therapeutic targets in order to improve fetal outcomes in diabetic pregnancy.
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Affiliation(s)
- Sukanya Shyamasundar
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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He B, Caudy A, Parsons L, Rosebrock A, Pane A, Raj S, Wieschaus E. Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster. Genome Res 2012; 22:2507-19. [PMID: 22745230 PMCID: PMC3514680 DOI: 10.1101/gr.137406.112] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes ("H-probes") for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin.
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Affiliation(s)
- Bing He
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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Finelli P, Sirchia SM, Masciadri M, Crippa M, Recalcati MP, Rusconi D, Giardino D, Monti L, Cogliati F, Faravelli F, Natacci F, Zoccante L, Bernardina BD, Russo S, Larizza L. Juxtaposition of heterochromatic and euchromatic regions by chromosomal translocation mediates a heterochromatic long-range position effect associated with a severe neurological phenotype. Mol Cytogenet 2012; 5:16. [PMID: 22475481 PMCID: PMC3395859 DOI: 10.1186/1755-8166-5-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/04/2012] [Indexed: 11/11/2022] Open
Abstract
Background The term "position effect" is used when the expression of a gene is deleteriously affected by an alteration in its chromosomal environment even though the integrity of the protein coding sequences is maintained. We describe a patient affected by epilepsy and severe neurodevelopment delay carrying a balanced translocation t(15;16)(p11.2;q12.1)dn that we assume caused a position effect as a result of the accidental juxtaposition of heterochromatin in the euchromatic region. Results FISH mapped the translocation breakpoints (bkps) to 15p11.2 within satellite III and the 16q12.1 euchromatic band within the ITFG1 gene. The expression of the genes located on both sides of the translocation were tested by means of real-time PCR and three, all located on der(16), were found to be variously perturbed: the euchromatic gene NETO2/BTCL2 was silenced, whereas VPS35 and SHCBP1, located within the major heterochromatic block of chromosome 16q11.2, were over-expressed. Pyrosequencing and chromatin immunoprecipitation of NETO2/BTCL2 and VPS35 confirmed the expression findings. Interphase FISH analysis showed that der(16) localised to regions occupied by the beta satellite heterochromatic blocks more frequently than der(15). Conclusions To the best of our knowledge, this is the first report of a heterochromatic position effect in humans caused by the juxtaposition of euchromatin/heterochromatin as a result of chromosomal rearrangement. The overall results are fully in keeping with the observations in Drosophila and suggest the occurrence of a human heterochromatin position effect associated with the nuclear repositioning of the der(16) and its causative role in the patient's syndromic phenotype.
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Affiliation(s)
- Palma Finelli
- Laboratory of Medical Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano, Cusano Milanino 20095, Italy.
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Xue K, Song J, Wei H, Chen L, Ma Y, Liu S, Li Y, Dai Y, Zhao Y, Li N. Synchronous behaviors of CBP and acetylations of lysine 18 and lysine 23 on histone H3 during porcine oocyte first meiotic division. Mol Reprod Dev 2010; 77:605-14. [PMID: 20575085 DOI: 10.1002/mrd.21190] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As a transcriptional coactivator and acetyltransferase, CREB-binding protein (CBP) is widely characterized due to its functions in cell proliferation and development. However, the activities of CBP in oocyte meiosis are not completely clear. Here we showed that the localization and expression of CBP changed regularly with the progression of porcine oocyte meiosis. The emergence of CBP in chromosomal domains is temporally coincident with the establishments of acetylated lysine 18 (AcH3/K18), lysine 23 (AcH3/K23) and dimethylated arginine 17 (dime-H3/R17) of histone H3 at meiotic stages from germinal vesicle breakdown (GVBD) to metaphase I (MI). Both CBP expression and these three histone modifications persisted to telophase I (TI). When trichostatin A (TSA) was used to enhance histone acetylations in porcine oocytes, we found that hyperacetylations of H3K18 and H3K23 occurred at meiotic stage from GVBD to TI, together with advanced and enhanced expression of CBP in the nucleus. In addition, disturbance of CBP activity by treatment with 2-Naphthol-AS-Ephosphate (KG-501, a drug targeting the KIX domain of CBP that disrupts the formation of CBP functional complex) led to synchronous decreases of CBP expression, AcH3/K18 and AcH3/K23 in chromosomal domains during oocyte meiosis. Therefore, these results indicate that the synchronous changes of CBP expression, AcH3/K18 and AcH3/K23 occur during porcine oocyte meiosis.
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Affiliation(s)
- Kai Xue
- State Key Laboratories for AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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21
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Silvers RM, Smith JA, Schowalter M, Litwin S, Liang Z, Geary K, Daniel R. Modification of integration site preferences of an HIV-1-based vector by expression of a novel synthetic protein. Hum Gene Ther 2010; 21:337-49. [PMID: 19877879 DOI: 10.1089/hum.2009.134] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
HIV-1-based lentiviral vectors are a promising tool for gene therapy. However, integration of a lentiviral vector into host cell genes may lead to the development of cancer. Therefore, control of integration site selection is critical to the successful outcome of gene therapy approaches that use these vectors. The discovery that integration site selection by HIV-1 and HIV-1-based vectors is controlled by the LEDGF/p75 protein has presented new opportunities to control integration site selection. In this study, we tested the hypothesis that a fusion protein containing the C-terminal HIV integrase-binding portion of LEDGF/p75, and the N-terminal chromodomain of heterochromatin protein-1alpha (HP1alpha), can target HIV-1 vector DNA outside of genes. We show that this fusion protein, termed TIHPLE, associates with the heterochromatin hallmark trimethylated Lys-9 of histone H3 (H3K9me3). Transient overexpression of TIHPLE alters integration site selection by an HIV-1-based vector and decreases the number of integration events that occur in genes. This change in integration site selection was achieved without a reduction in overall integration efficiency. Furthermore, we show that TIHPLE increases integration in the vicinity of H3K9me3 and in repetitive DNA sequences. These data provide a novel approach to address the problem of the tendency of retroviral vectors to integrate at undesirable sites of the human genome.
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Affiliation(s)
- Robert M Silvers
- Division of Infectious Diseases, Center for Human Virology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Sanyal A, Ammiraju JSS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J, San Miguel P, Mingsheng C, Wing RA, Jackson SA. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Mol Biol Evol 2010; 27:2487-506. [PMID: 20522726 DOI: 10.1093/molbev/msq133] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.
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Dimitri P, Caizzi R, Giordano E, Carmela Accardo M, Lattanzi G, Biamonti G. Constitutive heterochromatin: a surprising variety of expressed sequences. Chromosoma 2009; 118:419-35. [PMID: 19412619 DOI: 10.1007/s00412-009-0211-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
Abstract
The organization of chromosomes into euchromatin and heterochromatin is amongst the most important and enigmatic aspects of genome evolution. Constitutive heterochromatin is a basic yet still poorly understood component of eukaryotic chromosomes, and its molecular characterization by means of standard genomic approaches is intrinsically difficult. Although recent evidence indicates that the presence of transcribed genes in constitutive heterochromatin is a conserved trait that accompanies the evolution of eukaryotic genomes, the term heterochromatin is still considered by many as synonymous of gene silencing. In this paper, we comprehensively review data that provide a clearer picture of transcribed sequences within constitutive heterochromatin, with a special emphasis on Drosophila and humans.
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Affiliation(s)
- Patrizio Dimitri
- Laboratorio di Genomica Funzionale e Proteomica di Sistemi modello and Istituto Pasteur-Fondazione Bolognetti, Dipartimento di Genetica e Biologia Molecolare Charles Darwin, Università La Sapienza, 00185, Italy.
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Paço A, Adega F, Guedes-Pinto H, Chaves R. Hidden heterochromatin: Characterization in the Rodentia species Cricetus cricetus, Peromyscus eremicus (Cricetidae) and Praomys tullbergi (Muridae). Genet Mol Biol 2009; 32:58-68. [PMID: 21637647 PMCID: PMC3032958 DOI: 10.1590/s1415-47572009000100009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 07/14/2008] [Indexed: 11/22/2022] Open
Abstract
The use of in situ restriction endonuclease (RE) (which cleaves DNA at specific sequences) digestion has proven to be a useful technique in improving the dissection of constitutive heterochromatin (CH), and in the understanding of the CH evolution in different genomes. In the present work we describe in detail the CH of the three Rodentia species, Cricetus cricetus, Peromyscus eremicus (family Cricetidae) and Praomys tullbergi (family Muridae) using a panel of seven REs followed by C-banding. Comparison of the amount, distribution and molecular nature of C-positive heterochromatin revealed molecular heterogeneity in the heterochromatin of the three species. The large number of subclasses of CH identified in Praomys tullbergi chromosomes indicated that the karyotype of this species is the more derived when compared with the other two genomes analyzed, probably originated by a great number of complex chromosomal rearrangements. The high level of sequence heterogeneity identified in the CH of the three genomes suggests the coexistence of different satellite DNA families, or variants of these families in these genomes.
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Affiliation(s)
- Ana Paço
- Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real Portugal
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25
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Muhonen P, Holthofer H. Epigenetic and microRNA-mediated regulation in diabetes. Nephrol Dial Transplant 2009; 24:1088-96. [PMID: 19145005 PMCID: PMC2658734 DOI: 10.1093/ndt/gfn728] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Pirkko Muhonen
- Centre for BioAnalytical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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Abstract
The study of insect satellite DNAs (satDNAs) indicates the evolutionary conservation of certain features despite their sequence heterogeneity. Such features can include total length, monomer length, motifs, particular regions and/or secondary and tertiary structures. satDNAs may act as protein-binding sites, structural domains or sites for epigenetic modifications. The selective constraints in the evolution of satDNAs may be due to the satDNA sequence interaction with specific proteins important in heterochromatin formation and possible a role in controlling gene expression. The transcription of satDNA has been described in vertebrates, invertebrates and plants. In insects, differential satDNA expression has been observed in different cells, developmental stages, sex and caste of the individuals. These transcription differences may suggest their involvement in gene-regulation processes. In addition, the satDNA or its transcripts appear to be involved in heterochromatin formation and in chromatin-elimination processes. The importance of transposable elements to insect satDNA is shown by their presence as a constituent of satDNA in several species of insects (including possible active elements). In addition, they may be involved in the formation of centromeres and telomeres and in the homogenization and expansion of satDNA.
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Affiliation(s)
- T Palomeque
- Departamento de Biología Experimental, Area de Genética, Universidad de Jaén, Jaén, Spain.
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27
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Ceprani F, Raffa GD, Petrucci R, Piergentili R. Autosomal mutations affecting Y chromosome loops in Drosophila melanogaster. BMC Genet 2008; 9:32. [PMID: 18405358 PMCID: PMC2386818 DOI: 10.1186/1471-2156-9-32] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 04/11/2008] [Indexed: 11/17/2022] Open
Abstract
Background The Y chromosome of Drosophila melanogaster harbors several genes required for male fertility. The genes for these fertility factors are very large in size and contain conspicuous amounts of repetitive DNA and transposons. Three of these loci (ks-1, kl-3 and kl-5) have the ability to develop giant lampbrush-like loops in primary spermatocytes, a cytological manifestation of their active state in these cells. Y-loops bind a number of non-Y encoded proteins, but the mechanisms regulating their development and their specific functions are still to be elucidated. Results Here we report the results of a screen of 726 male sterile lines to identify novel autosomal genes controlling Y-loop function. We analyzed mutant testis preparations both in vivo and by immunofluorescence using antibodies directed against Y-loop-associated proteins. This screen enabled us to isolate 17 mutations at 15 loci whose wild-type function is required for proper Y-loop morphogenesis. Six of these loci are likely to specifically control loop development, while the others display pleiotropic effects on both loops and meiotic processes such as spermiogenesis, sperm development and maturation. We also determined the map position of the mutations affecting exclusively Y-loop morphology. Conclusion Our cytological screening permitted us to identify novel genetic functions required for male spermatogenesis, some of which show pleiotropic effects. Analysis of these mutations also shows that loop development can be uncoupled from meiosis progression. These data represent a useful framework for the characterization of Y-loop development at a molecular level and for the study of the genetic control of heterochromatin.
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Affiliation(s)
- Francesca Ceprani
- Dipartimento di Genetica e Biologia Molecolare, Sapienza - Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
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An investigation of heterochromatin domains on the fourth chromosome of Drosophila melanogaster. Genetics 2008; 178:1177-91. [PMID: 18245350 DOI: 10.1534/genetics.107.081828] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The banded portion of Drosophila melanogaster chromosome 4 exhibits euchromatic and heterochromatic characteristics. Reminiscent of heterochromatin, it contains a high percentage of repetitive elements, does not undergo recombination, and exhibits high levels of HP1 and histone-3 lysine-9 dimethylation. However, in the distal 1.2 Mb, the gene density is typical of euchromatin, and this region is polytene in salivary gland nuclei. Using P-element reporters carrying a copy of hsp70-white, alternative chromatin packaging domains can be distinguished by the eye color phenotype. Mapping studies identified the repetitive element 1360 as a candidate for heterochromatin targeting in the fourth chromosome Hcf region. We report here two new screens using this reporter to look for additional heterochromatin target sites. We confirm that reporter elements within 10 kb of 1360 are usually packaged as heterochromatin; however, heterochromatin packaging occurs in the sv region in the absence of 1360. Analyses of the sequences adjacent to P-element reporters show no simple association between specific repeated elements and transgene expression phenotype on a whole chromosome level. The data require that heterochromatin formation as a whole depends on a more complex pattern of sequence organization rather than the presence of a single sequence element.
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Abstract
A method for isolation of constitutive heterochromatin (chromocenters) from nuclei of mouse liver cells is described. This method is based on the higher resistance of chromocenters to low ionic strength treatment as compared with that of nucleoli and euchromatin. The method allows separation of chromocenters that are essentially free of nucleoli and other nuclear contaminants. In contrast to nuclei and nucleoli, isolated chromocenters are characterized by a simpler protein composition and contain a smaller number of proteins (especially of high molecular weight proteins). They possess telomeric DNA and telomerase activity that suggests a tight association of chromocenters with the telomerase complex in mouse hepatocyte nuclei.
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30
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Johnson LJ. The Genome Strikes Back: The Evolutionary Importance of Defence Against Mobile Elements. Evol Biol 2007. [DOI: 10.1007/s11692-007-9012-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Johnson L. Transposon silencing: the extraordinary epigenetics of a transposon trap. Heredity (Edinb) 2007; 100:5. [PMID: 17895904 DOI: 10.1038/sj.hdy.6801064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Adega F, Chaves R, Guedes-Pinto H. Chromosomal evolution and phylogenetic analyses in Tayassu pecari and Pecari tajacu (Tayassuidae): tales from constitutive heterochromatin. J Genet 2007; 86:19-26. [PMID: 17656845 DOI: 10.1007/s12041-007-0003-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The mammalian family Tayassuidae (peccaries) is confined to the New World and comprises three recognized extant species, white-lipped (Tayassu pecari), collared (Pecari tajacu) and chacoan (Catagonus wagneri) peccaries, which exhibit distinct morphological and chromosomal features. The phylogenetic relationships among the tayassuids are unclear and have instigated debate over the palaeontological, cytogenetic and molecular aspects. Constitutive heterochromatin analysis can be used in understanding the phylogenetic relationships between related species. Here we describe, for the first time, the constitutive heterochromatin (C-positive heterochromatin) of two tayassuid species, Tayassu pecari and Pecari tajacu. We demonstrate that in situ restriction endonuclease digestion with sequential C-banding could be a complementary tool in the study of constitutive heterochromatin heterogeneity in chromosomes of the Tayassuidae. Our characterization of peccary chromosomes suggests that the Pecari tajacu autosomal karyotype is more primitive and has accumulated great diversity in its constitutive heterochromatin. This idea is supported by several other studies that analysed nuclear and mitochondrial sequences of the living peccary species. Finally, the tayassuid X chromosome primitive form seems to be the one of Tayassu pecari.
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Affiliation(s)
- F Adega
- Laboratório Associado Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, P-5001-801 Vila Real, Portugal.
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Goetze S, Mateos-Langerak J, van Driel R. Three-dimensional genome organization in interphase and its relation to genome function. Semin Cell Dev Biol 2007; 18:707-14. [PMID: 17905616 DOI: 10.1016/j.semcdb.2007.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 08/22/2007] [Indexed: 01/10/2023]
Abstract
Higher order chromatin structure, i.e. the three-dimensional (3D) organization of the genome in the interphase nucleus, is an important component in the orchestration of gene expression in the mammalian genome. In this review we describe principles of higher order chromatin structure discussing three organizational parameters, i.e. chromatin folding, chromatin compaction and the nuclear position of the chromatin fibre. We argue that principles of 3D genome organization are probabilistic traits, reflected in a considerable cell-to-cell variation in 3D genome structure. It will be essential to understand how such higher order organizational aspects contribute to genome function to unveil global genome regulation.
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Affiliation(s)
- Sandra Goetze
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands.
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Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF, Dunham I, Komorowski J, Wadelius C. Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes. Genome Res 2007; 17:708-19. [PMID: 17567991 PMCID: PMC1891332 DOI: 10.1101/gr.5540007] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Butyrate is a histone deacetylase inhibitor (HDACi) with anti-neoplastic properties, which theoretically reactivates epigenetically silenced genes by increasing global histone acetylation. However, recent studies indicate that a similar number or even more genes are down-regulated than up-regulated by this drug. We treated hepatocarcinoma HepG2 cells with butyrate and characterized the levels of acetylation at DNA-bound histones H3 and H4 by ChIP-chip along the ENCODE regions. In contrast to the global increases of histone acetylation, many genomic regions close to transcription start sites were deacetylated after butyrate exposure. In order to validate these findings, we found that both butyrate and trichostatin A treatment resulted in histone deacetylation at selected regions, while nucleosome loss or changes in histone H3 lysine 4 trimethylation (H3K4me3) did not occur in such locations. Furthermore, similar histone deacetylation events were observed when colon adenocarcinoma HT-29 cells were treated with butyrate. In addition, genes with deacetylated promoters were down-regulated by butyrate, and this was mediated at the transcriptional level by affecting RNA polymerase II (POLR2A) initiation/elongation. Finally, the global increase in acetylated histones was preferentially localized to the nuclear periphery, indicating that it might not be associated to euchromatin. Our results are significant for the evaluation of HDACi as anti-tumourogenic drugs, suggesting that previous models of action might need to be revised, and provides an explanation for the frequently observed repression of many genes during HDACi treatment.
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Affiliation(s)
- Alvaro Rada-Iglesias
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-751 05 Sweden
- Corresponding authors.E-mail ; fax 46-18-471-4808
| | - Stefan Enroth
- Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, SE-751 05 Sweden
| | - Adam Ameur
- Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, SE-751 05 Sweden
| | | | | | - Patricia Respuela-Alonso
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-751 05 Sweden
| | - Sarah Wilcox
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Peter D. Ellis
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Ian Dunham
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Jan Komorowski
- Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, SE-751 05 Sweden
| | - Claes Wadelius
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, SE-751 05 Sweden
- Corresponding authors.E-mail ; fax 46-18-471-4808
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Carchilan M, Delgado M, Ribeiro T, Costa-Nunes P, Caperta A, Morais-Cecílio L, Jones RN, Viegas W, Houben A. Transcriptionally active heterochromatin in rye B chromosomes. THE PLANT CELL 2007; 19:1738-49. [PMID: 17586652 PMCID: PMC1955731 DOI: 10.1105/tpc.106.046946] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 05/23/2007] [Accepted: 05/31/2007] [Indexed: 05/02/2023]
Abstract
B chromosomes (Bs) are dispensable components of the genomes of numerous species. Thus far, there is a lack of evidence for any transcripts of Bs in plants, with the exception of some rDNA sequences. Here, we show that the Giemsa banding-positive heterochromatic subterminal domain of rye (Secale cereale) Bs undergoes decondensation during interphase. Contrary to the heterochromatic regions of A chromosomes, this domain is simultaneously marked by trimethylated H3K4 and by trimethylated H3K27, an unusual combination of apparently conflicting histone modifications. Notably, both types of B-specific high copy repeat families (E3900 and D1100) of the subterminal domain are transcriptionally active, although with different tissue type-dependent activity. No small RNAs were detected specifically for the presence of Bs. The lack of any significant open reading frame and the highly heterogeneous size of mainly polyadenylated transcripts indicate that the noncoding RNA may function as structural or catalytic RNA.
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Affiliation(s)
- Mariana Carchilan
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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36
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Abstract
Rice (Oryza sativa) has become an important model plant species in numerous research projects involving genome, molecular and evolutionary biology. In this review we describe the reasons why rice provides an excellent model system for centromere and heterochromatin research. In most multicellular eukaryotes, centromeres and heterochromatic domains contain long arrays of repetitive DNA elements that are recalcitrant to DNA sequencing. In contrast, three rice centromeres and the majority of the cytologically defined heterochromatin in the rice genome have been sequenced to high quality, providing an unparalleled resource compared to other model multicellular eukaryotes. Most importantly, active genes have been discovered in the functional domains of several rice centromeres. The centromeric genes and sequence resources provide an unprecedented opportunity to study function and evolution of centromeres and centromere-associated genes.
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Affiliation(s)
- Huihuang Yan
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
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37
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Goetze S, Mateos-Langerak J, Gierman HJ, de Leeuw W, Giromus O, Indemans MHG, Koster J, Ondrej V, Versteeg R, van Driel R. The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol Cell Biol 2007; 27:4475-87. [PMID: 17420274 PMCID: PMC1900058 DOI: 10.1128/mcb.00208-07] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The three-dimensional (3D) organization of the chromosomal fiber in the human interphase nucleus is an important but poorly understood aspect of gene regulation. Here we quantitatively analyze and compare the 3D structures of two types of genomic domains as defined by the human transcriptome map. While ridges are gene dense and show high expression levels, antiridges, on the other hand, are gene poor and carry genes that are expressed at low levels. We show that ridges are in general less condensed, more irregularly shaped, and located more closely to the nuclear center than antiridges. Six human cell lines that display different gene expression patterns and karyotypes share these structural parameters of chromatin. This shows that the chromatin structures of these two types of genomic domains are largely independent of tissue-specific variations in gene expression and differentiation state. Moreover, we show that there is remarkably little intermingling of chromatin from different parts of the same chromosome in a chromosome territory, neither from adjacent nor from distant parts. This suggests that the chromosomal fiber has a compact structure that sterically suppresses intermingling. Together, our results reveal novel general aspects of 3D chromosome architecture that are related to genome structure and function.
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Affiliation(s)
- Sandra Goetze
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 318, Amsterdam, The Netherlands
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38
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Marschner S, Kumke K, Houben A. B chromosomes of B. dichromosomatica show a reduced level of euchromatic histone H3 methylation marks. Chromosome Res 2007; 15:215-22. [PMID: 17285253 DOI: 10.1007/s10577-006-1114-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 11/27/2006] [Accepted: 11/27/2006] [Indexed: 12/28/2022]
Abstract
B chromosomes (Bs) are dispensable, less-transcriptionally active components of the genomes of numerous species. Little information is available on the chromatin composition of Bs and whether it differs in any way from that of the A chromosomes. Methylated isoforms of histone H3 are of particular interest because of their role in eu/heterochromatin formation. Immunofluorescence using site-specific antibodies demonstrates that the chromatin in A and both types of Bs of B. dichromosomatica differs markedly in euchromatic histone H3 methylation marks. While A chromosomes are labelled brightly, the micro B and large B chromosomes are faintly labelled with antibodies against H3K4me2/3, H3K9me3 and H3K27me2/3. The heteropycnotic, tandem-repeat enriched micro Bs were even less labelled with euchromatic histone H3 methylation marks than large Bs, most probably due to different DNA composition. No differences in immunolabelling intensity between A and B chromosomes were found as to the heterochromatic marks H3K9me1/2 and H3K27me1, indicating that Bs are not additionally labelled by heterochromatin typical histone H3 modifications. Analysis of DNA replication timing suggests that micro Bs are replicating throughout S-phase.
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Affiliation(s)
- Sylvia Marschner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
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39
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Dorsett D. Roles of the sister chromatid cohesion apparatus in gene expression, development, and human syndromes. Chromosoma 2007; 116:1-13. [PMID: 16819604 PMCID: PMC1783675 DOI: 10.1007/s00412-006-0072-6] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 05/02/2006] [Accepted: 05/03/2006] [Indexed: 11/27/2022]
Abstract
The sister chromatid cohesion apparatus mediates physical pairing of duplicated chromosomes. This pairing is essential for appropriate distribution of chromosomes into the daughter cells upon cell division. Recent evidence shows that the cohesion apparatus, which is a significant structural component of chromosomes during interphase, also affects gene expression and development. The Cornelia de Lange (CdLS) and Roberts/SC phocomelia (RBS/SC) genetic syndromes in humans are caused by mutations affecting components of the cohesion apparatus. Studies in Drosophila suggest that effects on gene expression are most likely responsible for developmental alterations in CdLS. Effects on chromatid cohesion are apparent in RBS/SC syndrome, but data from yeast and Drosophila point to the likelihood that changes in expression of genes located in heterochromatin could contribute to the developmental deficits.
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Affiliation(s)
- Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
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40
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Gvozdev VA, Abramov YA, Kogan GL, Lavrov SA. Distorted heterochromatin replication in Drosophila melanogaster polytene chromosomes as a result of euchromatin-heterochromatin rearrangements. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Schulze SR, Wallrath LL. Gene regulation by chromatin structure: paradigms established in Drosophila melanogaster. ANNUAL REVIEW OF ENTOMOLOGY 2007; 52:171-92. [PMID: 16881818 DOI: 10.1146/annurev.ento.51.110104.151007] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Studies in Drosophila melanogaster have revealed paradigms for regulating gene expression through chromatin structure, including mechanisms of gene activation and silencing. Regulation occurs at the level of individual genes, chromosomal domains, and entire chromosomes. The chromatin state is dynamic, allowing for changes in gene expression in response to cellular signals and/or environmental cues. Changes in chromatin result from the action of ATP-dependent chromatin-remodeling complexes, reversible epigenetic histone modifications, and the incorporation of histone variants. Many of the chromatin-based transcriptional regulatory mechanisms discovered in D. melanogaster are evolutionarily conserved and therefore serve as a foundation for studies in other organisms.
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Affiliation(s)
- Sandra R Schulze
- Department of Biology, Western Washington University, Bellingham, Washington 98225, USA.
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42
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Demakova OV, Pokholkova GV, Kolesnikova TD, Demakov SA, Andreyeva EN, Belyaeva ES, Zhimulev IF. The SU(VAR)3-9/HP1 complex differentially regulates the compaction state and degree of underreplication of X chromosome pericentric heterochromatin in Drosophila melanogaster. Genetics 2006; 175:609-20. [PMID: 17151257 PMCID: PMC1800617 DOI: 10.1534/genetics.106.062133] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In polytene chromosomes of Drosophila melanogaster, regions of pericentric heterochromatin coalesce to form a compact chromocenter and are highly underreplicated. Focusing on study of X chromosome heterochromatin, we demonstrate that loss of either SU(VAR)3-9 histone methyltransferase activity or HP1 protein differentially affects the compaction of different pericentric regions. Using a set of inversions breaking X chromosome heterochromatin in the background of the Su(var)3-9 mutations, we show that distal heterochromatin (blocks h26-h29) is the only one within the chromocenter to form a big "puff"-like structure. The "puffed" heterochromatin has not only unique morphology but also very special protein composition as well: (i) it does not bind proteins specific for active chromatin and should therefore be referred to as a pseudopuff and (ii) it strongly associates with heterochromatin-specific proteins SU(VAR)3-7 and SUUR, despite the fact that HP1 and HP2 are depleted particularly from this polytene structure. The pseudopuff completes replication earlier than when it is compacted as heterochromatin, and underreplication of some DNA sequences within the pseudopuff is strongly suppressed. So, we show that pericentric heterochromatin is heterogeneous in its requirement for SU(VAR)3-9 with respect to the establishment of the condensed state, time of replication, and DNA polytenization.
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Affiliation(s)
- Olga V Demakova
- Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
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43
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Rossi F, Moschetti R, Caizzi R, Corradini N, Dimitri P. Cytogenetic and molecular characterization of heterochromatin gene models in Drosophila melanogaster. Genetics 2006; 175:595-607. [PMID: 17110485 PMCID: PMC1800633 DOI: 10.1534/genetics.106.065441] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the past decade, genome-sequencing projects have yielded a great amount of information on DNA sequences in several organisms. The release of the Drosophila melanogaster heterochromatin sequence by the Drosophila Heterochromatin Genome Project (DHGP) has greatly facilitated studies of mapping, molecular organization, and function of genes located in pericentromeric heterochromatin. Surprisingly, genome annotation has predicted at least 450 heterochromatic gene models, a figure 10-fold above that defined by genetic analysis. To gain further insight into the locations and functions of D. melanogaster heterochromatic genes and genome organization, we have FISH mapped 41 gene models relative to the stained bands of mitotic chromosomes and the proximal divisions of polytene chromosomes. These genes are contained in eight large scaffolds, which together account for approximately 1.4 Mb of heterochromatic DNA sequence. Moreover, developmental Northern analysis showed that the expression of 15 heterochromatic gene models tested is similar to that of the vital heterochromatic gene Nipped-A, in that it is not limited to specific stages, but is present throughout all development, despite its location in a supposedly "silent" region of the genome. This result is consistent with the idea that genes resident in heterochromatin can encode essential functions.
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Affiliation(s)
- Fabrizio Rossi
- Laboratorio di Genomica Funzionale e Proteomica di Sistemi complessi, Dipartimento di Genetica e Biologia Molecolare Charles Darwin, Università La Sapienza, 00185 Roma, Italy
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44
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Corradini N, Rossi F, Giordano E, Caizzi R, Verní F, Dimitri P. Drosophila melanogaster as a model for studying protein-encoding genes that are resident in constitutive heterochromatin. Heredity (Edinb) 2006; 98:3-12. [PMID: 17080025 DOI: 10.1038/sj.hdy.6800877] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The organization of chromosomes into euchromatin and heterochromatin is one of the most enigmatic aspects of genome evolution. For a long time, heterochromatin was considered to be a genomic wasteland, incompatible with gene expression. However, recent studies--primarily conducted in Drosophila melanogaster--have shown that this peculiar genomic component performs important cellular functions and carries essential genes. New research on the molecular organization, function and evolution of heterochromatin has been facilitated by the sequencing and annotation of heterochromatic DNA. About 450 predicted genes have been identified in the heterochromatin of D. melanogaster, indicating that the number of active genes is higher than had been suggested by genetic analysis. Most of the essential genes are still unknown at the molecular level, and a detailed functional analysis of the predicted genes is difficult owing to the lack of mutant alleles. Far from being a peculiarity of Drosophila, heterochromatic genes have also been found in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Oryza sativa and Arabidopsis thaliana, as well as in humans. The presence of expressed genes in heterochromatin seems paradoxical because they appear to function in an environment that has been considered incompatible with gene expression. In the future, genetic, functional genomic and proteomic analyses will offer powerful approaches with which to explore the functions of heterochromatic genes and to elucidate the mechanisms driving their expression.
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Affiliation(s)
- N Corradini
- Laboratorio di Genomica Funzionale e Proteomica di Sistemi modello and Dipartimento di Genetica e Biologia Molecolare 'Charles Darwin', Università 'La Sapienza', Piazzale Aldo Moro 5, 00185 Roma, Italy
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45
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Vogel MJ, Guelen L, de Wit E, Hupkes DP, Lodén M, Talhout W, Feenstra M, Abbas B, Classen AK, van Steensel B. Human heterochromatin proteins form large domains containing KRAB-ZNF genes. Genome Res 2006; 16:1493-504. [PMID: 17038565 PMCID: PMC1665633 DOI: 10.1101/gr.5391806] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Heterochromatin is important for gene regulation and chromosome structure, but the genes that are occupied by heterochromatin proteins in the mammalian genome are largely unknown. We have adapted the DamID method to systematically identify target genes of the heterochromatin proteins HP1 and SUV39H1 in human and mouse cells. Unexpectedly, we found that CBX1 (formerly HP1beta) and SUV39H1 bind to genes encoding KRAB domain containing zinc finger (KRAB-ZNF) transcriptional repressors. These genes constitute one of the largest gene families and are organized in clusters in the human genome. Preference of CBX1 for this gene family was observed in both human and mouse cells. High-resolution mapping on human chromosome 19 revealed that CBX1 coats large domains 0.1-4 Mb in size, which coincide with the position of KRAB-ZNF gene clusters. These domains show an intricate CBX1 binding pattern: While CBX1 is globally elevated throughout the domains, it is absent from the promoters and binds more strongly to the 3' ends of KRAB-ZNF genes. KRAB-ZNF domains contain large numbers of LINE elements, which may contribute to CBX1 recruitment. These results uncover a surprising link between heterochromatin and a large family of regulatory genes in mammals. We suggest a role for heterochromatin in the evolution of the KRAB-ZNF gene family.
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Affiliation(s)
- Maartje J. Vogel
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lars Guelen
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniel Peric Hupkes
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Martin Lodén
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Wendy Talhout
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marike Feenstra
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ben Abbas
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anne-Kathrin Classen
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Corresponding author.E-mail ; fax +31.20.669.1383
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46
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47
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Kolesnikova TD, Andreeva EN, Pindyurin AV, Ananko NG, Belyakin SN, Shloma VV, Yurlova AA, Makunin IV, Pokholkova GV, Volkova EI, Zarutskaya EA, Kokoza EB, Semeshin VF, Belyaeva ES, Zhimulev IF. Contribution of the SuUR gene to the organization of epigenetically repressed regions of Drosophila melanogaster chromosomes. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406080011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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Schulze SR, McAllister BF, Sinclair DAR, Fitzpatrick KA, Marchetti M, Pimpinelli S, Honda BM. Heterochromatic genes in Drosophila: a comparative analysis of two genes. Genetics 2006; 173:1433-45. [PMID: 16648646 PMCID: PMC1526689 DOI: 10.1534/genetics.106.056069] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 04/29/2006] [Indexed: 01/04/2023] Open
Abstract
Centromeric heterochromatin comprises approximately 30% of the Drosophila melanogaster genome, forming a transcriptionally repressive environment that silences euchromatic genes juxtaposed nearby. Surprisingly, there are genes naturally resident in heterochromatin, which appear to require this environment for optimal activity. Here we report an evolutionary analysis of two genes, Dbp80 and RpL15, which are adjacent in proximal 3L heterochromatin of D. melanogaster. DmDbp80 is typical of previously described heterochromatic genes: large, with repetitive sequences in its many introns. In contrast, DmRpL15 is uncharacteristically small. The orthologs of these genes were examined in D. pseudoobscura and D. virilis. In situ hybridization and whole-genome assembly analysis show that these genes are adjacent, but not centromeric in the genome of D. pseudoobscura, while they are located on different chromosomal elements in D. virilis. Dbp80 gene organization differs dramatically among these species, while RpL15 structure is conserved. A bioinformatic analysis in five additional Drosophila species demonstrates active repositioning of these genes both within and between chromosomal elements. This study shows that Dbp80 and RpL15 can function in contrasting chromatin contexts on an evolutionary timescale. The complex history of these genes also provides unique insight into the dynamic nature of genome evolution.
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Affiliation(s)
- Sandra R Schulze
- Department of Molecular Biology snd Biochemistry, Simon Fraser University, Canada
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49
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Ashburner M, Bergman CM. Drosophila melanogaster: a case study of a model genomic sequence and its consequences. Genome Res 2006; 15:1661-7. [PMID: 16339363 DOI: 10.1101/gr.3726705] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The sequencing and annotation of the Drosophila melanogaster genome, first published in 2000 through collaboration between Celera Genomics and the Drosophila Genome Projects, has provided a number of important contributions to genome research. By demonstrating the utility of methods such as whole-genome shotgun sequencing and genome annotation by a community "jamboree," the Drosophila genome established the precedents for the current paradigm used by most genome projects. Subsequent releases of the initial genome sequence have been improved by the Berkeley Drosophila Genome Project and annotated by FlyBase, the Drosophila community database, providing one of the highest-quality genome sequences and annotations for any organism. We discuss the impact of the growing number of genome sequences now available in the genus on current Drosophila research, and some of the biological questions that these resources will enable to be solved in the future.
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Affiliation(s)
- Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom.
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50
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Gvozdev VA, Kogan GL, Usakin LA. The Y chromosome as a target for acquired and amplified genetic material in evolution. Bioessays 2006; 27:1256-62. [PMID: 16299764 DOI: 10.1002/bies.20321] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The special properties of the Y chromosome stem form the fact that it is a non-recombining degenerate derivative of the X chromosome. The absence of homologous recombination between the X and the Y chromosome leads to gradual degeneration of various Y chromosome genes on an evolutionary timescale. The absence of recombination, however, also favors the accumulation of transposable elements on the Y chromosome during its evolution, as seen with both Drosophila and mammalian Y chromosomes. Alongside these processes, the acquisition and amplification of autosomal male benefit genes occur. This review will focus on recent studies that reveal the autosome-acquired genes on the Y chromosome of both Drosophila and humans. The evolution of the acquired and amplified genes on the Y chromosome is also discussed. Molecular and comparative analyses of Y-linked repeats in the Drosophila melanogaster genome demonstrate that there was a period of their degeneration followed by a period of their integration into RNAi silencing, which was beneficial for male fertility. Finally, the function of non-coding RNA produced by amplified Y chromosome genetic elements will be discussed.
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Affiliation(s)
- Vladimir A Gvozdev
- Institute of Molecular Genetic of the Russian Academy of Science, Russia.
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