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Chavez J, Murillo-Maldonado JM, Bahena V, Cruz AK, Castañeda-Sortibrán A, Rodriguez-Arnaiz R, Zurita M, Valadez-Graham V. dAdd1 and dXNP prevent genome instability by maintaining HP1a localization at Drosophila telomeres. Chromosoma 2017; 126:697-712. [PMID: 28688038 DOI: 10.1007/s00412-017-0634-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 12/16/2022]
Abstract
Telomeres are important contributors to genome stability, as they prevent linear chromosome end degradation and contribute to the avoidance of telomeric fusions. An important component of the telomeres is the heterochromatin protein 1a (HP1a). Mutations in Su(var)205, the gene encoding HP1a in Drosophila, result in telomeric fusions, retrotransposon regulation loss and larger telomeres, leading to chromosome instability. Previously, it was found that several proteins physically interact with HP1a, including dXNP and dAdd1 (orthologues to the mammalian ATRX gene). In this study, we found that mutations in the genes encoding the dXNP and dAdd1 proteins affect chromosome stability, causing chromosomal aberrations, including telomeric defects, similar to those observed in Su(var)205 mutants. In somatic cells, we observed that dXNP and dAdd1 participate in the silencing of the telomeric HTT array of retrotransposons, preventing anomalous retrotransposon transcription and integration. Furthermore, the lack of dAdd1 results in the loss of HP1a from the telomeric regions without affecting other chromosomal HP1a binding sites; mutations in dxnp also affected HP1a localization but not at all telomeres, suggesting a specialized role for dAdd1 and dXNP proteins in locating HP1a at the tips of the chromosomes. These results place dAdd1 as an essential regulator of HP1a localization and function in the telomere heterochromatic domain.
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Affiliation(s)
- Joselyn Chavez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Juan Manuel Murillo-Maldonado
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Vanessa Bahena
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Ana Karina Cruz
- Laboratorio de Genética. Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Universidad 3000, Col. Copilco-Universidad, Ciudad de México, Mexico
| | - América Castañeda-Sortibrán
- Laboratorio de Genética. Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Universidad 3000, Col. Copilco-Universidad, Ciudad de México, Mexico
| | - Rosario Rodriguez-Arnaiz
- Laboratorio de Genética. Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Universidad 3000, Col. Copilco-Universidad, Ciudad de México, Mexico
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico.
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Duc C, Benoit M, Détourné G, Simon L, Poulet A, Jung M, Veluchamy A, Latrasse D, Le Goff S, Cotterell S, Tatout C, Benhamed M, Probst AV. Arabidopsis ATRX Modulates H3.3 Occupancy and Fine-Tunes Gene Expression. THE PLANT CELL 2017; 29:1773-1793. [PMID: 28684426 PMCID: PMC5559740 DOI: 10.1105/tpc.16.00877] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/24/2017] [Accepted: 06/28/2017] [Indexed: 05/23/2023]
Abstract
Histones are essential components of the nucleosome, the major chromatin subunit that structures linear DNA molecules and regulates access of other proteins to DNA. Specific histone chaperone complexes control the correct deposition of canonical histones and their variants to modulate nucleosome structure and stability. In this study, we characterize the Arabidopsis thaliana Alpha Thalassemia-mental Retardation X-linked (ATRX) ortholog and show that ATRX is involved in histone H3 deposition. Arabidopsis ATRX mutant alleles are viable, but show developmental defects and reduced fertility. Their combination with mutants of the histone H3.3 chaperone HIRA (Histone Regulator A) results in impaired plant survival, suggesting that HIRA and ATRX function in complementary histone deposition pathways. Indeed, ATRX loss of function alters cellular histone H3.3 pools and in consequence modulates the H3.1/H3.3 balance in the cell. H3.3 levels are affected especially at genes characterized by elevated H3.3 occupancy, including the 45S ribosomal DNA (45S rDNA) loci, where loss of ATRX results in altered expression of specific 45S rDNA sequence variants. At the genome-wide scale, our data indicate that ATRX modifies gene expression concomitantly to H3.3 deposition at a set of genes characterized both by elevated H3.3 occupancy and high expression. Together, our results show that ATRX is involved in H3.3 deposition and emphasize the role of histone chaperones in adjusting genome expression.
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Affiliation(s)
- Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Matthias Benoit
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Gwénaëlle Détourné
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Matthieu Jung
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 67404 Illkirch, France
| | - Alaguraj Veluchamy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
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Dosage Compensation in Drosophila-a Model for the Coordinate Regulation of Transcription. Genetics 2017; 204:435-450. [PMID: 27729494 DOI: 10.1534/genetics.115.185108] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/25/2016] [Indexed: 12/20/2022] Open
Abstract
The sex chromosomes have special significance in the history of genetics. The chromosomal basis of inheritance was firmly established when Calvin Bridges demonstrated that exceptions to Mendel's laws of segregation were accompanied at the cytological level by exceptional sex chromosome segregation. The morphological differences between X and Y exploited in Bridges' experiments arose as a consequence of the evolution of the sex chromosomes. Originally a homologous chromosome pair, the degeneration of the Y chromosome has been accompanied by a requirement for increased expression of the single X chromosome in males. Drosophila has been a model for the study of this dosage compensation and has brought key strengths, including classical genetics, the exceptional cytology of polytene chromosomes, and more recently, comprehensive genomics. The impact of these studies goes beyond sex chromosome regulation, providing valuable insights into mechanisms for the establishment and maintenance of chromatin domains, and for the coordinate regulation of transcription.
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Boldyreva LV, Goncharov FP, Demakova OV, Zykova TY, Levitsky VG, Kolesnikov NN, Pindyurin AV, Semeshin VF, Zhimulev IF. Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines. Curr Genomics 2017; 18:214-226. [PMID: 28367077 PMCID: PMC5345337 DOI: 10.2174/1389202917666160512164913] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. RESULTS Here, we describe the properties of these chromatin types across different cell lines. We show that aquamarine chromatin tends to harbor transcription start sites (TSSs) and 5' untranslated regions (5'UTRs) of the genes, is enriched in diverse "open" chromatin proteins, histone modifications, nucleosome remodeling complexes and transcription factors. It encompasses most of the tRNA genes and shows enrichment for non-coding RNAs and miRNA genes. Lazurite chromatin typically encompasses gene bodies. It is rich in proteins involved in transcription elongation. Frequency of both point mutations and natural deletion breakpoints is elevated within lazurite chromatin. Malachite chromatin shows higher frequency of insertions of natural transposons. Finally, ruby chromatin is enriched for proteins and histone modifications typical for the "closed" chromatin. Ruby chromatin has a relatively low frequency of point mutations and is essentially devoid of miRNA and tRNA genes. Aquamarine and ruby chromatin types are highly stable across cell lines and have contrasting properties. Lazurite and malachite chromatin types also display characteristic protein composition, as well as enrichment for specific genomic features. We found that two types of chromatin, aquamarine and ruby, retain their complementary protein patterns in four Drosophila cell lines.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Igor F. Zhimulev
- Address correspondence to this author at the Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Tel: +7 383 363-90-41; Fax: +7 383 363-90-78; E-mail:
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55
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Galectin-3 is a non-classic RNA binding protein that stabilizes the mucin MUC4 mRNA in the cytoplasm of cancer cells. Sci Rep 2017; 7:43927. [PMID: 28262838 PMCID: PMC5338267 DOI: 10.1038/srep43927] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Pancreatic cancer cells express high levels of MUC1, MUC4 and MUC16 mRNAs that encode membrane-bound mucins. These mRNAs share unusual features such as a long half-life. However, it remains unknown how mucin mRNA stability is regulated. Galectin-3 (Gal-3) is an endogenous lectin playing important biological functions in epithelial cells. Gal-3 is encoded by LGALS3 which is up-regulated in pancreatic cancer. Despite the absence of a RNA-recognition motif, Gal-3 interacts indirectly with pre-mRNAs in the nucleus and promotes constitutive splicing. However a broader role of Gal-3 in mRNA fate is unexplored. We report herein that Gal-3 increases MUC4 mRNA stability through an intermediate, hnRNP-L which binds to a conserved CA repeat element in the 3′UTR in a Gal-3 dependent manner and also controls Muc4 mRNA levels in epithelial tissues of Gal3−/− mice. Gal-3 interacts with hnRNP-L in the cytoplasm, especially during cell mitosis, but only partly associates with protein markers of P-Bodies or Stress Granules. By RNA-IP plus RNA-seq analysis and imaging, we demonstrate that Gal-3 binds to mature spliced MUC4 mRNA in the perinuclear region, probably in hnRNP-L-containing RNA granules. Our findings highlight a new role for Gal-3 as a non-classic RNA-binding protein that regulates MUC4 mRNA post-transcriptionally.
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56
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Akhund-Zade J, Bergland AO, Crowe SO, Unckless RL. The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention. JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:iew094. [PMID: 28042107 PMCID: PMC5270406 DOI: 10.1093/jisesa/iew094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention.
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Affiliation(s)
- Jamilla Akhund-Zade
- Department of Biology, Stanford University, 371 Serra Street, Palo Alto, CA 94305
- Department of Organismal and Evolutionary Biology, Harvard University, Northwest Labs 248, Cambridge, MA 02138
| | - Alan O Bergland
- Department of Biology, Stanford University, 371 Serra Street, Palo Alto, CA 94305
- Department of Biology, University of Virginia, 063A Gilmer Hall, Charlottesville, VA 22903
| | - Sarah O Crowe
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, 14853 NY
| | - Robert L Unckless
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, 14853 NY
- Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, Lawrence, KS 66045
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57
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Jung YL, Kang H, Park PJ, Kuroda MI. Correspondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains. Fly (Austin) 2016; 9:178-82. [PMID: 26940990 DOI: 10.1080/19336934.2016.1151988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Youngsook L Jung
- a Department of Biomedical Informatics ; Harvard Medical School ; Boston , MA 02115
| | - Hyuckjoon Kang
- b Division of Genetics; Brigham and Women's Hospital ; Boston , MA 02115.,c Department of Genetics ; Harvard Medical School ; Boston , MA 02115
| | - Peter J Park
- a Department of Biomedical Informatics ; Harvard Medical School ; Boston , MA 02115
| | - Mitzi I Kuroda
- b Division of Genetics; Brigham and Women's Hospital ; Boston , MA 02115.,c Department of Genetics ; Harvard Medical School ; Boston , MA 02115
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58
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Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH. The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 2016; 5:e16096. [PMID: 27514026 PMCID: PMC4981497 DOI: 10.7554/elife.16096] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.
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Affiliation(s)
- Joel M Swenson
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Amy R Strom
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Sylvain V Costes
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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59
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Liu Y, Ge Q, Chan B, Liu H, Singh SR, Manley J, Lee J, Weideman AM, Hou G, Hou SX. Whole-animal genome-wide RNAi screen identifies networks regulating male germline stem cells in Drosophila. Nat Commun 2016; 7:12149. [PMID: 27484291 PMCID: PMC4976209 DOI: 10.1038/ncomms12149] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
Stem cells are regulated both intrinsically and externally, including by signals from the local environment and distant organs. To identify genes and pathways that regulate stem-cell fates in the whole organism, we perform a genome-wide transgenic RNAi screen through ubiquitous gene knockdowns, focusing on regulators of adult Drosophila testis germline stem cells (GSCs). Here we identify 530 genes that regulate GSC maintenance and differentiation. Of these, we further knock down 113 selected genes using cell-type-specific Gal4s and find that more than half were external regulators, that is, from the local microenvironment or more distal sources. Some genes, for example, versatile (vers), encoding a heterochromatin protein, regulates GSC fates differentially in different cell types and through multiple pathways. We also find that mitosis/cytokinesis proteins are especially important for male GSC maintenance. Our findings provide valuable insights and resources for studying stem cell regulation at the organismal level.
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Affiliation(s)
- Ying Liu
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Qinglan Ge
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Brian Chan
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Hanhan Liu
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Shree Ram Singh
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Jacob Manley
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Jae Lee
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Ann Marie Weideman
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Gerald Hou
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
| | - Steven X Hou
- Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, 1050 Boyles Street, Building 560, Room 12-70, Frederick, Maryland 21702, USA
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Wierer M, Mann M. Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes. Hum Mol Genet 2016; 25:R106-R114. [PMID: 27402878 PMCID: PMC5036873 DOI: 10.1093/hmg/ddw208] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/24/2016] [Indexed: 01/30/2023] Open
Abstract
High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the identification of soluble protein complexes and large-scale affinity purification screens can decode entire protein interaction networks. In contrast, protein complexes residing on chromatin have been much more challenging, because they are difficult to purify and often of very low abundance. However, this is changing due to recent methodological and technological advances in proteomics. Proteins interacting with chromatin marks can directly be identified by pulldowns with synthesized histone tails containing posttranslational modifications (PTMs). Similarly, pulldowns with DNA baits harbouring single nucleotide polymorphisms or DNA modifications reveal the impact of those DNA alterations on the recruitment of transcription factors. Accurate quantitation – either isotope-based or label free – unambiguously pinpoints proteins that are significantly enriched over control pulldowns. In addition, protocols that combine classical chromatin immunoprecipitation (ChIP) methods with mass spectrometry (ChIP-MS) target gene regulatory complexes in their in-vivo context. Similar to classical ChIP, cells are crosslinked with formaldehyde and chromatin sheared by sonication or nuclease digested. ChIP-MS baits can be proteins in tagged or endogenous form, histone PTMs, or lncRNAs. Locus-specific ChIP-MS methods would allow direct purification of a single genomic locus and the proteins associated with it. There, loci can be targeted either by artificial DNA-binding sites and corresponding binding proteins or via proteins with sequence specificity such as TAL or nuclease deficient Cas9 in combination with a specific guide RNA. We predict that advances in MS technology will soon make such approaches generally applicable tools in epigenetics.
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Affiliation(s)
- Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
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61
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Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry. Proc Natl Acad Sci U S A 2016; 113:1784-9. [PMID: 26831069 DOI: 10.1073/pnas.1522750113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Posttranslational modifications (PTMs) are key contributors to chromatin function. The ability to comprehensively link specific histone PTMs with specific chromatin factors would be an important advance in understanding the functions and genomic targeting mechanisms of those factors. We recently introduced a cross-linked affinity technique, BioTAP-XL, to identify chromatin-bound protein interactions that can be difficult to capture with native affinity techniques. However, BioTAP-XL was not strictly compatible with similarly comprehensive analyses of associated histone PTMs. Here we advance BioTAP-XL by demonstrating the ability to quantify histone PTMs linked to specific chromatin factors in parallel with the ability to identify nonhistone binding partners. Furthermore we demonstrate that the initially published quantity of starting material can be scaled down orders of magnitude without loss in proteomic sensitivity. We also integrate hydrophilic interaction chromatography to mitigate detergent carryover and improve liquid chromatography-mass spectrometric performance. In summary, we greatly extend the practicality of BioTAP-XL to enable comprehensive identification of protein complexes and their local chromatin environment.
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62
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Politz JCR, Scalzo D, Groudine M. The redundancy of the mammalian heterochromatic compartment. Curr Opin Genet Dev 2015; 37:1-8. [PMID: 26706451 DOI: 10.1016/j.gde.2015.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 01/05/2023]
Abstract
Two chromatin compartments are present in most mammalian cells; the first contains primarily euchromatic, early replicating chromatin and the second, primarily late-replicating heterochromatin, which is the subject of this review. Heterochromatin is concentrated in three intranuclear regions: the nuclear periphery, the perinucleolar space and in pericentromeric bodies. We review recent evidence demonstrating that the heterochromatic compartment is critically involved in global nuclear organization and the maintenance of genome stability, and discuss models regarding how this compartment is formed and maintained. We also evaluate our understanding of how heterochromatic sequences (herein named heterochromatic associated regions (HADs)) might be tethered within these regions and review experiments that reveal the stochastic nature of individual HAD positioning within the compartment. These investigations suggest a substantial level of functional redundancy within the heterochromatic compartment.
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Affiliation(s)
| | - David Scalzo
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mark Groudine
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
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63
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Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA. The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev 2015. [PMID: 26220994 PMCID: PMC4526735 DOI: 10.1101/gad.267583.115] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
NUT midline carcinoma (NMC), a subtype of squamous cell cancer, is one of the most aggressive human solid malignancies known. NMC is driven by the creation of a translocation oncoprotein, BRD4-NUT, which blocks differentiation and drives growth of NMC cells. BRD4-NUT forms distinctive nuclear foci in patient tumors, which we found correlate with ∼100 unprecedented, hyperacetylated expanses of chromatin that reach up to 2 Mb in size. These "megadomains" appear to be the result of aberrant, feed-forward loops of acetylation and binding of acetylated histones that drive transcription of underlying DNA in NMC patient cells and naïve cells induced to express BRD4-NUT. Megadomain locations are typically cell lineage-specific; however, the cMYC and TP63 regions are targeted in all NMCs tested and play functional roles in tumor growth. Megadomains appear to originate from select pre-existing enhancers that progressively broaden but are ultimately delimited by topologically associating domain (TAD) boundaries. Therefore, our findings establish a basis for understanding the powerful role played by large-scale chromatin organization in normal and aberrant lineage-specific gene transcription.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Erica M Walsh
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xin Wang
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Adlai R Grayson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter T Hsi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA; Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts 02115, USA; Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells. Genome Biol 2015; 16:213. [PMID: 26415775 PMCID: PMC4587738 DOI: 10.1186/s13059-015-0760-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/25/2015] [Indexed: 11/22/2022] Open
Abstract
Background Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. Results Here we identify Heterochromatin Protein 1β (HP1β) as an essential protein for proper differentiation, and, unexpectedly, for the maintenance of pluripotency in ESCs. In pluripotent and differentiated cells HP1β is differentially localized and differentially associated with chromatin. Deletion of HP1β, but not HP1α, in ESCs provokes a loss of the morphological and proliferative characteristics of embryonic pluripotent cells, reduces expression of pluripotency factors and causes aberrant differentiation. However, in differentiated cells, loss of HP1β has the opposite effect, perturbing maintenance of the differentiation state and facilitating reprogramming to an induced pluripotent state. Microscopy, biochemical fractionation and chromatin immunoprecipitation reveal a diffuse nucleoplasmic distribution, weak association with chromatin and high expression levels for HP1β in ESCs. The minor fraction of HP1β that is chromatin-bound in ESCs is enriched within exons, unlike the situation in differentiated cells, where it binds heterochromatic satellite repeats and chromocenters. Conclusions We demonstrate an unexpected duality in the role of HP1β: it is essential in ESCs for maintaining pluripotency, while it is required for proper differentiation in differentiated cells. Thus, HP1β function both depends on, and regulates, the pluripotent state. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0760-8) contains supplementary material, which is available to authorized users.
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Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI. Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev 2015; 29:1136-50. [PMID: 26063573 PMCID: PMC4470282 DOI: 10.1101/gad.260562.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, Kang et al. investigate how PcG complexes form repressive chromatin domains. The findings show that Scm, a transcriptional repressor, is an important regulator of PRC1, PRC2, and transcriptional silencing and suggest that Scm coordinates PcG complexes and polymerizes, resulting in PcG silencing. The Polycomb group (PcG) proteins are key regulators of development in Drosophila and are strongly implicated in human health and disease. How PcG complexes form repressive chromatin domains remains unclear. Using cross-linked affinity purifications of BioTAP-Polycomb (Pc) or BioTAP-Enhancer of zeste [E(z)], we captured all PcG-repressive complex 1 (PRC1) or PRC2 core components and Sex comb on midleg (Scm) as the only protein strongly enriched with both complexes. Although previously not linked to PRC2, we confirmed direct binding of Scm and PRC2 using recombinant protein expression and colocalization of Scm with PRC1, PRC2, and H3K27me3 in embryos and cultured cells using ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing). Furthermore, we found that RNAi knockdown of Scm and overexpression of the dominant-negative Scm-SAM (sterile α motif) domain both affected the binding pattern of E(z) on polytene chromosomes. Aberrant localization of the Scm-SAM domain in long contiguous regions on polytene chromosomes revealed its independent ability to spread on chromatin, consistent with its previously described ability to oligomerize in vitro. Pull-downs of BioTAP-Scm captured PRC1 and PRC2 and additional repressive complexes, including PhoRC, LINT, and CtBP. We propose that Scm is a key mediator connecting PRC1, PRC2, and transcriptional silencing. Combined with previous structural and genetic analyses, our results strongly suggest that Scm coordinates PcG complexes and polymerizes to produce broad domains of PcG silencing.
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Affiliation(s)
- Hyuckjoon Kang
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kyle A McElroy
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Youngsook Lucy Jung
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Artyom A Alekseyenko
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Barry M Zee
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
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Proximity ligation assays of protein and RNA interactions in the male-specific lethal complex on Drosophila melanogaster polytene chromosomes. Chromosoma 2015; 124:385-95. [PMID: 25694028 PMCID: PMC4548014 DOI: 10.1007/s00412-015-0509-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 01/18/2023]
Abstract
In Drosophila, the male-specific lethal (MSL) complex specifically targets the male X chromosome and participates in a twofold increase in expression output leading to functional dosage compensation. The complex includes five proteins and two non-coding RNAs (ncRNAs). A number of additional associated factors have also been identified. However, the components’ roles and interactions have not been fully elucidated. The in situ proximity ligation assay (PLA) provides a sensitive means to determine whether proteins and other factors have bound to chromosomes in close proximity to each other, and thus may interact. Thus, we modified, tested, and applied the assay to probe interactions of MSL complex components on polytene chromosomes. We show that in situ PLA can detect and map both protein-protein and protein-ncRNA interactions on polytene chromosomes at high resolution. We further show that all five protein components of the MSL complex are in close proximity to each other, and the ncRNAs roX1 and roX2 bind the complex in close proximity to MLE. Our results also indicate that JIL1, a histone H3 Ser10 kinase enriched on the male X chromosome, interacts with MSL1 and MSL2, but not MSL3 of the MSL complex. In addition, we corroborate proposed interactions of the MSL complex with both CLAMP and TopoII.
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Alekseyenko AA, McElroy KA, Kang H, Zee BM, Kharchenko PV, Kuroda MI. BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes. ACTA ACUST UNITED AC 2015; 109:21.30.1-21.30.32. [PMID: 25559106 DOI: 10.1002/0471142727.mb2130s109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In order to understand how chromatin complexes function in the nucleus, it is important to obtain a comprehensive picture of their protein, DNA, and RNA components, as well as their mutual interactions. This unit presents a chromatin cross-linking approach (BioTAP-XL) that utilizes a special BioTAP-tagged transgenic protein bait along with mass spectrometry to identify protein complex components, and high-throughput sequencing to identify RNA components and DNA binding sites. Full protocols are provided for Drosophila cells and for human cells in culture, along with an additional protocol for Drosophila embryos as the source material. A key element of the approach in all cases is the generation of control data from input chromatin samples.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Kyle A McElroy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Barry M Zee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts.,Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
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López-Falcón B, Meyer-Nava S, Hernández-Rodríguez B, Campos A, Montero D, Rudiño E, Vázquez M, Zurita M, Valadez-Graham V. Characterization of the Drosophila group ortholog to the amino-terminus of the alpha-thalassemia and mental retardation X-Linked (ATRX) vertebrate protein. PLoS One 2014; 9:e113182. [PMID: 25437195 PMCID: PMC4249797 DOI: 10.1371/journal.pone.0113182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/21/2014] [Indexed: 12/11/2022] Open
Abstract
The human ATRX gene encodes hATRX, a chromatin-remodeling protein harboring an helicase/ATPase and ADD domains. The ADD domain has two zinc fingers that bind to histone tails and mediate hATRX binding to chromatin. dAtrx, the putative ATRX homolog in Drosophila melanogaster, has a conserved helicase/ATPase domain but lacks the ADD domain. A bioinformatic search of the Drosophila genome using the human ADD sequence allowed us to identify the CG8290 annotated gene, which encodes three ADD harboring- isoforms generated by alternative splicing. This Drosophila ADD domain is highly similar in structure and in the amino acids which mediate the histone tail contacts to the ADD domain of hATRX as shown by 3D modeling. Very recently the CG8290 annotated gene has been named dadd1. We show through pull-down and CoIP assays that the products of the dadd1 gene interact physically with dAtrxL and HP1a and all of them mainly co-localize in the chromocenter, although euchromatic localization can also be observed through the chromosome arms. We confirm through ChIP analyses that these proteins are present in vivo in the same heterochromatic regions. The three isoforms are expressed throughout development. Flies carrying transheterozygous combinations of the dadd1 and atrx alleles are semi-viable and have different phenotypes including the appearance of melanotic masses. Interestingly, the dAdd1-b and c isoforms have extra domains, such as MADF, which suggest newly acquired functions of these proteins. These results strongly support that, in Drosophila, the atrx gene diverged and that the dadd1-encoded proteins participate with dAtrx in some cellular functions such as heterochromatin maintenance.
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Affiliation(s)
- Brenda López-Falcón
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Silvia Meyer-Nava
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Benjamín Hernández-Rodríguez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adam Campos
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Montero
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Rudiño
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Vázquez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (VVG); (MZ)
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (VVG); (MZ)
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