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Alekseyenko AA, Zee BM, Dhoondia Z, Kang H, Makofske JL, Kuroda MI. Cell state-dependent chromatin targeting in NUT carcinoma. Genetics 2023; 224:iyad083. [PMID: 37119804 PMCID: PMC10691748 DOI: 10.1093/genetics/iyad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/07/2023] [Accepted: 04/20/2023] [Indexed: 05/01/2023] Open
Abstract
Aberrant transcriptional programming and chromatin dysregulation are common to most cancers. Whether by deranged cell signaling or environmental insult, the resulting oncogenic phenotype is typically manifested in transcriptional changes characteristic of undifferentiated cell growth. Here we analyze targeting of an oncogenic fusion protein, BRD4-NUT, composed of 2 normally independent chromatin regulators. The fusion causes the formation of large hyperacetylated genomic regions or megadomains, mis-regulation of c-MYC, and an aggressive carcinoma of squamous cell origin. Our previous work revealed largely distinct megadomain locations in different NUT carcinoma patient cell lines. To assess whether this was due to variations in individual genome sequences or epigenetic cell state, we expressed BRD4-NUT in a human stem cell model and found that megadomains formed in dissimilar patterns when comparing cells in the pluripotent state with the same cell line following induction along a mesodermal lineage. Thus, our work implicates initial cell state as the critical factor in the locations of BRD4-NUT megadomains. These results, together with our analysis of c-MYC protein-protein interactions in a patient cell line, are consistent with a cascade of chromatin misregulation underlying NUT carcinoma.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Disease Biology Department, Triana Biomedicine, Lexington, MA 02421, USA
| | - Barry M Zee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Proteomics Department, Cell Signaling Technology, Danvers, MA 01923, USA
| | - Zuzer Dhoondia
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica L Makofske
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Oncology Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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2
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Alekseyenko AA, Zee BM, Dhoondia Z, Kang H, Makofske JL, Kuroda MI. Cell state-dependent chromatin targeting in NUT carcinoma. bioRxiv 2023:2023.04.18.537367. [PMID: 37131839 PMCID: PMC10153199 DOI: 10.1101/2023.04.18.537367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Aberrant transcriptional programming and chromatin dysregulation are common to most cancers. Whether by deranged cell signaling or environmental insult, the resulting oncogenic phenotype is typically manifested in transcriptional changes characteristic of undifferentiated cell growth. Here we analyze targeting of an oncogenic fusion protein, BRD4-NUT, composed of two normally independent chromatin regulators. The fusion causes the formation of large hyperacetylated genomic regions or megadomains, mis-regulation of c-MYC , and an aggressive carcinoma of squamous cell origin. Our previous work revealed largely distinct megadomain locations in different NUT carcinoma patient cell lines. To assess whether this was due to variations in individual genome sequences or epigenetic cell state, we expressed BRD4-NUT in a human stem cell model and found that megadomains formed in dissimilar patterns when comparing cells in the pluripotent state with the same cell line following induction along a mesodermal lineage. Thus, our work implicates initial cell state as the critical factor in the locations of BRD4-NUT megadomains. These results, together with our analysis of c-MYC protein-protein interactions in a patient cell line, are consistent with a cascade of chromatin misregulation underlying NUT carcinoma.
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Affiliation(s)
- Artyom A Alekseyenko
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
- Triana Biomedicine, Lexington, MA
| | - Barry M Zee
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
- Cell Signaling Technology, Danvers, MA
| | - Zuzer Dhoondia
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
| | - Hyuckjoon Kang
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
| | - Jessica L Makofske
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
- Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Mitzi I Kuroda
- Div. of Genetics, Dept. of Medicine, Brigham and Women's Hospital, Boston, MA
- Dept. of Genetics, Harvard Medical School, Boston, MA
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3
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Shiota H, Alekseyenko AA, Wang ZA, Filic I, Knox TM, Luong NM, Huang Y, Scott DA, Jones KL, Gokhale PC, Lemieux ME, Cole PA, Kuroda MI, French CA. Chemical Screen Identifies Diverse and Novel Histone Deacetylase Inhibitors as Repressors of NUT Function: Implications for NUT Carcinoma Pathogenesis and Treatment. Mol Cancer Res 2021; 19:1818-1830. [PMID: 34285087 DOI: 10.1158/1541-7786.mcr-21-0259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/23/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022]
Abstract
NUT carcinoma (NC), characterized most commonly by the BRD4-NUTM1 fusion, is a rare, aggressive variant of squamous carcinoma with no effective treatment. BRD4-NUT drives growth and maintains the poorly differentiated state of NC by activating pro-growth genes such as MYC, through the formation of massive, hyperacetylated, superenhancer-like domains termed megadomains. BRD4-NUT-mediated hyperacetylation of chromatin is facilitated by the chromatin-targeting tandem bromodomains of BRD4, combined with NUT, which recruits the histone acetyltransferase, p300. Here, we developed a high-throughput small-molecule screen to identify inhibitors of transcriptional activation by NUT. In this dCAS9-based GFP-reporter assay, the strongest hits were diverse histone deacetylase (HDAC) inhibitors. Two structurally unrelated HDAC inhibitors, panobinostat and the novel compound, IRBM6, both repressed growth and induced differentiation of NC cells in proportion to their inhibition of NUT transcriptional activity. These two compounds repressed transcription of megadomain-associated oncogenic genes, such as MYC and SOX2, while upregulating pro-differentiation, non-megadomain-associated genes, including JUN, FOS, and key cell-cycle regulators, such as CDKN1A. The transcriptional changes correlate with depletion of BRD4-NUT from megadomains, and redistribution of the p300/CBP-associated chromatin acetylation mark, H3K27ac, away from megadomains toward regular enhancer regions previously populated by H3K27ac. In NC xenograft models, we demonstrated that suppression of tumor growth by panobinostat was comparable with that of bromodomain inhibition, and when combined they improved both survival and growth suppression. IMPLICATIONS: The findings provide mechanistic and preclinical rationale for the use of HDAC inhibitors, alone or combined with other agents, in the treatment of NUT carcinoma.
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Affiliation(s)
- Hitoshi Shiota
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - 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
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Ivona Filic
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tatiana M Knox
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nhi M Luong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yeying Huang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - David A Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Kristen L Jones
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 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
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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Shiota H, Elya JE, Alekseyenko AA, Chou PM, Gorman SA, Barbash O, Becht K, Danga K, Kuroda MI, Nardi V, French CA. "Z4" Complex Member Fusions in NUT Carcinoma: Implications for a Novel Oncogenic Mechanism. Mol Cancer Res 2018; 16:1826-1833. [PMID: 30139738 DOI: 10.1158/1541-7786.mcr-18-0474] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/11/2018] [Accepted: 08/13/2018] [Indexed: 12/16/2022]
Abstract
Nuclear protein in testis (NUT) carcinoma (NC) is a rare, distinctly aggressive subtype of squamous carcinoma defined by the presence of NUT-fusion oncogenes resulting from chromosomal translocation. In most cases, the NUT gene (NUTM1) is fused to bromodomain containing 4 (BRD4) forming the BRD4-NUT oncogene. Here, a novel fusion partner to NUT was discovered using next-generation sequencing and FISH from a young patient with an undifferentiated malignant round cell tumor. Interestingly, the NUT fusion identified involved ZNF592, a zinc finger containing protein, which was previously identified as a component of the BRD4-NUT complex. In BRD4-NUT-expressing NC cells, wild-type ZNF592 and other associated "Z4" complex proteins, including ZNF532 and ZMYND8, colocalize with BRD4-NUT in characteristic nuclear foci. Furthermore, ectopic expression of BRD4-NUT in a non-NC cell line induces sequestration of Z4 factors to BRD4-NUT foci. Finally, the data demonstrate the specific dependency of NC cells on Z4 modules, ZNF532 and ZNF592. IMPLICATIONS: This study establishes the oncogenic role of Z4 factors in NC, offering potential new targeted therapeutic strategies in this incurable cancer.Visual Overview: http://mcr.aacrjournals.org/content/molcanres/16/12/1826/F1.large.jpg.
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Affiliation(s)
- Hitoshi Shiota
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Janine E Elya
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - 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
| | - Pauline M Chou
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Shelby A Gorman
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Olena Barbash
- Cancer Epigenetics DPU, Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Kelly Becht
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kristina Danga
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 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
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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Shiota H, Elya JE, Danga K, Becht K, Chou P, Alekseyenko AA, Nardi V, French CA. Abstract 2487: Novel ZNF-fusions in NUT carcinoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
INTRODUCTION. NUT Carcinoma (NC) is a rare, aggressive squamous carcinoma characterized by chromosome translocations involving rearrangement of the NUT gene (also known as NUTM1) on chromosome 15. While the BRD4-NUT fusion oncoprotein drives the majority of NCs, approximately 25% of NCs harbor non-BRD4 fusion partner genes, including BRD3-, NSD3-, and ZNF532-NUT. All of these partner genes encode proteins that are key components of the BRD4-NUT oncogenic complex and have led to greater understanding of the oncogenic mechanism of NC. Despite these advances, several NCs harbor NUT-fusions with genes of unknown identity, here termed NUT-variant, offering further opportunity to discover additional NUT-fusion partners that may play a key role in BRD4-NUT complex function.
METHODS. In this study, we identified 7 NCs with NUT-variant fusions. Archer® FusionPlex®, a next generation sequencing-based derivation of rapid amplification of cDNA ends (RACE), was used to identify the NUT-fusions using RNA extracted from formalin-fixed paraffin-embedded (FFPE) archival tumor tissue. Confirmatory studies included RT-PCR, Sanger sequencing, and fluorescence in situ hybridization (FISH).
RESULTS. Of the 7 NCs with unknown NUT- fusion partners, Archer® FusionPlex® identified two tumors with classic BRD4-NUT fusions, two BRD3-NUT, one non-fusion, one technical failure, and one novel ZNF592-NUT fusion. The tumor harboring the ZNF592-NUT fusion was biopsied from a pelvic tumor in an 18 year old female patient. She was initially diagnosed with NC based on positive NUT immunohistochemical staining of her pelvic tumor, and died 13 months later. RT-PCR and Sanger sequencing confirmed the ZNF592-NUT fusion detected in Archer® FusionPlex® analysis. The ZNF592-NUT fusion was further confirmed by DNA-FISH performed on the same tissue. ZNF592 is known to form a “Z4” coregulator complex with ZNF532 (a NUT-fusion partner), ZNF687 and ZMYND8. Interestingly, we have previously reported that all Z4 members co-purify with the BRD4-NUT chromatin complex. Here we show that wild type ZNF532 and wild type ZNF592 co-localize with BRD4-NUT by immunofluorescence in the BRD4-NUT NC cell line TC-797. Furthermore, knockdown of ZNF532 and ZNF592 reduced cell viability/growth of TC-797 cells, indicating these are critical factors for NC growth and/or viability.
CONCLUSION. Here we report, through the identification of a novel NUT-fusion partner, ZNF592, evidence that supports a critical role of Z4 factors in BRD4-NUT complex oncogenic function, providing the opportunity for future mechanistic insights and targeted therapeutic inhibition. Secondly, the findings suggest that Archer® FusionPlex® may in certain circumstances have a greater sensitivity for the detection of NUT-fusions than conventional FISH, and should be considered as an alternative approach for fusion-partner detection and discovery in NC.
Citation Format: Hitoshi Shiota, Janine E. Elya, Kristina Danga, Kelly Becht, Pauline Chou, Artyom A. Alekseyenko, Valentina Nardi, Christopher A. French. Novel ZNF-fusions in NUT carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2487.
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Affiliation(s)
- Hitoshi Shiota
- 1Brigham andWomen's Hospital, Harvard Medical School, Boston, MA
| | - Janine E. Elya
- 1Brigham andWomen's Hospital, Harvard Medical School, Boston, MA
| | - Kristina Danga
- 1Brigham andWomen's Hospital, Harvard Medical School, Boston, MA
| | - Kelly Becht
- 1Brigham andWomen's Hospital, Harvard Medical School, Boston, MA
| | - Pauline Chou
- 2Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Valentina Nardi
- 3Massachusetts General Hospital, Harvard Medical School, Boston, MA
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Kuroda MI, Alekseyenko AA, Walsh EM, Wang X, Grayson A, Hsi PT, Kharchenko PV, French CA. Abstract 2655: Oncogenic chromatin factors drive cell type-specific transcription within megadomains in NUT midline carcinoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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 find 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. Megadomains drive transcription of underlying DNA in NMC patient cells and in naïve cells induced to express BRD4-NUT. Here we characterize the constituents of BRD4-NUT chromatin complexes using a crosslinking approach, BioTAP-XL. We find many transcriptional activating proteins known to associate with BRD4, along with novel interactors including p300/CBP and a previously uncharacterized BRD4-NUT Megadomain Associated Protein (BMAP1). BMAP1 is expressed in primary NMC tissue and a subset of more common head and neck squamous cell carcinomas (HNSQC). Concurrently, we discovered a patient-derived NMC harboring a novel BMAP1-NUT fusion. BMAP-NUT blocks differentiation, and like BRD4-NUT recruits p300 to form hyperacetylated megadomains, including at the MYC locus. Thus, our proteomic and genetic approaches have converged on a novel mechanism that involves reprogramming very large regulatory regions to drive oncogenic transcription.
Citation Format: Mitzi I. Kuroda, Artyom A. Alekseyenko, Erica M. Walsh, Xin Wang, Adlai Grayson, Peter T. Hsi, Peter V. Kharchenko, Christopher A. French. Oncogenic chromatin factors drive cell type-specific transcription within megadomains in NUT midline carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2655.
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Affiliation(s)
| | | | | | - Xin Wang
- 2Harvard Medical School, Boston, MA
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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: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI. Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs. Genes Dev 2014; 28:1445-60. [PMID: 24990964 PMCID: PMC4083088 DOI: 10.1101/gad.241950.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Heterochromatin protein 1 (HP1a) plays conserved roles in gene silencing and heterochromatin and is also implicated in transcription, DNA replication, and repair. Using BioTAP-XL mass spectrometry and sequencing across multiple life stages of Drosophila, Alekseyenko et al. identify HP1a chromatin-associated protein and RNA interactions. They discover 13 novel candidates among the top interactions. Furthermore, HP1a selectively associates with a broad set of RNAs transcribed from repetitive regions. The validation of several novel HP1a protein interactors reveals new HP1a links to chromatin organization and function. Heterochromatin protein 1 (HP1a) has conserved roles in gene silencing and heterochromatin and is also implicated in transcription, DNA replication, and repair. Here we identify chromatin-associated protein and RNA interactions of HP1a by BioTAP-XL mass spectrometry and sequencing from Drosophila S2 cells, embryos, larvae, and adults. Our results reveal an extensive list of known and novel HP1a-interacting proteins, of which we selected three for validation. A strong novel interactor, dADD1 (Drosophila ADD1) (CG8290), is highly enriched in heterochromatin, harbors an ADD domain similar to human ATRX, displays selective binding to H3K9me2 and H3K9me3, and is a classic genetic suppressor of position-effect variegation. Unexpectedly, a second hit, HIPP1 (HP1 and insulator partner protein-1) (CG3680), is strongly connected to CP190-related complexes localized at putative insulator sequences throughout the genome in addition to its colocalization with HP1a in heterochromatin. A third interactor, the histone methyltransferase MES-4, is also enriched in heterochromatin. In addition to these protein–protein interactions, we found that HP1a selectively associated with a broad set of RNAs transcribed from repetitive regions. We propose that this rich network of previously undiscovered interactions will define how HP1a complexes perform their diverse functions in cells and developing organisms.
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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
| | - Andrey A Gorchakov
- 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; Institute of Molecular and Cellular Biology, Novosibirsk 630090, Russia
| | - Barry M Zee
- 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
| | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, Massachusetts 02155, 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
| | - 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
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11
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Zhou Q, Ellison CE, Kaiser VB, Alekseyenko AA, Gorchakov AA, Bachtrog D. The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation. PLoS Biol 2013; 11:e1001711. [PMID: 24265597 PMCID: PMC3825665 DOI: 10.1371/journal.pbio.1001711] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 10/04/2013] [Indexed: 11/19/2022] Open
Abstract
This study shows how young sex chromosomes have altered their chromatin structure in Drosophila, and what genomic changes have led to silencing of the Y, and hyper-transcription of the X. Sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure. Drosophila Y chromosomes are composed entirely of silent heterochromatin, while male X chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation. Here, we dissect the molecular mechanisms and functional pressures driving heterochromatin formation and dosage compensation of the recently formed neo-sex chromosomes of Drosophila miranda. We show that the onset of heterochromatin formation on the neo-Y is triggered by an accumulation of repetitive DNA. The neo-X has evolved partial dosage compensation and we find that diverse mutational paths have been utilized to establish several dozen novel binding consensus motifs for the dosage compensation complex on the neo-X, including simple point mutations at pre-binding sites, insertion and deletion mutations, microsatellite expansions, or tandem amplification of weak binding sites. Spreading of these silencing or activating chromatin modifications to adjacent regions results in massive mis-expression of neo-sex linked genes, and little correspondence between functionality of genes and their silencing on the neo-Y or dosage compensation on the neo-X. Intriguingly, the genomic regions being targeted by the dosage compensation complex on the neo-X and those becoming heterochromatic on the neo-Y show little overlap, possibly reflecting different propensities along the ancestral chromosome that formed the sex chromosome to adopt active or repressive chromatin configurations. Our findings have broad implications for current models of sex chromosome evolution, and demonstrate how mechanistic constraints can limit evolutionary adaptations. Our study also highlights how evolution can follow predictable genetic trajectories, by repeatedly acquiring the same 21-bp consensus motif for recruitment of the dosage compensation complex, yet utilizing a diverse array of random mutational changes to attain the same phenotypic outcome. Sex chromosomes differ from non-sex chromosomes (“autosomes”) at the genomic, transcriptomic, and epigenomic level, yet the X and Y share a common evolutionary origin. The Drosophila Y chromosome is gene-poor and associated with a compact and transcriptionally inactive form of genetic material called heterochromatin. The X, in contrast, is enriched for activating chromatin marks and is consequently hyper-transcribed, a process thought to be an adaptation to decay and silencing of genes on the Y, resulting in “dosage compensation.” How sex chromosomes have altered their chromatin structure, and what genomic changes led to this dramatically different epigenetic makeup, however, has remained a mystery. By studying the genome, epigenome, and transcriptome of a species with a very recently evolved pair of sex chromosomes (the neo-X and neo-Y of a fruit fly, Drosophila miranda), we here recapitulate how both dosage compensation and heterochromatin formation evolve in Drosophila and establish several novel and important principles governing the evolution of chromatin structure. We dissect the evolutionary history of over 60 novel binding sites for the dosage compensation complex that evolved by natural selection on the neo-X within the last one million years. We show that the 21-bp consensus motifs for recruiting the dosage compensation complex were acquired by diverse molecular mechanisms along the neo-X, while the onset of heterochromatin formation is triggered by the accumulation of transposable elements, leading to silencing of adjacent neo-Y genes. We find that spreading of these chromatin modifications results in massive mis-expression of neo-sex linked genes, and that little correspondence exists between functional activity of genes on the neo-Y and whether they are dosage-compensated on the neo-X. Intriguingly, the genomic regions being targeted by the dosage compensation complex on the neo-X and those that are heterochromatic on the neo-Y show little overlap, possibly reflecting different propensities of the ancestral chromosome that formed the sex chromosome to evolve active versus repressive chromatin configurations. These findings have broad implications for current models of sex chromosome evolution.
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Affiliation(s)
- Qi Zhou
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Christopher E. Ellison
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Vera B. Kaiser
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Artyom A. Alekseyenko
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrey A. Gorchakov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Laboratory of Chromosome Engineering, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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12
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Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, Kuroda MI. "Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts. Cell Rep 2013; 5:629-36. [PMID: 24183666 DOI: 10.1016/j.celrep.2013.09.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/13/2013] [Accepted: 09/25/2013] [Indexed: 01/14/2023] Open
Abstract
Dosage compensation in Drosophila is mediated by the MSL complex, which increases male X-linked gene expression approximately 2-fold. The MSL complex preferentially binds the bodies of active genes on the male X, depositing H4K16ac with a 3' bias. Two models have been proposed for the influence of the MSL complex on transcription: one based on promoter recruitment of RNA polymerase II (Pol II), and a second featuring enhanced transcriptional elongation. Here, we utilize nascent RNA sequencing to document dosage compensation during transcriptional elongation. We also compare X and autosomes from published data on paused and elongating polymerase in order to assess the role of Pol II recruitment. Our results support a model for differentially regulated elongation, starting with release from 5' pausing and increasing through X-linked gene bodies. Our results highlight facilitated transcriptional elongation as a key mechanism for the coordinated regulation of a diverse set of genes.
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Affiliation(s)
- Francesco Ferrari
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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13
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Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D, Kuroda MI. Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. Genes Dev 2013; 27:853-8. [PMID: 23630075 DOI: 10.1101/gad.215426.113] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Dosage compensation has arisen in response to the evolution of distinct male (XY) and female (XX) karyotypes. In Drosophila melanogaster, the MSL complex increases male X transcription approximately twofold. X-specific targeting is thought to occur through sequence-dependent binding to chromatin entry sites (CESs), followed by spreading in cis to active genes. We tested this model by asking how newly evolving sex chromosome arms in Drosophila miranda acquired dosage compensation. We found evidence for the creation of new CESs, with the analogous sequence and spacing as in D. melanogaster, providing strong support for the spreading model in the establishment of dosage compensation.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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14
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Ferrari F, Jung YL, Kharchenko PV, Plachetka A, Alekseyenko AA, Kuroda MI, Park PJ. Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters". Science 2013; 340:273. [PMID: 23599463 DOI: 10.1126/science.1231815] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Conrad et al. (Reports, 10 August 2012, p. 742) reported a doubling of RNA polymerase II (Pol II) occupancy at X-linked promoters to support 5' recruitment as the key mechanism for dosage compensation in Drosophila. However, they employed an erroneous data-processing step, overestimating Pol II differences. Reanalysis of the data fails to support the authors' model for dosage compensation.
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Affiliation(s)
- F Ferrari
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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15
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Wang CI, Alekseyenko AA, LeRoy G, Elia AEH, Gorchakov AA, Britton LMP, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI. Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 2013; 20:202-9. [PMID: 23295261 DOI: 10.1038/nsmb.2477] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 11/21/2012] [Indexed: 12/28/2022]
Abstract
X-chromosome dosage compensation by the MSL (male-specific lethal) complex is required in Drosophila melanogaster to increase gene expression from the single male X to equal that of both female X chromosomes. Instead of focusing solely on protein complexes released from DNA, here we used chromatin-interacting protein MS (ChIP-MS) to identify MSL interactions on cross-linked chromatin. We identified MSL-enriched histone modifications, including histone H4 Lys16 acetylation and histone H3 Lys36 methylation, and CG4747, a putative Lys36-trimethylated histone H3 (H3K36me3)-binding protein. CG4747 is associated with the bodies of active genes, coincident with H3K36me3, and is mislocalized in the Set2 mutant lacking H3K36me3. CG4747 loss of function in vivo results in partial mislocalization of the MSL complex to autosomes, and RNA interference experiments confirm that CG4747 and Set2 function together to facilitate targeting of the MSL complex to active genes, validating the ChIP-MS approach.
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Affiliation(s)
- Charlotte I Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
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16
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Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SCR, Kuroda MI, Park PJ, Savitsky M, Karpen GH, Pirrotta V. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res 2012; 22:2188-98. [PMID: 22767387 PMCID: PMC3483548 DOI: 10.1101/gr.138156.112] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together, these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes.
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Affiliation(s)
- Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden.
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17
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Alekseyenko AA, Ho JWK, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SCR, Karpen GH, Pirrotta V, Kuroda MI, Park PJ. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet 2012; 8:e1002646. [PMID: 22570616 PMCID: PMC3343056 DOI: 10.1371/journal.pgen.1002646] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 02/22/2012] [Indexed: 11/23/2022] Open
Abstract
The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at “entry sites” that contain a consensus sequence motif (“MSL recognition element” or MRE). However, this motif is only ∼2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC content in the surrounding sequences, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome. The genomes of complex organisms encompass hundreds of millions of base pairs of DNA, and regulatory molecules must distinguish specific targets within this vast landscape. In general, regulatory factors find target genes through sequence-specific interactions with the underlying DNA. However, sequence-specific factors typically bind only a fraction of the candidate genomic regions containing their specific target sequence motif. Here we identify potential roles for chromatin environment and flanking sequence composition in helping regulatory factors find their appropriate binding sites, using targeting of the Drosophila dosage compensation complex as a model. The initial stage of dosage compensation involves binding of the Male Specific Lethal (MSL) complex to a sequence motif called the MSL recognition element [1]. Using data from a large chromatin mapping effort (the modENCODE project), we successfully identify an active chromatin environment as predictive of selective MRE binding by the MSL complex. Our study provides a framework for using genome-wide datasets to analyze and predict functional protein–DNA binding site selection.
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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, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joshua W. K. Ho
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shouyong Peng
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marnie Gelbart
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Y. Tolstorukov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Plachetka
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter V. Kharchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Youngsook L. Jung
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrey A. Gorchakov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Tingting Gu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Aki Minoda
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Nicole C. Riddle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | | | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Mitzi I. Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MIK); (PJP)
| | - Peter J. Park
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MIK); (PJP)
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18
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Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 2011; 21:147-63. [PMID: 21177972 PMCID: PMC3032919 DOI: 10.1101/gr.110098.110] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 12/08/2010] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the "silencing" marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin-heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin patterns reveals distinct profiles for euchromatin, pericentric heterochromatin, and the 4th chromosome. Both silent and active protein-coding genes in heterochromatin display complex patterns of chromosomal proteins and histone modifications; a majority of the active genes exhibit both "activation" marks (e.g., H3K4me3 and H3K36me3) and "silencing" marks (e.g., H3K9me2 and HP1a). The hallmark of active genes in heterochromatic domains appears to be a loss of H3K9 methylation at the transcription start site. We also observe complex epigenomic profiles of intergenic regions, repeated transposable element (TE) sequences, and genes in the heterochromatic extensions. An unexpectedly large fraction of sequences in the euchromatic chromosome arms exhibits a heterochromatic chromatin signature, which differs in size, position, and impact on gene expression among cell types. We conclude that patterns of heterochromatin/euchromatin packaging show greater complexity and plasticity than anticipated. This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin.
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Affiliation(s)
- Nicole C. Riddle
- Department of Biology, Washington University St. Louis, Missouri 63130, USA
| | - Aki Minoda
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Peter V. Kharchenko
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Artyom A. Alekseyenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yuri B. Schwartz
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
- Department of Molecular Biology, Umea University, 90187 Umea, Sweden
| | - Michael Y. Tolstorukov
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Andrey A. Gorchakov
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jacob D. Jaffe
- Proteomics Group, The Broad Institute, Cambridge, Massachusetts 02139, USA
| | - Cameron Kennedy
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
| | - Daniela Linder-Basso
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Sally E. Peach
- Proteomics Group, The Broad Institute, Cambridge, Massachusetts 02139, USA
| | - Gregory Shanower
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Resource, Center for Advanced Biotechnology and Medicine, University of Dentistry and Medicine of New Jersey, Piscataway, New Jersey 08854, USA
| | - Mitzi I. Kuroda
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vincenzo Pirrotta
- Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08901, USA
| | - Peter J. Park
- Center for Biomedical Informatics, Harvard Medical School and Informatics Program, Children's Hospital, Boston, Massachusetts 02115, USA
| | - Sarah C.R. Elgin
- Department of Biology, Washington University St. Louis, Missouri 63130, USA
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California at Berkeley and Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
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Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SCR, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010; 330:1787-97. [PMID: 21177974 PMCID: PMC3192495 DOI: 10.1126/science.1198374] [Citation(s) in RCA: 899] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
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Affiliation(s)
| | - Sushmita Roy
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Jason Ernst
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Peter V. Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Nicolas Negre
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Matthew L. Eaton
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jane M. Landolin
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Christopher A. Bristow
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Michael F. Lin
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Stefan Washietl
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Bradley I. Arshinoff
- Department of Molecular Genetics, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1, Canada
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Ferhat Ay
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Patrick E. Meyer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Machine Learning Group, Université Libre de Bruxelles, CP212, Brussels 1050, Belgium
| | - Nicolas Robine
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | | | - Luisa Di Stefano
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Eugene Berezikov
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands
| | - Christopher D. Brown
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Rogerio Candeias
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Joseph W. Carlson
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Adrian Carr
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Daniel Marbach
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Rachel Sealfon
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Michael Y. Tolstorukov
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Sebastian Will
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Artyom A. Alekseyenko
- Department of Medicine and Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Carlo Artieri
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Benjamin W. Booth
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Angela N. Brooks
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Qi Dai
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - Carrie A. Davis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael O. Duff
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, 263 Farmington, CT 06030–6403, USA
| | - Xin Feng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Andrey A. Gorchakov
- Department of Medicine and Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tingting Gu
- Department of Biology CB-1137, Washington University, Saint Louis, MO 63130, USA
| | - Jorja G. Henikoff
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | | | - Renhua Li
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Heather K. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - John Malone
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Aki Minoda
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | | | - Katsutomo Okamura
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - Marc Perry
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Sara K. Powell
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicole C. Riddle
- Department of Biology CB-1137, Washington University, Saint Louis, MO 63130, USA
| | - Akiko Sakai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Anastasia Samsonova
- Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jeremy E. Sandler
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Yuri B. Schwartz
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Noa Sher
- White-head Institute, Cambridge, MA 02142, USA
| | - Rebecca Spokony
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - David Sturgill
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Marijke van Baren
- Center for Genome Sciences, Washington University, 4444 Forest Park Boulevard, Saint Louis, MO 63108, USA
| | - Kenneth H. Wan
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Li Yang
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, 263 Farmington, CT 06030–6403, USA
| | - Charles Yu
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Elise Feingold
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Peter Good
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Mark Guyer
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Rebecca Lowdon
- Division of Extramural Research, National Human Genome Research Institute, NIH, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA
| | - Kami Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Justen Andrews
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Michael R. Brent
- Center for Genome Sciences, Washington University, 4444 Forest Park Boulevard, Saint Louis, MO 63108, USA
| | - Lucy Cherbas
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
- Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - Sarah C. R. Elgin
- Department of Biology CB-1137, Washington University, Saint Louis, MO 63130, USA
| | - Thomas R. Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Affymetrix, Santa Clara, CA 95051, USA
| | - Robert Grossman
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Roger A. Hoskins
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Thomas C. Kaufman
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - William Kent
- Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute (HHMI), University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mitzi I. Kuroda
- Department of Medicine and Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Norbert Perrimon
- Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - James W. Posakony
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bing Ren
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Steven Russell
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Peter Cherbas
- Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
- Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA
| | - Brenton R. Graveley
- Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, 263 Farmington, CT 06030–6403, USA
| | - Suzanna Lewis
- Genome Sciences Division, LBNL, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Gos Micklem
- Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Peter J. Park
- Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Susan E. Celniker
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Gary H. Karpen
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Eric C. Lai
- Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA
| | - David M. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada
| | - Kevin P. White
- Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA
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20
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Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SCR, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 2010; 471:480-5. [PMID: 21179089 PMCID: PMC3109908 DOI: 10.1038/nature09725] [Citation(s) in RCA: 647] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 12/06/2010] [Indexed: 12/17/2022]
Abstract
Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.
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Affiliation(s)
- Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
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21
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Gorchakov AA, Alekseyenko AA, Kharchenko PV, Park PJ, Kuroda MI. Dosage compensation in drosophila: Sequence-specific initiation and sequence-independent spreading of MSL complex to the active genes on the male X chromosome. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410100303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI. Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev 2009; 23:2266-71. [PMID: 19797766 DOI: 10.1101/gad.1840409] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dosage compensation in Drosophila melanogaster males is achieved via targeting of male-specific lethal (MSL) complex to X-linked genes. This is proposed to involve sequence-specific recognition of the X at approximately 150-300 chromatin entry sites, and subsequent spreading to active genes. Here we ask whether the spreading step requires transcription and is sequence-independent. We find that MSL complex binds, acetylates, and up-regulates autosomal genes inserted on X, but only if transcriptionally active. We conclude that a long-sought specific DNA sequence within X-linked genes is not obligatory for MSL binding. Instead, linkage and transcription play the pivotal roles in MSL targeting irrespective of gene origin and DNA sequence.
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Affiliation(s)
- Andrey A Gorchakov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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23
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Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI. MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell 2008; 28:121-33. [PMID: 17936709 DOI: 10.1016/j.molcel.2007.08.011] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2007] [Revised: 06/05/2007] [Accepted: 08/03/2007] [Indexed: 11/30/2022]
Abstract
In Drosophila, X chromosome dosage compensation requires the male-specific lethal (MSL) complex, which associates with actively transcribed genes on the single male X chromosome to upregulate transcription approximately 2-fold. We found that on the male X chromosome, or when MSL complex is ectopically localized to an autosome, histone H3K36 trimethylation (H3K36me3) is a strong predictor of MSL binding. We isolated mutants lacking Set2, the H3K36me3 methyltransferase, and found that Set2 is an essential gene in both sexes of Drosophila. In set2 mutant males, MSL complex maintains X specificity but exhibits reduced binding to target genes. Furthermore, recombinant MSL3 protein preferentially binds nucleosomes marked by H3K36me3 in vitro. Our results support a model in which MSL complex uses high-affinity sites to initially recognize the X chromosome and then associates with many of its targets through sequence-independent features of transcribed genes.
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Affiliation(s)
- Erica Larschan
- Howard Hughes Medical Institute, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
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24
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Belyaeva ES, Demakov SA, Pokholkova GV, Alekseyenko AA, Kolesnikova TD, Zhimulev IF. DNA underreplication in intercalary heterochromatin regions in polytene chromosomes of Drosophila melanogaster correlates with the formation of partial chromosomal aberrations and ectopic pairing. Chromosoma 2006; 115:355-66. [PMID: 16583218 DOI: 10.1007/s00412-006-0063-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 02/26/2006] [Accepted: 03/06/2006] [Indexed: 11/25/2022]
Abstract
We studied the influence of the Suppressor of Underreplication (SuUR) gene expression on the intercalary heterochromatin (IH) regions of Drosophila melanogaster polytene chromosomes. We observed a strong positive correlation between increased SuUR expression, underreplication extent, amount of DNA truncation, and formation of ectopic contacts in IH regions. SuUR overexpression from heat shock-driven transgene results in the formation of partial chromosomal aberrations whose breakpoints map exclusively to the regions of intercalary and pericentric heterochromatin. It is important to note that all these effects are seen only if SuUR overexpression is induced during early stages of chromosome polytenization. Therefore, we developed the idea that ectopic pairing results from the joining of free DNA ends, which are formed as a consequence of underreplication.
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Affiliation(s)
- Elena S Belyaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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25
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Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MI. High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev 2006; 20:848-57. [PMID: 16547173 PMCID: PMC1472287 DOI: 10.1101/gad.1400206] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
X-chromosome dosage compensation in Drosophila requires the male-specific lethal (MSL) complex, which up-regulates gene expression from the single male X chromosome. Here, we define X-chromosome-specific MSL binding at high resolution in two male cell lines and in late-stage embryos. We find that the MSL complex is highly enriched over most expressed genes, with binding biased toward the 3' end of transcription units. The binding patterns are largely similar in the distinct cell types, with approximately 600 genes clearly bound in all three cases. Genes identified as clearly bound in one cell type and not in another indicate that attraction of MSL complex correlates with expression state. Thus, sequence alone is not sufficient to explain MSL targeting. We propose that the MSL complex recognizes most X-linked genes, but only in the context of chromatin factors or modifications indicative of active transcription. Distinguishing expressed genes from the bulk of the genome is likely to be an important function common to many chromatin organizing and modifying activities.
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Affiliation(s)
- Artyom A Alekseyenko
- Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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26
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Larschan E, Alekseyenko AA, Lai WR, Park PJ, Kuroda MI. MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome. Cold Spring Harb Symp Quant Biol 2006; 71:385-94. [PMID: 17381321 DOI: 10.1101/sqb.2006.71.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Dosage compensation in Drosophila serves as a model system for understanding the targeting of chromatin-modifying complexes to their sites of action. The MSL (male-specific lethal) complex up-regulates transcription of the single male X chromosome, thereby equalizing levels of transcription of X-linked genes between the sexes. Recruitment of the MSL complex to its binding sites on the male X chromosome requires each of the MSL proteins and at least one of the two large noncoding roX RNAs. To better understand how the MSL complex specifically targets the X chromosome, we have defined the binding using high-resolution genomic tiling arrays. Our results indicate that the MSL complex largely associates with transcribed genes that are present in clusters along the X chromosome. We hypothesize that after initial recruitment of the MSL complex to the X chromosome by unknown mechanisms, nascent transcripts or chromatin marks associated with active transcription attract the MSL complex to its final targets. Defining MSL-complex-binding sites will provide a tool for understanding functions of large noncoding RNAs that have remained elusive.
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Affiliation(s)
- E Larschan
- Harvard-Partners Center for Genetics and Genomics, Brigham & Women's Hospital, Boston, Massachusetts 02115, USA
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27
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Belyakin SN, Christophides GK, Alekseyenko AA, Kriventseva EV, Belyaeva ES, Nanayev RA, Makunin IV, Kafatos FC, Zhimulev IF. Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proc Natl Acad Sci U S A 2005; 102:8269-74. [PMID: 15928082 PMCID: PMC1149430 DOI: 10.1073/pnas.0502702102] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In Drosophila polytene chromosomes, most late-replicating regions remain underreplicated. A loss-of-function mutant of the suppressor of underreplication [Su(UR)] gene suppresses underreplication (UR), whereas extra copies of this gene enhance the level and number of regions showing UR. By combining DNA microarray analysis with manipulation of the number of Su(UR) gene copies, we achieved genomic-scale molecular identification of 1,036 genes that are arranged in clusters located in 52 UR chromosomal regions. These regions overlap extensively (96%) but are not completely identical with late-replicating regions of mitotically dividing Kc cells in culture. Reanalysis of published gene expression profiles revealed that genomic regions defined by replication properties include clusters of coordinately expressed genes. Genomic regions that are UR in polytene chromosomes and late replicated in Kc cell chromosomes show a particularly common association with transcriptional territories that are expressed in testis/males but not ovary/females or embryos. An attractive hypothesis for future testing is that factors involved in replication control, such as SU(UR), may interact physically with those involved in epigenetic silencing of transcription territories.
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Affiliation(s)
- Stepan N Belyakin
- Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia
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Bai X, Alekseyenko AA, Kuroda MI. Sequence-specific targeting of MSL complex regulates transcription of the roX RNA genes. EMBO J 2004; 23:2853-61. [PMID: 15229655 PMCID: PMC514957 DOI: 10.1038/sj.emboj.7600299] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Accepted: 06/07/2004] [Indexed: 11/09/2022] Open
Abstract
In Drosophila, dosage compensation is controlled by the male-specific lethal (MSL) complex consisting of at least five proteins and two noncoding RNAs, roX1 and roX2. The roX RNAs function in targeting MSL complex to the X chromosome, and roX transgenes can nucleate spreading of the MSL complex into flanking chromatin when inserted on an autosome. An MSL-binding site (DHS, DNaseI hypersensitive site) has been identified in each roX gene. Here, we investigate the functions of the DHS using transgenic deletion analyses and reporter assays. We find that MSL interaction with the DHS counteracts constitutive repression at roX1, resulting in male-specific expression of roX1 RNA. Surprisingly, the DHS is not required for initiation of cis spreading of MSL complex, instead local transcription of roX RNAs correlates with extensive spreading.
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Affiliation(s)
- Xiaoying Bai
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Genetics, Howard Hughes Medical Institute, Harvard-Partners Center for Genetics & Genomics, Harvard Medical School, Boston, MA, USA
| | - Artyom A Alekseyenko
- Department of Genetics, Howard Hughes Medical Institute, Harvard-Partners Center for Genetics & Genomics, Harvard Medical School, Boston, MA, USA
| | - Mitzi I Kuroda
- Department of Genetics, Howard Hughes Medical Institute, Harvard-Partners Center for Genetics & Genomics, Harvard Medical School, Boston, MA, USA
- Harvard-Partners Center for Genetics & Genomics, NRB Room 168, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Tel.: +1 617 525 4520; Fax: +1 617 525 4522; E-mail:
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Affiliation(s)
- Artyom A Alekseyenko
- Howard Hughes Medical Institute, Harvard-Partners Center for Genetics & Genomics, Harvard Medical School, Boston, MA 02115, USA.
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Belyaeva ES, Boldyreva LV, Volkova EI, Nanayev RA, Alekseyenko AA, Zhimulev IF. Effect of the Suppressor of Underreplication (SuUR) Gene on Position-Effect Variegation Silencing in Drosophila melanogaster. Genetics 2003; 165:1209-20. [PMID: 14668376 PMCID: PMC1462842 DOI: 10.1093/genetics/165.3.1209] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
It has been previously shown that the SuUR gene encodes a protein located in intercalary and pericentromeric heterochromatin in Drosophila melanogaster polytene chromosomes. The SuUR mutation suppresses the formation of ectopic contacts and DNA underreplication in polytene chromosomes; SuUR+ in extra doses enhances the expression of these characters. This study demonstrates that heterochromatin-dependent PEV silencing is also influenced by SuUR. The SuUR protein localizes to chromosome regions compacted as a result of PEV; the SuUR mutation suppresses DNA underreplication arising in regions of polytene chromosomes undergoing PEV. The SuUR mutation also suppresses variegation of both adult morphological characters and chromatin compaction observed in rearranged chromosomes. In contrast, SuUR+ in extra doses and its overexpression enhance variegation. Thus, SuUR affects PEV silencing in a dose-dependent manner. However, its effect is expressed weaker than that of the strong modifier Su(var)2-5.
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Affiliation(s)
- E S Belyaeva
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
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Demakova OV, Kotlikova IV, Gordadze PR, Alekseyenko AA, Kuroda MI, Zhimulev IF. The MSL complex levels are critical for its correct targeting to the chromosomes in Drosophila melanogaster. Chromosoma 2003; 112:103-15. [PMID: 14579126 DOI: 10.1007/s00412-003-0249-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2003] [Revised: 06/28/2003] [Accepted: 07/01/2003] [Indexed: 11/26/2022]
Abstract
In Drosophila, dosage compensation requires assembly of the Male Specific Lethal (MSL) protein complex for doubling transcription of most X-linked genes in males. The recognition of the X chromosome by the MSL complex has been suggested to include initial assembly at approximately 35 chromatin entry sites and subsequent spreading of mature complexes in cis to numerous additional sites along the chromosome. To understand this process further we examined MSL patterns in a range of wild-type and mutant backgrounds producing different amounts of MSL components. Our data support a model in which MSL complex binding to the X is directed by a hierarchy of target sites that display different affinities for the MSL proteins. Chromatin entry sites differ in their ability to provide local intensive binding of complexes to adjacent regions, and need high MSL complex titers to achieve this. We also mapped a set of definite autosomal regions (approximately 70) competent to associate with the functional MSL complex in wild-type males. Overexpression of both MSL1 and MSL2 stabilizes this binding and results in inappropriate MSL binding to the chromocenter and the 4th chromosome. Thus, wild-type MSL complex titers are critical for correct targeting to the X chromosome.
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Affiliation(s)
- Olga V Demakova
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Zhimulev IF, Belyaeva ES, Makunin IV, Pirrotta V, Volkova EI, Alekseyenko AA, Andreyeva EN, Makarevich GF, Boldyreva LV, Nanayev RA, Demakova OV. Influence of the SuUR gene on intercalary heterochromatin in Drosophila melanogaster polytene chromosomes. Chromosoma 2003; 111:377-98. [PMID: 12644953 DOI: 10.1007/s00412-002-0218-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2002] [Revised: 10/02/2002] [Accepted: 10/15/2002] [Indexed: 10/22/2022]
Abstract
Salivary gland polytene chromosomes of Drosophila melanogaster have a reproducible set of intercalary heterochromatin (IH) sites, characterized by late DNA replication, underreplicated DNA, breaks and frequent ectopic contacts. The SuUR mutation has been shown to suppress underreplication, and wild-type SuUR protein is found at late-replicating IH sites and in pericentric heterochromatin. Here we show that the SuUR gene influences all four IH features. The SuUR mutation leads to earlier completion of DNA replication. Using transgenic strains with two, four or six additional SuUR(+) doses (4-8xSuUR(+)) we show that wild-type SuUR is an enhancer of DNA underreplication, causing many late-replicating sites to become underreplicated. We map the underreplication sites and show that their number increases from 58 in normal strains (2xSuUR(+)) to 161 in 4-8xSuUR(+) strains. In one of these new sites (1AB) DNA polytenization decreases from 100% in the wild type to 51%-85% in the 4xSuUR (+) strain. In the 4xSuUR(+) strain, 60% of the weak points coincide with the localization of Polycomb group (PcG) proteins. At the IH region 89E1-4 (the Bithorax complex), a typical underreplication site, the degree of underreplication increases with four doses of SuUR(+) but the extent of the underreplicated region is the same as in wild type and corresponds to the region containing PcG binding sites. We conclude that the polytene chromosome regions known as IH are binding sites for SuUR protein and in many cases PcG silencing proteins. We propose that these stable silenced regions are late replicated and, in the presence of SuUR protein, become underreplicated.
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia.
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Zhimulev IF, Belyaeva ES, Makunin IV, Pirrotta V, Semeshin VF, Alekseyenko AA, Belyakin SN, Volkova EI, Koryakov DE, Andreyeva EN, Demakova OV, Kotlikova IV, Kolesnikova TD, Boldyreva LV, Nanayev RA. Intercalary heterochromatin in Drosophila melanogaster polytene chromosomes and the problem of genetic silencing. Genetica 2003; 117:259-70. [PMID: 12723705 DOI: 10.1023/a:1022912716376] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The morphological characteristics of intercalary heterochromatin (IH) are compared with those of other types of silenced chromatin in the Drosophila melanogaster genome: pericentric heterochromatin (PH) and regions subject to position effect variegation (PEV). We conclude that IH regions in polytene chromosomes are binding sites of silencing complexes such as PcG complexes and of SuUR protein. Binding of these proteins results in the appearance of condensed chromatin and late replication of DNA, which in turn may result in DNA underreplication. IH and PH as well as regions subject to PEV have in common the condensed chromatin appearance, the localization of specific proteins, late replication, underreplication in polytene chromosomes, and ectopic pairing.
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Affiliation(s)
- Igor F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 10, 630090, Novosibirsk, Russia.
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Alekseyenko AA, Demakova OV, Belyaeva ES, Makarevich GF, Kotlikova IV, Nöthiger R, Zhimulev IF. Dosage compensation and intercalary heterochromatin in X chromosomes of Drosophila melanogaster. Chromosoma 2002; 111:106-13. [PMID: 12111333 DOI: 10.1007/s00412-002-0191-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2001] [Accepted: 03/08/2002] [Indexed: 11/30/2022]
Abstract
Regions of intercalary heterochromatin (IH) are dispersed in the euchromatic arms of polytene chromosomes and share the main properties of heterochromatin, namely chromosome constrictions resulting from DNA underreplication. These constrictions are frequent on the paired X chromosomes of females, but are practically absent from the single X chromosome of males. These sex-specific differences have been proposed to reflect the different levels of transcription and chromosome compaction due to dosage compensation, which in turn may affect the degree of underreplication in IH regions. To test this hypothesis, we induced dosage compensation in females by ectopic expression of MSL-2 protein. We then measured the extent of underreplication in IH regions by determining frequencies of constrictions, or by Southern blot analysis using a fragment of the ten (a) gene which is located in IH region 11A6-9. Females transheterozygous for Sxl (fhv1)/ Sxl (f1) or carrying a constitutive msl-2 transgene are known to hypertranscribe their X chromosomes. In such females, both the frequency of constrictions and DNA underreplication were reduced. Suppression of underreplication occurs only when a complete functional MSL complex assembles on the X chromosomes. We also used three strains that carried constitutive transgenes of msl-2 with mutations in the 5' untranslated regions. These strains produced normal levels of SXL protein, but variable levels of MSL-2 protein. The SXL protein did not prevent the formation of an MSL complex in these transgenic females. We found that the extent of underreplication of ten (a) DNA in IH region 11A6-9 negatively correlates with the amount of MSL complex.
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Affiliation(s)
- Artyom A Alekseyenko
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Koptyuga Avenue 2, Novosibirsk 630090, Russia
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Moshkin YM, Alekseyenko AA, Semeshin VF, Spierer A, Spierer P, Makarevich GF, Belyaeva ES, Zhimulev IF. The Bithorax Complex of Drosophila melanogaster: Underreplication and morphology in polytene chromosomes. Proc Natl Acad Sci U S A 2001; 98:570-4. [PMID: 11136231 PMCID: PMC14628 DOI: 10.1073/pnas.98.2.570] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The level of polyteny of the Drosophila salivary gland chromosomes was determined throughout the chromosome region 89E1-4, the locus of the Bithorax Complex. A zone of underreplication spans the 300 kb of DNA from the Ubx to Abd-B loci. From the centromere proximal end of the complex, a 70-kb-long gradual decrease of polytenization starts with the Ubx transcription unit and, after a floor corresponding to the abd-A locus, raises gradually back to the maximum over 70 kb in the region of the Abd-B transcription unit. In flies carrying the mutation Suppressor of DNA Underreplication [Su(UR)ES], the underreplication of the Bithorax Complex is fully suppressed. In the wild type, the Bithorax Complex forms a weak point featuring thinner bands separated by clefts or constrictions. In Su(UR)ES strain in contrast, the 89E1-4 band looks like a single solid band consisting of homogenous dense material. We speculate that the wild-type Su(UR)ES protein hampers DNA replication of silenced domains and leads to their underreplication in salivary gland polytene chromosomes.
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Affiliation(s)
- Y M Moshkin
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
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Koryakov DE, Alekseyenko AA, Zhimulev IF. Dynamic organization of the beta-heterochromatin in the Drosophila melanogaster polytene X chromosome. Mol Gen Genet 1999; 260:503-9. [PMID: 9928929 DOI: 10.1007/s004380050923] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Region 20 of the polytene X chromosome of Drosophila melanogaster was studied in salivary glands (SG) and pseudonurse cells (PNC) of otu mutants. In SG chromosomes the morphology of the region strongly depends on two modifiers of position effect variegation: temperature and amount of heterochromatin. It is banded in XYY males at 25 degrees C and beta-heterochromatic in X0 males at 14 degrees C, i.e. it shows dynamic transitions. In PNC chromosomes region 20 is not heterochromatic, but demonstrates a clear banding pattern. Some molecular markers of mitotic heterochromatin were localized by means of in situ hybridization on PNC chromosomes: DNA of the gene su(f) in section 20C, the nucleolar organizer and 359-bp satellite in 20F. The 359-bp satellite, which has been considered to be specific for heterochromatin of the mitotic X chromosome, was found at two additional sites on chromosome 3L, proximally to 80C. The right arm of the X chromosome in SG chromosomes was localized in the inversion In(ILR)pn2b: the telomeric HeT-A DNA and AAGAG satellite from the right arm are polytenized, having been relocated from heterochromatin to euchromatin.
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Affiliation(s)
- D E Koryakov
- Department of Cytology and Genetics, Novosibirsk State University, Russia
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Belyaeva ES, Zhimulev IF, Volkova EI, Alekseyenko AA, Moshkin YM, Koryakov DE. Su(UR)ES: a gene suppressing DNA underreplication in intercalary and pericentric heterochromatin of Drosophila melanogaster polytene chromosomes. Proc Natl Acad Sci U S A 1998; 95:7532-7. [PMID: 9636184 PMCID: PMC22673 DOI: 10.1073/pnas.95.13.7532] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A genetic locus suppressing DNA underreplication in intercalary heterochromatin (IH) and pericentric heterochromatin (PH) of the polytene chromosomes of Drosophila melanogaster salivary glands, has been described. Found in the In(1)scV2 strain, the mutation, designated as Su(UR)ES, was located on chromosome 3L at position 34. 8 and cytologically mapped to region 68A3-B4. A cytological phenotype was observed in the salivary gland chromosomes of larvae homozygous and hemizygous for Su(UR)ES: (i) in the IH regions, that normally are incompletely polytenized and so they often break to form "weak points," underreplication is suppressed, breaks and ectopic contacts disappear; (ii) the degree of polytenization in PH grows higher. That is why the regions in chromosome arm basements, normally beta-heterochromatic, acquire a distinct banding pattern, i. e., become euchromatic by morphological criteria; (iii) an additional bulk of polytenized material arises between the arms of chromosome 3 to form a fragment with a typical banding pattern. Chromosome 2 PH reveals additional alpha-heterochromatin. Su(UR)ES does not affect the viability, fertility, or morphological characters of the imago, and has semidominant expression in the heterozygote and distinct maternal effect. The results obtained provide evidence that the processes leading to DNA underreplication in IH and PH are affected by the same genetic mechanism.
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Affiliation(s)
- E S Belyaeva
- Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
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Abstract
The formation of alpha and beta heterochromatin in chromosomes of Drosophila melanogaster was studied in salivary glands (SGs) and pseudonurse cells (PNCs). In SGs of X0, XY, XYY, XX and XXY individuals the amounts of alpha heterochromatin were similar, suggesting that the Y chromosome does not substantially contribute to alpha heterochromatin formation. Pericentric heterochromatin developed a linear sequence of blocks in PNCs, showing morphology of both alpha and beta heterochromatin. In situ hybridization with Rsp sequences (Ho clone) revealed that the most proximal heterochromatic segment of the mitotic map (region h39) formed a polytenized block in PNCs. Dot analysis showed that the clone had a hybridization rate with PNC-DNA very close to that with DNA from mainly diploid head cells, whereas the homologous SG-DNA was dramatically underrepresented. A similar increase of DNA representation in PNC was found for AAGAC satellite DNA. The mitotic region h44 was found not to polytenize in the SG chromosome, whereas in PNC chromosome 2 this region was partly polytenized and presented as an array of several blocks of alpha and beta heterochromatin. The mapping of deficiencies with proximal breakpoints in the most distal heterochromatin segments h35 in arm 2L and h46 in 2R showed that the mitotic eu-heterochromatin transitions were located in SG chromosomes distally to the polytene 40E and 41C regions, respectively. Thus, the transition zones between mitotic hetero- and euchromatin are located in banded polytene euchromatin. A scheme for dynamic organization of pericentric heterochromatin in nuclei with polytene chromosomes is proposed.
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Affiliation(s)
- D E Koryakov
- Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk 630090, Russia
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