publication . Article . 2017

The Drosophila CLAMP protein associates with diverse proteins on chromatin.

Jennifer A. Urban; John M. Urban; Guray Kuzu; Erica N. Larschan;
Open Access English
  • Published: 01 Dec 2017 Journal: PLoS ONE (issn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
Abstract
Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP). More recently, we established that CLAMP has non-sex-specific roles as an essential protein that ...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Biology and Life Sciences, Cell Biology, Chromosome Biology, Chromatin, Genetics, Epigenetics, Gene Expression, RNA interference, Genetic interference, Biochemistry, Nucleic acids, RNA, Research and Analysis Methods, Precipitation Techniques, Immunoprecipitation, Physical Sciences, Chemistry, Physical Chemistry, Chemical Bonding, Cross-Linking, Experimental Organism Systems, Model Organisms, Drosophila Melanogaster, Animal Models, Organisms, Eukaryota, Animals, Invertebrates, Arthropoda, Insects, Drosophila, Genomics, Animal Genomics, Invertebrate Genomics, Gene Regulation, Proteins, DNA-binding proteins, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine
Related Organizations
Funded by
NIH| Establishing coordinate gene regulation during Drosophila dosage compensation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM098461-05
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
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43 references, page 1 of 3

1 Wang CI, Alekseyenko A a, Leroy G, Elia AE, Gorchakov A a, Britton L-MP, et al Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol. Nature Publishing Group; 2013;20: 202–9. doi: 10.1038/nsmb.2477 23295261 [OpenAIRE] [PubMed]

2 Lucchesi J. Gene dosage compensation and the evolution of sex chromosomes. Science (80-). 1978;202: 711–716. doi: 10.1126/science.715437 715437 [OpenAIRE] [PubMed]

3 Lucchesi JC, Kelly WG, Panning B. Chromatin remodeling in dosage compensation. Annu Rev Genet. Annual Reviews; 2005;39: 615–51. doi: 10.1146/annurev.genet.39.073003.094210 16285873 [PubMed]

4 Fauth T, Müller-Planitz F, König C, Straub T, Becker PB. The DNA binding CXC domain of MSL2 is required for faithful t argeting the Dosage Compensation Complex to the X chromosome. Nucleic Acids Res. 2010;38: 3209–21. doi: 10.1093/nar/gkq026 20139418 [OpenAIRE] [PubMed]

5 Larschan E, Soruco MML, Lee O-K, Peng S, Bishop E, Chery J, et al Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation. PLoS Genet. 2012;8: e1002830 doi: 10.1371/journal.pgen.1002830 22844249 [OpenAIRE] [PubMed]

6 Soruco MML, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, et al The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 2013;27: 1551–6. doi: 10.1101/gad.214585.113 23873939 [OpenAIRE] [PubMed]

7 Urban JA, Doherty CA, Jordan WT, Bliss JE, Feng J, Soruco MM, et al The essential Drosophila CLAMP protein differentially regulates non-coding roX RNAs in male and females. Chromosom Res. 2016; 1–13. doi: 10.1007/s10577-016-9541-9 27995349 [OpenAIRE] [PubMed]

8 Belote J, Lucchesi J. Male-specific lethal mutations of Drosophila melanogaster. Genetics. 1980; 165–185. 6781985 [OpenAIRE] [PubMed]

9 Mendjan S, Taipale M, Kind J, Holz H, Gebhardt P, Schelder M, et al Nuclear Pore Components Are Involved in the Transcriptional Regulation of Dosage Compensation in Drosophila. Mol Cell. Elsevier Inc; 2006;21: 811–823. doi: 10.1016/j.molcel.2006.02.007 16543150 [OpenAIRE] [PubMed]

10 Alekseyenko AA, McElroy KA, Kang H, Zee BM, Kharchenko P V, Kuroda MI. BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes. Curr Protoc Mol Biol. NIH Public Access; 2015;109: 21.30.1–32. doi: 10.1002/0471142727.mb2130s109 25559106 [OpenAIRE] [PubMed]

11 Urban J, Kuzu G, Bowman S, Scruggs B, Henriques T, Kingston R, et al Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PLoS Genet. 2017; [OpenAIRE]

12 Quinn JJ, Ilik IA, Qu K, Georgiev P, Chu C, Akhtar A, et al Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol. 2014;32: 933–940. doi: 10.1038/nbt.2943 24997788 [OpenAIRE] [PubMed]

13 Li J, Liu Y, Rhee HS, Ghosh SKB, Bai L, Pugh BF, et al Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing. Mol Cell. 2013;50: 711–722. doi: 10.1016/j.molcel.2013.05.016 23746353 [OpenAIRE] [PubMed]

14 Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov A V., Moresco JJ, Blokhina T, et al The GAGA factor regulatory network: Identification of GAGA factor associated proteins. Cavalli G, editor. PLoS One. 2017;12: e0173602 doi: 10.1371/journal.pone.0173602 28296955 [OpenAIRE] [PubMed]

15 Guruharsha KG, Rual J-F, Zhai B, Mintseris J, Vaidya P, Vaidya N, et al A Protein Complex Network of Drosophila melanogaster. Cell. 2011;147: 690–703. doi: 10.1016/j.cell.2011.08.047 22036573 [OpenAIRE] [PubMed]

43 references, page 1 of 3
Abstract
Gaining new insights into gene regulation involves an in-depth understanding of protein-protein interactions on chromatin. A powerful model for studying mechanisms of gene regulation is dosage compensation, a process that targets the X-chromosome to equalize gene expression between XY males and XX females. We previously identified a zinc finger protein in Drosophila melanogaster that plays a sex-specific role in targeting the Male-specific lethal (MSL) dosage compensation complex to the male X-chromosome, called the Chromatin-Linked Adapter for MSL Proteins (CLAMP). More recently, we established that CLAMP has non-sex-specific roles as an essential protein that ...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Biology and Life Sciences, Cell Biology, Chromosome Biology, Chromatin, Genetics, Epigenetics, Gene Expression, RNA interference, Genetic interference, Biochemistry, Nucleic acids, RNA, Research and Analysis Methods, Precipitation Techniques, Immunoprecipitation, Physical Sciences, Chemistry, Physical Chemistry, Chemical Bonding, Cross-Linking, Experimental Organism Systems, Model Organisms, Drosophila Melanogaster, Animal Models, Organisms, Eukaryota, Animals, Invertebrates, Arthropoda, Insects, Drosophila, Genomics, Animal Genomics, Invertebrate Genomics, Gene Regulation, Proteins, DNA-binding proteins, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine
Related Organizations
Funded by
NIH| Establishing coordinate gene regulation during Drosophila dosage compensation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM098461-05
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
Download fromView all 4 versions
PLoS ONE
Article . 2017
PLoS ONE
Article . 2017
Provider: Crossref
PLoS ONE
Article
Provider: UnpayWall
43 references, page 1 of 3

1 Wang CI, Alekseyenko A a, Leroy G, Elia AE, Gorchakov A a, Britton L-MP, et al Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol. Nature Publishing Group; 2013;20: 202–9. doi: 10.1038/nsmb.2477 23295261 [OpenAIRE] [PubMed]

2 Lucchesi J. Gene dosage compensation and the evolution of sex chromosomes. Science (80-). 1978;202: 711–716. doi: 10.1126/science.715437 715437 [OpenAIRE] [PubMed]

3 Lucchesi JC, Kelly WG, Panning B. Chromatin remodeling in dosage compensation. Annu Rev Genet. Annual Reviews; 2005;39: 615–51. doi: 10.1146/annurev.genet.39.073003.094210 16285873 [PubMed]

4 Fauth T, Müller-Planitz F, König C, Straub T, Becker PB. The DNA binding CXC domain of MSL2 is required for faithful t argeting the Dosage Compensation Complex to the X chromosome. Nucleic Acids Res. 2010;38: 3209–21. doi: 10.1093/nar/gkq026 20139418 [OpenAIRE] [PubMed]

5 Larschan E, Soruco MML, Lee O-K, Peng S, Bishop E, Chery J, et al Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation. PLoS Genet. 2012;8: e1002830 doi: 10.1371/journal.pgen.1002830 22844249 [OpenAIRE] [PubMed]

6 Soruco MML, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, et al The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 2013;27: 1551–6. doi: 10.1101/gad.214585.113 23873939 [OpenAIRE] [PubMed]

7 Urban JA, Doherty CA, Jordan WT, Bliss JE, Feng J, Soruco MM, et al The essential Drosophila CLAMP protein differentially regulates non-coding roX RNAs in male and females. Chromosom Res. 2016; 1–13. doi: 10.1007/s10577-016-9541-9 27995349 [OpenAIRE] [PubMed]

8 Belote J, Lucchesi J. Male-specific lethal mutations of Drosophila melanogaster. Genetics. 1980; 165–185. 6781985 [OpenAIRE] [PubMed]

9 Mendjan S, Taipale M, Kind J, Holz H, Gebhardt P, Schelder M, et al Nuclear Pore Components Are Involved in the Transcriptional Regulation of Dosage Compensation in Drosophila. Mol Cell. Elsevier Inc; 2006;21: 811–823. doi: 10.1016/j.molcel.2006.02.007 16543150 [OpenAIRE] [PubMed]

10 Alekseyenko AA, McElroy KA, Kang H, Zee BM, Kharchenko P V, Kuroda MI. BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes. Curr Protoc Mol Biol. NIH Public Access; 2015;109: 21.30.1–32. doi: 10.1002/0471142727.mb2130s109 25559106 [OpenAIRE] [PubMed]

11 Urban J, Kuzu G, Bowman S, Scruggs B, Henriques T, Kingston R, et al Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PLoS Genet. 2017; [OpenAIRE]

12 Quinn JJ, Ilik IA, Qu K, Georgiev P, Chu C, Akhtar A, et al Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol. 2014;32: 933–940. doi: 10.1038/nbt.2943 24997788 [OpenAIRE] [PubMed]

13 Li J, Liu Y, Rhee HS, Ghosh SKB, Bai L, Pugh BF, et al Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing. Mol Cell. 2013;50: 711–722. doi: 10.1016/j.molcel.2013.05.016 23746353 [OpenAIRE] [PubMed]

14 Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov A V., Moresco JJ, Blokhina T, et al The GAGA factor regulatory network: Identification of GAGA factor associated proteins. Cavalli G, editor. PLoS One. 2017;12: e0173602 doi: 10.1371/journal.pone.0173602 28296955 [OpenAIRE] [PubMed]

15 Guruharsha KG, Rual J-F, Zhai B, Mintseris J, Vaidya P, Vaidya N, et al A Protein Complex Network of Drosophila melanogaster. Cell. 2011;147: 690–703. doi: 10.1016/j.cell.2011.08.047 22036573 [OpenAIRE] [PubMed]

43 references, page 1 of 3
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