메뉴 건너뛰기




Volumn 112, Issue 12, 2015, Pages 3841-3846

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

Author keywords

Chromatin; Genomics; Proteomics

Indexed keywords

HISTONE H3; LYSINE; PROTEIN; TRANSCRIPTION FACTOR; CHROMATIN; CROSS LINKING REAGENT; HISTONE; PROTEOME;

EID: 84925397437     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1502971112     Document Type: Article
Times cited : (122)

References (45)
  • 1
    • 84897138228 scopus 로고    scopus 로고
    • Looping back to leap forward: Transcription enters a new era
    • Levine M, Cattoglio C, Tjian R (2014) Looping back to leap forward: Transcription enters a new era. Cell 157(1):13-25.
    • (2014) Cell , vol.157 , Issue.1 , pp. 13-25
    • Levine, M.1    Cattoglio, C.2    Tjian, R.3
  • 2
    • 62549128139 scopus 로고    scopus 로고
    • A census of human transcription factors: Function, expression and evolution
    • Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM (2009) A census of human transcription factors: Function, expression and evolution. Nat Rev Genet 10(4):252-263.
    • (2009) Nat Rev Genet , vol.10 , Issue.4 , pp. 252-263
    • Vaquerizas, J.M.1    Kummerfeld, S.K.2    Teichmann, S.A.3    Luscombe, N.M.4
  • 3
    • 84863621527 scopus 로고    scopus 로고
    • Cancer epigenetics: From mechanism to therapy
    • Dawson MA, Kouzarides T (2012) Cancer epigenetics: From mechanism to therapy. Cell 150(1):12-27.
    • (2012) Cell , vol.150 , Issue.1 , pp. 12-27
    • Dawson, M.A.1    Kouzarides, T.2
  • 5
    • 78650304236 scopus 로고    scopus 로고
    • Charting histone modifications and the functional organization of mammalian genomes
    • Zhou VW, Goren A, Bernstein BE (2011) Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet 12(1):7-18.
    • (2011) Nat Rev Genet , vol.12 , Issue.1 , pp. 7-18
    • Zhou, V.W.1    Goren, A.2    Bernstein, B.E.3
  • 6
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Dunham I, et al.; ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
    • ENCODE Project Consortium1    Dunham, I.2
  • 7
    • 84884829249 scopus 로고    scopus 로고
    • Mapping human epigenomes
    • Rivera CM, Ren B (2013) Mapping human epigenomes. Cell 155(1):39-55.
    • (2013) Cell , vol.155 , Issue.1 , pp. 39-55
    • Rivera, C.M.1    Ren, B.2
  • 8
    • 77956643239 scopus 로고    scopus 로고
    • Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers
    • Vermeulen M, et al. (2010) Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142(6):967-980.
    • (2010) Cell , vol.142 , Issue.6 , pp. 967-980
    • Vermeulen, M.1
  • 9
    • 33751092246 scopus 로고    scopus 로고
    • A protein interaction network for pluripotency of embryonic stem cells
    • Wang J, et al. (2006) A protein interaction network for pluripotency of embryonic stem cells. Nature 444(7117):364-368.
    • (2006) Nature , vol.444 , Issue.7117 , pp. 364-368
    • Wang, J.1
  • 10
    • 84861897793 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics and network biology
    • Bensimon A, Heck AJR, Aebersold R (2012) Mass spectrometry-based proteomics and network biology. Annu Rev Biochem 81(81):379-405.
    • (2012) Annu Rev Biochem , vol.81 , Issue.81 , pp. 379-405
    • Bensimon, A.1    Heck, A.J.R.2    Aebersold, R.3
  • 11
    • 84873569148 scopus 로고    scopus 로고
    • Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila
    • Wang CI, et al. (2013) Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 20(2):202-209.
    • (2013) Nat Struct Mol Biol , vol.20 , Issue.2 , pp. 202-209
    • Wang, C.I.1
  • 12
    • 84874627227 scopus 로고    scopus 로고
    • The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components
    • Soldi M, Bonaldi T (2013) The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components. Mol Cell Proteomics 12(3):764-780.
    • (2013) Mol Cell Proteomics , vol.12 , Issue.3 , pp. 764-780
    • Soldi, M.1    Bonaldi, T.2
  • 13
    • 84899155587 scopus 로고    scopus 로고
    • The ChroP approach combines ChIP and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin
    • Soldi M, Bonaldi T (2014) The ChroP approach combines ChIP and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin. J Vis Exp 86.
    • (2014) J Vis Exp , pp. 86
    • Soldi, M.1    Bonaldi, T.2
  • 14
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    • Mikkelsen TS, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153):553-560.
    • (2007) Nature , vol.448 , Issue.7153 , pp. 553-560
    • Mikkelsen, T.S.1
  • 15
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghton MP, et al. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107(50):21931-21936.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.50 , pp. 21931-21936
    • Creyghton, M.P.1
  • 16
    • 33847070442 scopus 로고    scopus 로고
    • The role of chromatin during transcription
    • Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128(4):707-719.
    • (2007) Cell , vol.128 , Issue.4 , pp. 707-719
    • Li, B.1    Carey, M.2    Workman, J.L.3
  • 17
    • 34249299791 scopus 로고    scopus 로고
    • The complex language of chromatin regulation during transcription
    • Berger SL (2007) The complex language of chromatin regulation during transcription. Nature 447(7143):407-412.
    • (2007) Nature , vol.447 , Issue.7143 , pp. 407-412
    • Berger, S.L.1
  • 18
    • 73349092441 scopus 로고    scopus 로고
    • Histones: Annotating chromatin
    • Campos EI, Reinberg D (2009) Histones: Annotating chromatin. Annu Rev Genet 43:559-599.
    • (2009) Annu Rev Genet , vol.43 , pp. 559-599
    • Campos, E.I.1    Reinberg, D.2
  • 19
    • 84888015137 scopus 로고    scopus 로고
    • Super-enhancers in the control of cell identity and disease
    • Hnisz D, et al. (2013) Super-enhancers in the control of cell identity and disease. Cell 155(4):934-947.
    • (2013) Cell , vol.155 , Issue.4 , pp. 934-947
    • Hnisz, D.1
  • 20
    • 33947245128 scopus 로고    scopus 로고
    • RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3
    • Christensen J, et al. (2007) RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3. Cell 128(6):1063-1076.
    • (2007) Cell , vol.128 , Issue.6 , pp. 1063-1076
    • Christensen, J.1
  • 21
    • 77954954200 scopus 로고    scopus 로고
    • PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression
    • Liu W, et al. (2010) PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature 466(7305):508-512.
    • (2010) Nature , vol.466 , Issue.7305 , pp. 508-512
    • Liu, W.1
  • 22
    • 33847613217 scopus 로고    scopus 로고
    • Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins
    • Seward DJ, et al. (2007) Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat Struct Mol Biol 14(3):240-242.
    • (2007) Nat Struct Mol Biol , vol.14 , Issue.3 , pp. 240-242
    • Seward, D.J.1
  • 23
    • 84873420044 scopus 로고    scopus 로고
    • LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation
    • Fang R, et al. (2013) LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell 49(3):558-570.
    • (2013) Mol Cell , vol.49 , Issue.3 , pp. 558-570
    • Fang, R.1
  • 24
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides T (2007) Chromatin modifications and their function. Cell 128(4):693-705.
    • (2007) Cell , vol.128 , Issue.4 , pp. 693-705
    • Kouzarides, T.1
  • 25
    • 78049480691 scopus 로고    scopus 로고
    • GeneCards version 3: The human gene integrator
    • Safran M, et al. (2010) GeneCards version 3: The human gene integrator. Database, baq020.
    • (2010) Database , pp. baq020
    • Safran, M.1
  • 26
    • 79955615662 scopus 로고    scopus 로고
    • The transcriptional and signalling networks of pluripotency
    • Ng H-H, Surani MA (2011) The transcriptional and signalling networks of pluripotency. Nat Cell Biol 13(5):490-496.
    • (2011) Nat Cell Biol , vol.13 , Issue.5 , pp. 490-496
    • Ng, H.-H.1    Surani, M.A.2
  • 27
    • 79952660821 scopus 로고    scopus 로고
    • Control of the embryonic stem cell state
    • Young RA (2011) Control of the embryonic stem cell state. Cell 144(6):940-954.
    • (2011) Cell , vol.144 , Issue.6 , pp. 940-954
    • Young, R.A.1
  • 28
    • 77957139539 scopus 로고    scopus 로고
    • Mediator and cohesin connect gene expression and chromatin architecture
    • Kagey MH, et al. (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467(7314):430-435.
    • (2010) Nature , vol.467 , Issue.7314 , pp. 430-435
    • Kagey, M.H.1
  • 29
    • 84876571339 scopus 로고    scopus 로고
    • BioGPS and MyGene.info: Organizing online, genecentric information
    • Wu C, Macleod I, Su AI (2013) BioGPS and MyGene.info: Organizing online, genecentric information. Nucleic Acids Res 41(Database issue, D1):D561-D565.
    • (2013) Nucleic Acids Res , vol.41 , Issue.DATABASE ISSUE D1 , pp. D561-D565
    • Wu, C.1    Macleod, I.2    Su, A.I.3
  • 30
    • 0030249381 scopus 로고    scopus 로고
    • The role of general initiation factors in transcription by RNA polymerase II
    • Roeder RG (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 21(9):327-335.
    • (1996) Trends Biochem Sci , vol.21 , Issue.9 , pp. 327-335
    • Roeder, R.G.1
  • 31
  • 32
    • 84861857476 scopus 로고    scopus 로고
    • RNA polymerase II elongation control
    • Zhou Q, Li T, Price DH (2012) RNA polymerase II elongation control. Annu Rev Biochem 81(81):119-143.
    • (2012) Annu Rev Biochem , vol.81 , Issue.81 , pp. 119-143
    • Zhou, Q.1    Li, T.2    Price, D.H.3
  • 33
    • 84887161037 scopus 로고    scopus 로고
    • Control of transcriptional elongation
    • Kwak H, Lis JT (2013) Control of transcriptional elongation. Annu Rev Genet 47(47):483-508.
    • (2013) Annu Rev Genet , vol.47 , Issue.47 , pp. 483-508
    • Kwak, H.1    Lis, J.T.2
  • 35
    • 84877721757 scopus 로고    scopus 로고
    • SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase
    • Ji X, et al. (2013) SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell 153(4):855-868.
    • (2013) Cell , vol.153 , Issue.4 , pp. 855-868
    • Ji, X.1
  • 36
    • 84922394133 scopus 로고    scopus 로고
    • Integrator Regulates Transcriptional Initiation and Pause Release following Activation
    • Gardini A, et al. (2014) Integrator Regulates Transcriptional Initiation and Pause Release following Activation. Mol Cell 56:1-12.
    • (2014) Mol Cell , vol.56 , pp. 1-12
    • Gardini, A.1
  • 37
    • 84907527348 scopus 로고    scopus 로고
    • Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA
    • Schwartz S, et al. (2014) Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159(1):148-162.
    • (2014) Cell , vol.159 , Issue.1 , pp. 148-162
    • Schwartz, S.1
  • 38
    • 84922180958 scopus 로고    scopus 로고
    • Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
    • Carlile TM, et al. (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515(7525):143-146.
    • (2014) Nature , vol.515 , Issue.7525 , pp. 143-146
    • Carlile, T.M.1
  • 39
    • 0036468364 scopus 로고    scopus 로고
    • Multisubunit RNA polymerases
    • Cramer P (2002) Multisubunit RNA polymerases. Curr Opin Struct Biol 12(1):89-97.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.1 , pp. 89-97
    • Cramer, P.1
  • 40
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
    • Forbes SA, et al. (2011) COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39(Database issue):D945-D950.
    • (2011) Nucleic Acids Res , vol.39 , Issue.DATABASE ISSUE , pp. D945-D950
    • Forbes, S.A.1
  • 41
    • 84892833777 scopus 로고    scopus 로고
    • Discovery and saturation analysis of cancer genes across 21 tumour types
    • Lawrence MS, et al. (2014) Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505(7484):495-501.
    • (2014) Nature , vol.505 , Issue.7484 , pp. 495-501
    • Lawrence, M.S.1
  • 42
    • 84875198920 scopus 로고    scopus 로고
    • Transcriptional regulation and its misregulation in disease
    • Lee TI, Young RA (2013) Transcriptional regulation and its misregulation in disease. Cell 152(6):1237-1251.
    • (2013) Cell , vol.152 , Issue.6 , pp. 1237-1251
    • Lee, T.I.1    Young, R.A.2
  • 43
    • 0040920369 scopus 로고    scopus 로고
    • (Johns Hopkins University, Baltimore). Available at omim.org/. Accessed September 1, 2014
    • Online Mendelian Inheritance in Man OM-NIoGM (2014) (Johns Hopkins University, Baltimore). Available at omim.org/. Accessed September 1, 2014.
    • (2014) Online Mendelian Inheritance in Man OM-NIoGM
  • 44
    • 80052942443 scopus 로고    scopus 로고
    • Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification
    • Tan M, et al. (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146(6):1016-1028.
    • (2011) Cell , vol.146 , Issue.6 , pp. 1016-1028
    • Tan, M.1
  • 45
    • 84876216563 scopus 로고    scopus 로고
    • Master transcription factors and mediator establish super-enhancers at key cell identity genes
    • Whyte WA, et al. (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153(2):307-319.
    • (2013) Cell , vol.153 , Issue.2 , pp. 307-319
    • Whyte, W.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.