메뉴 건너뛰기




Volumn 47, Issue 11, 2015, Pages 1249-1259

Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DNA; HISTONE; RNA; TRANSCRIPTION FACTOR PU 1; LYSINE;

EID: 84945490164     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3402     Document Type: Article
Times cited : (64)

References (42)
  • 1
    • 84866975037 scopus 로고    scopus 로고
    • Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification
    • Samstein, R.M., et al. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 151, 153-166 (2012).
    • (2012) Cell , vol.151 , pp. 153-166
    • Samstein, R.M.1
  • 2
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz, S., et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
    • (2010) Mol. Cell , vol.38 , pp. 576-589
    • Heinz, S.1
  • 3
    • 77956648493 scopus 로고    scopus 로고
    • Pioneer factors in embryonic stem cells and differentiation
    • Smale, S.T. Pioneer factors in embryonic stem cells and differentiation. Curr. Opin. Genet. Dev. 20, 519-526 (2010).
    • (2010) Curr. Opin. Genet. Dev. , vol.20 , pp. 519-526
    • Smale, S.T.1
  • 4
    • 84899958196 scopus 로고    scopus 로고
    • The chromatin landscape and transcription factors in T cell programming
    • Rothenberg, E.V. The chromatin landscape and transcription factors in T cell programming. Trends Immunol. 35, 195-204 (2014).
    • (2014) Trends Immunol. , vol.35 , pp. 195-204
    • Rothenberg, E.V.1
  • 5
    • 84907419194 scopus 로고    scopus 로고
    • Chromatin state dynamics during blood formation
    • Lara-Astiaso, D., et al. Chromatin state dynamics during blood formation. Science 345, 943-949 (2014).
    • (2014) Science , vol.345 , pp. 943-949
    • Lara-Astiaso, D.1
  • 6
    • 79956326274 scopus 로고    scopus 로고
    • Chromatin 'prepattern' and histone modifiers in a fate choice for liver and pancreas
    • Xu, C.R., et al. Chromatin 'prepattern' and histone modifiers in a fate choice for liver and pancreas. Science 332, 963-966 (2011).
    • (2011) Science , vol.332 , pp. 963-966
    • Xu, C.R.1
  • 7
    • 33646070846 scopus 로고    scopus 로고
    • A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    • Bernstein, B.E., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).
    • (2006) Cell , vol.125 , pp. 315-326
    • Bernstein, B.E.1
  • 8
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • Rada-Iglesias, A., et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2011).
    • (2011) Nature , vol.470 , pp. 279-283
    • Rada-Iglesias, A.1
  • 9
    • 78650758676 scopus 로고    scopus 로고
    • Histone H3K27ac separates active from poised enhancers and predicts developmental state
    • Creyghton, M.P., et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. USA 107, 21931-21936 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 21931-21936
    • Creyghton, M.P.1
  • 10
    • 84888015137 scopus 로고    scopus 로고
    • Super-enhancers in the control of cell identity and disease
    • Hnisz, D., et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-947 (2013).
    • (2013) Cell , vol.155 , pp. 934-947
    • Hnisz, D.1
  • 11
    • 84876216563 scopus 로고    scopus 로고
    • Master transcription factors and mediator establish super-enhancers at key cell identity genes
    • Whyte, W.A., et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319 (2013).
    • (2013) Cell , vol.153 , pp. 307-319
    • Whyte, W.A.1
  • 12
    • 84887072795 scopus 로고    scopus 로고
    • Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants
    • Parker, S.C., et al. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc. Natl. Acad. Sci. USA 110, 17921-17926 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 17921-17926
    • Parker, S.C.1
  • 13
    • 84892622973 scopus 로고    scopus 로고
    • NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers
    • Wang, H., et al. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers. Proc. Natl. Acad. Sci. USA 111, 705-710 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 705-710
    • Wang, H.1
  • 14
    • 84905392053 scopus 로고    scopus 로고
    • H3K4me3 breadth is linked to cell identity and transcriptional consistency
    • Benayoun, B.A., et al. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 158, 673-688 (2014).
    • (2014) Cell , vol.158 , pp. 673-688
    • Benayoun, B.A.1
  • 15
    • 84882766972 scopus 로고    scopus 로고
    • Developmental fate and cellular maturity encoded in human regulatory DNA landscapes
    • Stergachis, A.B., et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 154, 888-903 (2013).
    • (2013) Cell , vol.154 , pp. 888-903
    • Stergachis, A.B.1
  • 16
    • 84873310426 scopus 로고    scopus 로고
    • Genome-wide chromatin state transitions associated with developmental and environmental cues
    • Zhu, J., et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642-654 (2013).
    • (2013) Cell , vol.152 , pp. 642-654
    • Zhu, J.1
  • 17
    • 84923362619 scopus 로고    scopus 로고
    • Integrative analysis of 111 reference human epigenomes
    • Roadmap Epigenomics Consortium.
    • Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015).
    • (2015) Nature , vol.518 , pp. 317-330
  • 18
    • 79955564639 scopus 로고    scopus 로고
    • Measuring reproducibility of high-Dhroughput experiments
    • Li, Q.H., Brown, J.B., Huang, H.Y., & Bickel, P.J. Measuring reproducibility of high-Dhroughput experiments. Ann. Appl. Stat. 5, 1752-1779 (2011).
    • (2011) Ann. Appl. Stat. , vol.5 , pp. 1752-1779
    • Li, Q.H.1    Brown, J.B.2    Huang, H.Y.3    Bickel, P.J.4
  • 19
    • 76749133610 scopus 로고    scopus 로고
    • Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate
    • Zheng, Y., et al. Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. Nature 463, 808-812 (2010).
    • (2010) Nature , vol.463 , pp. 808-812
    • Zheng, Y.1
  • 20
    • 84888246827 scopus 로고    scopus 로고
    • Transcriptional regulation of the Ikzf1 locus
    • Yoshida, T., et al. Transcriptional regulation of the Ikzf1 locus. Blood 122, 3149-3159 (2013).
    • (2013) Blood , vol.122 , pp. 3149-3159
    • Yoshida, T.1
  • 21
    • 84930092058 scopus 로고    scopus 로고
    • Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
    • Mifsud, B., et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47, 598-606 (2015).
    • (2015) Nat. Genet. , vol.47 , pp. 598-606
    • Mifsud, B.1
  • 22
    • 84894589713 scopus 로고    scopus 로고
    • Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation
    • Kieffer-Kwon, K.R., et al. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155, 1507-1520 (2013).
    • (2013) Cell , vol.155 , pp. 1507-1520
    • Kieffer-Kwon, K.R.1
  • 23
    • 84901292280 scopus 로고    scopus 로고
    • Long range regulation of the sonic hedgehog gene
    • Anderson, E., & Hill, R.E. Long range regulation of the sonic hedgehog gene. Curr. Opin. Genet. Dev. 27, 54-59 (2014).
    • (2014) Curr. Opin. Genet. Dev. , vol.27 , pp. 54-59
    • Anderson, E.1    Hill, R.E.2
  • 24
    • 84927763931 scopus 로고    scopus 로고
    • The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
    • Schoenfelder, S., et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 25, 582-597 (2015).
    • (2015) Genome Res. , vol.25 , pp. 582-597
    • Schoenfelder, S.1
  • 25
    • 34548441932 scopus 로고    scopus 로고
    • Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome
    • Xi, H., et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3, e136 (2007).
    • (2007) PLoS Genet. , vol.3 , pp. e136
    • Xi, H.1
  • 26
    • 84930607386 scopus 로고    scopus 로고
    • SeqGL identifies context-dependent binding signals in genome-wide regulatory element maps
    • Setty, M., & Leslie, C.S. SeqGL identifies context-dependent binding signals in genome-wide regulatory element maps. PLoS Comput. Biol. 11, e1004271 (2015).
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004271
    • Setty, M.1    Leslie, C.S.2
  • 28
    • 84886790466 scopus 로고    scopus 로고
    • T-bet: A bridge between innate and adaptive immunity
    • Lazarevic, V., Glimcher, L.H., & Lord, G.M. T-bet: a bridge between innate and adaptive immunity. Nat. Rev. Immunol. 13, 777-789 (2013).
    • (2013) Nat. Rev. Immunol. , vol.13 , pp. 777-789
    • Lazarevic, V.1    Glimcher, L.H.2    Lord, G.M.3
  • 29
    • 0028801328 scopus 로고
    • Overexpression of the zinc finger protein MZF1 inhibits hematopoietic development from embryonic stem cells: Correlation with negative regulation of CD34 and c-myb promoter activity
    • Perrotti, D., et al. Overexpression of the zinc finger protein MZF1 inhibits hematopoietic development from embryonic stem cells: correlation with negative regulation of CD34 and c-myb promoter activity. Mol. Cell. Biol. 15, 6075-6087 (1995).
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 6075-6087
    • Perrotti, D.1
  • 30
    • 0033551666 scopus 로고    scopus 로고
    • CCAAT/enhancer-binding protein activates the CD14 promoter and mediates transforming growth factor b signaling in monocyte development
    • Pan, Z., Hetherington, C.J., & Zhang, D.E. CCAAT/enhancer-binding protein activates the CD14 promoter and mediates transforming growth factor b signaling in monocyte development. J. Biol. Chem. 274, 23242-23248 (1999).
    • (1999) J. Biol. Chem. , vol.274 , pp. 23242-23248
    • Pan, Z.1    Hetherington, C.J.2    Zhang, D.E.3
  • 31
    • 84870027825 scopus 로고    scopus 로고
    • STATs shape the active enhancer landscape of T cell populations
    • Vahedi, G., et al. STATs shape the active enhancer landscape of T cell populations. Cell 151, 981-993 (2012).
    • (2012) Cell , vol.151 , pp. 981-993
    • Vahedi, G.1
  • 32
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M.D., McCarthy, D.J., & Smyth, G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 34
    • 84925283769 scopus 로고    scopus 로고
    • What are super-enhancers?
    • Pott, S., & Lieb, J.D. What are super-enhancers? Nat. Genet. 47, 8-12 (2015).
    • (2015) Nat Genet. , vol.47 , pp. 8-12
    • Pott, S.1    Lieb, J.D.2
  • 35
    • 84865800494 scopus 로고    scopus 로고
    • The long-range interaction landscape of gene promoters
    • Sanyal, A., Lajoie, B.R., Jain, G., & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109-113 (2012).
    • (2012) Nature , vol.489 , pp. 109-113
    • Sanyal, A.1    Lajoie, B.R.2    Jain, G.3    Dekker, J.4
  • 36
    • 84916880365 scopus 로고    scopus 로고
    • Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
    • Dowen, J.M., et al. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159, 374-387 (2014).
    • (2014) Cell , vol.159 , pp. 374-387
    • Dowen, J.M.1
  • 37
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst, J., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 38
    • 84865755978 scopus 로고    scopus 로고
    • The accessible chromatin landscape of the human genome
    • Thurman, R.E., et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
    • (2012) Nature , vol.489 , pp. 75-82
    • Thurman, R.E.1
  • 39
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen, Y., et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012).
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 40
    • 84881487110 scopus 로고    scopus 로고
    • Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers
    • Malin, J., Aniba, M.R., & Hannenhalli, S. Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. Nucleic Acids Res. 41, 6828-6838 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. 6828-6838
    • Malin, J.1    Aniba, M.R.2    Hannenhalli, S.3
  • 41
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-Dype-specific gene expression
    • Heintzman, N.D., et al. Histone modifications at human enhancers reflect global cell-Dype-specific gene expression. Nature 459, 108-112 (2009).
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1
  • 42
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., & Greenleaf, W.J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.