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Volumn 18, Issue 1, 2017, Pages

Functional assessment of human enhancer activities using whole-genome STARR-sequencing

Author keywords

Enhancers; Non coding regions; Regulatory elements; STARR seq

Indexed keywords

ARTICLE; CHROMATIN; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; ENHANCER REGION; FEASIBILITY STUDY; FUNCTIONAL ASSESSMENT; GENE LIBRARY; GENOME SIZE; HUMAN; HUMAN CELL; HUMAN GENOME; MALE; PROSTATE CANCER CELL LINE; RNA SEQUENCE; UPREGULATION; WHOLE GENOME SEQUENCING; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

EID: 85034609603     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-017-1345-5     Document Type: Article
Times cited : (67)

References (39)
  • 1
    • 84861529303 scopus 로고    scopus 로고
    • Enhancers as information integration hubs in development: lessons from genomics
    • Buecker C, Wysocka J. Enhancers as information integration hubs in development: lessons from genomics. Trends Genet. 2012;28:276-84.
    • (2012) Trends Genet , vol.28 , pp. 276-284
    • Buecker, C.1    Wysocka, J.2
  • 2
    • 84939259847 scopus 로고    scopus 로고
    • STARR-seq - principles and applications
    • Muerdter F, Boryn LM, Arnold CD. STARR-seq - principles and applications. Genomics. 2015;106:145-50.
    • (2015) Genomics , vol.106 , pp. 145-150
    • Muerdter, F.1    Boryn, L.M.2    Arnold, C.D.3
  • 3
    • 84871693720 scopus 로고    scopus 로고
    • Deciphering the transcriptional cis-regulatory code
    • Yanez-Cuna JO, Kvon EZ, Stark A. Deciphering the transcriptional cis-regulatory code. Trends Genet. 2013;29:11-22.
    • (2013) Trends Genet , vol.29 , pp. 11-22
    • Yanez-Cuna, J.O.1    Kvon, E.Z.2    Stark, A.3
  • 4
    • 84939255435 scopus 로고    scopus 로고
    • Decoding enhancers using massively parallel reporter assays
    • Inoue F, Ahituv N. Decoding enhancers using massively parallel reporter assays. Genomics. 2015;106:159-64.
    • (2015) Genomics , vol.106 , pp. 159-164
    • Inoue, F.1    Ahituv, N.2
  • 5
    • 84923362619 scopus 로고    scopus 로고
    • Integrative analysis of 111 reference human epigenomes
    • Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518:317-30.
    • (2015) Nature , vol.518 , pp. 317-330
    • Kundaje, A.1    Meuleman, W.2    Ernst, J.3    Bilenky, M.4    Yen, A.5
  • 6
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 7
    • 84899450857 scopus 로고    scopus 로고
    • Transcriptional enhancers: from properties to genome-wide predictions
    • Shlyueva D, Stampfel G, Stark A. Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet. 2014;15:272-86.
    • (2014) Nat Rev Genet , vol.15 , pp. 272-286
    • Shlyueva, D.1    Stampfel, G.2    Stark, A.3
  • 8
    • 84907516453 scopus 로고    scopus 로고
    • High-throughput functional testing of ENCODE segmentation predictions
    • Kwasnieski JC, Fiore C, Chaudhari HG, Cohen BA. High-throughput functional testing of ENCODE segmentation predictions. Genome Res. 2014;24:1595-602.
    • (2014) Genome Res , vol.24 , pp. 1595-1602
    • Kwasnieski, J.C.1    Fiore, C.2    Chaudhari, H.G.3    Cohen, B.A.4
  • 10
    • 84899692444 scopus 로고    scopus 로고
    • Function-based identification of mammalian enhancers using site-specific integration
    • Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, Afzal V, et al. Function-based identification of mammalian enhancers using site-specific integration. Nat Methods. 2014;11:566-71.
    • (2014) Nat Methods , vol.11 , pp. 566-571
    • Dickel, D.E.1    Zhu, Y.2    Nord, A.S.3    Wylie, J.N.4    Akiyama, J.A.5    Afzal, V.6
  • 11
    • 84899670369 scopus 로고    scopus 로고
    • FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells
    • Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X, Wang Y, et al. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nat Methods. 2014;11:559-65.
    • (2014) Nat Methods , vol.11 , pp. 559-565
    • Murtha, M.1    Tokcaer-Keskin, Z.2    Tang, Z.3    Strino, F.4    Chen, X.5    Wang, Y.6
  • 13
    • 84883457107 scopus 로고    scopus 로고
    • Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
    • Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, et al. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet. 2013;45:1021-8.
    • (2013) Nat Genet , vol.45 , pp. 1021-1028
    • Smith, R.P.1    Taher, L.2    Patwardhan, R.P.3    Kim, M.J.4    Inoue, F.5    Shendure, J.6
  • 14
    • 84877147962 scopus 로고    scopus 로고
    • Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
    • Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, et al. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res. 2013;23:800-11.
    • (2013) Genome Res , vol.23 , pp. 800-811
    • Kheradpour, P.1    Ernst, J.2    Melnikov, A.3    Rogov, P.4    Wang, L.5    Zhang, X.6
  • 15
    • 84874381107 scopus 로고    scopus 로고
    • Genome-wide quantitative enhancer activity maps identified by STARR-seq
    • Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 2013;339:1074-7.
    • (2013) Science , vol.339 , pp. 1074-1077
    • Arnold, C.D.1    Gerlach, D.2    Stelzer, C.3    Boryn, L.M.4    Rath, M.5    Stark, A.6
  • 16
    • 84898025687 scopus 로고    scopus 로고
    • Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin
    • Shlyueva D, Stelzer C, Gerlach D, Yanez-Cuna JO, Rath M, Boryn LM, et al. Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin. Mol Cell. 2014;54:180-92.
    • (2014) Mol Cell , vol.54 , pp. 180-192
    • Shlyueva, D.1    Stelzer, C.2    Gerlach, D.3    Yanez-Cuna, J.O.4    Rath, M.5    Boryn, L.M.6
  • 17
    • 84925543087 scopus 로고    scopus 로고
    • Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation
    • Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, et al. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature. 2015;518:556-9.
    • (2015) Nature , vol.518 , pp. 556-559
    • Zabidi, M.A.1    Arnold, C.D.2    Schernhuber, K.3    Pagani, M.4    Rath, M.5    Frank, O.6
  • 18
    • 84903640603 scopus 로고    scopus 로고
    • Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution
    • Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, et al. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet. 2014;46:685-92.
    • (2014) Nat Genet , vol.46 , pp. 685-692
    • Arnold, C.D.1    Gerlach, D.2    Spies, D.3    Matts, J.A.4    Sytnikova, Y.A.5    Pagani, M.6
  • 20
    • 85031914498 scopus 로고    scopus 로고
    • Nuclear receptor-mediated transcriptional regulation in prostate cancer cells
    • Proquest Dissertations Publishing. 3628087
    • Liu Y. Nuclear receptor-mediated transcriptional regulation in prostate cancer cells. Proquest Dissertations Publishing; 2014. 3628087
    • (2014)
    • Liu, Y.1
  • 21
    • 85031944833 scopus 로고    scopus 로고
    • Functional genomic analysis of nuclear receptors in MCF7 cells
    • Proquest DissertationsPublishing. 3627912
    • Zhou J. Functional genomic analysis of nuclear receptors in MCF7 cells. Proquest DissertationsPublishing; 2014. 3627912.
    • (2014)
    • Zhou, J.1
  • 22
    • 33646070846 scopus 로고    scopus 로고
    • A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    • Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125:315-26.
    • (2006) Cell , vol.125 , pp. 315-326
    • Bernstein, B.E.1    Mikkelsen, T.S.2    Xie, X.3    Kamal, M.4    Huebert, D.J.5    Cuff, J.6
  • 25
    • 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, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576-89.
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1    Benner, C.2    Spann, N.3    Bertolino, E.4    Lin, Y.C.5    Laslo, P.6
  • 26
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 27
    • 85009062687 scopus 로고    scopus 로고
    • A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
    • Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, et al. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res. 2017;27:38-52.
    • (2017) Genome Res , vol.27 , pp. 38-52
    • Inoue, F.1    Kircher, M.2    Martin, B.3    Cooper, G.M.4    Witten, D.M.5    McManus, M.T.6
  • 28
    • 84988985113 scopus 로고    scopus 로고
    • High-resolution interrogation of functional elements in the noncoding genome
    • Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, et al. High-resolution interrogation of functional elements in the noncoding genome. Science. 2016;353:1545-9.
    • (2016) Science , vol.353 , pp. 1545-1549
    • Sanjana, N.E.1    Wright, J.2    Zheng, K.3    Shalem, O.4    Fontanillas, P.5    Joung, J.6
  • 29
    • 84990852918 scopus 로고    scopus 로고
    • Systematic mapping of functional enhancer-promoter connections with CRISPR interference
    • Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, et al. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science. 2016;354:769-73.
    • (2016) Science , vol.354 , pp. 769-773
    • Fulco, C.P.1    Munschauer, M.2    Anyoha, R.3    Munson, G.4    Grossman, S.R.5    Perez, E.M.6
  • 30
    • 85017510953 scopus 로고    scopus 로고
    • A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
    • Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, et al. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods. 2017;14:629-35.
    • (2017) Nat Methods , vol.14 , pp. 629-635
    • Diao, Y.1    Fang, R.2    Li, B.3    Meng, Z.4    Yu, J.5    Qiu, Y.6
  • 31
    • 85034579175 scopus 로고    scopus 로고
    • Section 31.2: The greater complexity of eukaryotic genomes requires elaborate mechanisms for gene regulation
    • 5th ed, New York: W H Freeman
    • Berg JM, Tymoczko JL, Stryer L. Section 31.2: The greater complexity of eukaryotic genomes requires elaborate mechanisms for gene regulation. In: Biochemistry. 5th ed. New York: W H Freeman; 2002. Available from: https://www.ncbi.nlm.nih.gov/books/NBK22479/.
    • (2002) Biochemistry
    • Berg, J.M.1    Tymoczko, J.L.2    Stryer, L.3
  • 32
    • 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 JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013;10:1213-8.
    • (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
  • 34
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 35
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562-78.
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 36
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 37
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;17:10-2.
    • (2011) EMBnetjournal , vol.17 , pp. 10-12
    • Martin, M.1
  • 38
    • 54949147307 scopus 로고    scopus 로고
    • F-Seq: a feature density estimator for high-throughput sequence tags
    • Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008;24:2537-8.
    • (2008) Bioinformatics , vol.24 , pp. 2537-2538
    • Boyle, A.P.1    Guinney, J.2    Crawford, G.E.3    Furey, T.S.4
  • 39
    • 85034574854 scopus 로고    scopus 로고
    • Genome-wide functional assessment of enhancer activities in the human genome
    • Liu Y, Yu S, Dhiman V, Brunetti T, Scott H, White K. Genome-wide functional assessment of enhancer activities in the human genome. Gene Expression Omnibus. 2017. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE82204.
    • (2017) Gene Expression Omnibus.
    • Liu, Y.1    Yu, S.2    Dhiman, V.3    Brunetti, T.4    Scott, H.5    White, K.6


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