-
1
-
-
79551655285
-
Functional and mechanistic diversity of distal transcription enhancers
-
Bulger, M. & Groudine, M. Functional and mechanistic diversity of distal transcription enhancers. Cell 144, 327-339 (2011).
-
(2011)
Cell
, vol.144
, pp. 327-339
-
-
Bulger, M.1
Groudine, M.2
-
2
-
-
84895887720
-
Enhancer biology and enhanceropathies
-
Smith, E. & Shilatifard, A. Enhancer biology and enhanceropathies. Nat Struct Mol Biol 21, 210-219 (2014).
-
(2014)
Nat Struct Mol Biol
, vol.21
, pp. 210-219
-
-
Smith, E.1
Shilatifard, A.2
-
3
-
-
84870182699
-
Noncoding transcription at enhancers: General principles and functional models
-
Natoli, G. & Andrau, J. C. Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet 46, 1-19 (2012).
-
(2012)
Annu Rev Genet
, vol.46
, pp. 1-19
-
-
Natoli, G.1
Andrau, J.C.2
-
4
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
-
5
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers
-
De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8, e1000384 (2010).
-
(2010)
PLoS Biol
, vol.8
-
-
De Santa, F.1
-
6
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455-461 (2014).
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
-
7
-
-
84865800494
-
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
-
8
-
-
84881526410
-
Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription
-
Kaikkonen, M. U. et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 51, 310-325 (2013).
-
(2013)
Mol Cell
, vol.51
, pp. 310-325
-
-
Kaikkonen, M.U.1
-
9
-
-
84879694221
-
Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
-
Lam, M. T. et al. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498, 511-515 (2013).
-
(2013)
Nature
, vol.498
, pp. 511-515
-
-
Lam, M.T.1
-
10
-
-
84879695128
-
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
-
Li, W. et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498, 516-520 (2013).
-
(2013)
Nature
, vol.498
, pp. 516-520
-
-
Li, W.1
-
11
-
-
84883756441
-
ERNAs promote transcription by establishing chromatin accessibility at defined genomic loci
-
Mousavi, K. et al. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell 51, 606-617 (2013).
-
(2013)
Mol Cell
, vol.51
, pp. 606-617
-
-
Mousavi, K.1
-
12
-
-
84873456575
-
ERNAs are required for p53-dependent enhancer activity and gene transcription
-
Melo, C. A. et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 49, 524-535 (2013).
-
(2013)
Mol Cell
, vol.49
, pp. 524-535
-
-
Melo, C.A.1
-
13
-
-
84901020399
-
Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation
-
Hsieh, C. L. et al. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proc Natl Acad Sci USA 111, 7319-7324 (2014).
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 7319-7324
-
-
Hsieh, C.L.1
-
14
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
-
15
-
-
84890397089
-
Predicting enhancer transcription and activity from chromatin modifications
-
Zhu, Y. et al. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Res 41, 10032-10043 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 10032-10043
-
-
Zhu, Y.1
-
16
-
-
84881171344
-
Enhancer transcripts mark active estrogen receptor binding sites
-
Hah, N., Murakami, S., Nagari, A., Danko, C. G. & Kraus, W. L. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res 23, 1210-1223 (2013).
-
(2013)
Genome Res
, vol.23
, pp. 1210-1223
-
-
Hah, N.1
Murakami, S.2
Nagari, A.3
Danko, C.G.4
Kraus, W.L.5
-
17
-
-
77957243921
-
Long noncoding RNAs with enhancer-like function in human cells
-
Orom, U. A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46-58 (2010).
-
(2010)
Cell
, vol.143
, pp. 46-58
-
-
Orom, U.A.1
-
18
-
-
79953748673
-
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
-
Wang, K. C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-124 (2011).
-
(2011)
Nature
, vol.472
, pp. 120-124
-
-
Wang, K.C.1
-
19
-
-
84874368349
-
Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
-
Lai, F. et al. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494, 497-501 (2013).
-
(2013)
Nature
, vol.494
, pp. 497-501
-
-
Lai, F.1
-
20
-
-
33751251990
-
Small dsRNAs induce transcriptional activation in human cells
-
Li, L. C. et al. Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci USA 103, 17337-17342 (2006).
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 17337-17342
-
-
Li, L.C.1
-
21
-
-
40349094597
-
MicroRNA-373 induces expression of genes with complementary promoter sequences
-
Place, R. F., Li, L. C., Pookot, D., Noonan, E. J. & Dahiya, R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA 105, 1608-1613 (2008).
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 1608-1613
-
-
Place, R.F.1
Li, L.C.2
Pookot, D.3
Noonan, E.J.4
Dahiya, R.5
-
22
-
-
84883191893
-
MIR-200a enhances the migrations of A549 and SK-MES-1 cells by regulating the expression of TSPAN1
-
Chen, Y. et al. MiR-200a enhances the migrations of A549 and SK-MES-1 cells by regulating the expression of TSPAN1. J Biosci 38, 523-532 (2013).
-
(2013)
J Biosci
, vol.38
, pp. 523-532
-
-
Chen, Y.1
-
23
-
-
84863229533
-
Upregulation of Cyclin B1 by miRNA and its implications in cancer
-
Huang, V. et al. Upregulation of Cyclin B1 by miRNA and its implications in cancer. Nucleic Acids Res 40, 1695-1707 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 1695-1707
-
-
Huang, V.1
-
24
-
-
78650117232
-
MicroRNA-205-directed transcriptional activation of tumor suppressor genes in prostate cancer
-
Majid, S. et al. MicroRNA-205-directed transcriptional activation of tumor suppressor genes in prostate cancer. Cancer 116, 5637-5649 (2010).
-
(2010)
Cancer
, vol.116
, pp. 5637-5649
-
-
Majid, S.1
-
25
-
-
84911489718
-
Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs
-
Zhang, Y. et al. Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs. Rna 20, 1878-1889 (2014).
-
(2014)
RNA
, vol.20
, pp. 1878-1889
-
-
Zhang, Y.1
-
26
-
-
84864462544
-
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
-
27
-
-
79961022267
-
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters
-
Koch, F. et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 18, 956-963 (2011).
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 956-963
-
-
Koch, F.1
-
28
-
-
84926658082
-
Long ncRNA expression associates with tissue-specific enhancers
-
Vucicevic, D., Corradin, O., Ntini, E., Scacheri, P. C. & Orom, U. A. Long ncRNA expression associates with tissue-specific enhancers. Cell cycle 14, 253-260 (2015).
-
(2015)
Cell Cycle
, vol.14
, pp. 253-260
-
-
Vucicevic, D.1
Corradin, O.2
Ntini, E.3
Scacheri, P.C.4
Orom, U.A.5
-
29
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang, D., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37, 1-13 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1-13
-
-
Huang, D.1
Sherman, B.T.2
Lempicki, R.A.3
-
30
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57 (2009).
-
(2009)
Nat Protoc
, vol.4
, pp. 44-57
-
-
Huang, D.1
Sherman, B.T.2
Lempicki, R.A.3
-
31
-
-
84890037468
-
Infernal 1.1: 100-fold faster RNA homology searches
-
Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933-2935 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
32
-
-
84876216563
-
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
-
33
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
34
-
-
77955963884
-
Comprehensive modeling of microRNA targets predicts functional nonconserved and non-canonical sites
-
Betel, D., Koppal, A., Agius, P., Sander, C. & Leslie, C. Comprehensive modeling of microRNA targets predicts functional nonconserved and non-canonical sites. Genome Biol 11, R90 (2010).
-
(2010)
Genome Biol
, vol.11
, pp. R90
-
-
Betel, D.1
Koppal, A.2
Agius, P.3
Sander, C.4
Leslie, C.5
-
35
-
-
84897446230
-
Enhancer RNAs and regulated transcriptional programs
-
Lam, M. T., Li, W., Rosenfeld, M. G. & Glass, C. K. Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 39, 170-182 (2014).
-
(2014)
Trends Biochem Sci
, vol.39
, pp. 170-182
-
-
Lam, M.T.1
Li, W.2
Rosenfeld, M.G.3
Glass, C.K.4
-
36
-
-
84891767394
-
RefSeq: An update on mammalian reference sequences
-
Pruitt, K. D. et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 42, D756-763 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D756-763
-
-
Pruitt, K.D.1
-
37
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Bernstein, B. E. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.E.1
-
38
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628 (2008).
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
39
-
-
84874266637
-
Rfam 11.0: 10 years of RNA families
-
Burge, S. W. et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41, D226-232 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D226-232
-
-
Burge, S.W.1
|