-
1
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang ET, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456(7221):470-476.
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 470-476
-
-
Wang, E.T.1
-
2
-
-
0036534129
-
Alternative splicing: Multiple control mechanisms and involvement in human disease
-
Cáceres JF, Kornblihtt AR (2002) Alternative splicing: Multiple control mechanisms and involvement in human disease. Trends Genet 18(4):186-193.
-
(2002)
Trends Genet
, vol.18
, Issue.4
, pp. 186-193
-
-
Cáceres, J.F.1
Kornblihtt, A.R.2
-
3
-
-
67650299463
-
Control of alternative splicing through siRNA-mediated transcriptional gene silencing
-
Alló M, et al. (2009) Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat Struct Mol Biol 16(7):717-724.
-
(2009)
Nat Struct Mol Biol
, vol.16
, Issue.7
, pp. 717-724
-
-
Alló, M.1
-
4
-
-
80052411399
-
Chromatin and alternative splicing
-
spring Harb Symp Quant Biol
-
Alló M, et al. (2010) Chromatin and alternative splicing. Cold Spring Harb Symp Quant Biol 75:103-111.
-
(2010)
Cold
, vol.75
, pp. 103-111
-
-
Alló, M.1
-
5
-
-
84880248267
-
Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation
-
Bertucci PY, et al. (2013) Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation. Nucleic Acids Res 41(12):6072-6086.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.12
, pp. 6072-6086
-
-
Bertucci, P.Y.1
-
6
-
-
80052445151
-
Splicing enhances recruitment of methyltransferase HYPB/ Setd2 and methylation of histone H3 Lys36
-
de Almeida SF, et al. (2011) Splicing enhances recruitment of methyltransferase HYPB/ Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol 18(9):977-983.
-
(2011)
Nat Struct Mol Biol
, vol.18
, Issue.9
, pp. 977-983
-
-
De Almeida, S.F.1
-
7
-
-
78650961149
-
Epigenetics in alternative pre-mRNA splicing
-
Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T (2011) Epigenetics in alternative pre-mRNA splicing. Cell 144(1):16-26.
-
(2011)
Cell
, vol.144
, Issue.1
, pp. 16-26
-
-
Luco, R.F.1
Allo, M.2
Schor, I.E.3
Kornblihtt, A.R.4
Misteli, T.5
-
8
-
-
77149175671
-
Regulation of alternative splicing by histone modifications
-
Luco RF, et al. (2010) Regulation of alternative splicing by histone modifications. Science 327(5968):996-1000.
-
(2010)
Science
, vol.327
, Issue.5968
, pp. 996-1000
-
-
Luco, R.F.1
-
9
-
-
63149192174
-
Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing
-
Schor IE, Rascovan N, Pelisch F, Alló M, Kornblihtt AR (2009) Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc Natl Acad Sci USA 106(11):4325-4330.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.11
, pp. 4325-4330
-
-
Schor, I.E.1
Rascovan, N.2
Pelisch, F.3
Alló, M.4
Kornblihtt, A.R.5
-
10
-
-
84867230570
-
Argonaute proteins couple chromatin silencing to alternative splicing
-
Ameyar-Zazoua M, et al. (2012) Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol 19(10):998-1004.
-
(2012)
Nat Struct Mol Biol
, vol.19
, Issue.10
, pp. 998-1004
-
-
Ameyar-Zazoua, M.1
-
11
-
-
83555164884
-
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila
-
Cernilogar FM, et al. (2011) Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 480(7377):391-395.
-
(2011)
Nature
, vol.480
, Issue.7377
, pp. 391-395
-
-
Cernilogar, F.M.1
-
12
-
-
84874279332
-
Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: Alternative pre-mRNA splicing and transcriptional repression
-
Taliaferro JM, et al. (2013) Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: Alternative pre-mRNA splicing and transcriptional repression. Genes Dev 27(4):378-389.
-
(2013)
Genes Dev
, vol.27
, Issue.4
, pp. 378-389
-
-
Taliaferro, J.M.1
-
13
-
-
84884692746
-
Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells
-
Huang V, et al. (2013) Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. PLoS Genet 9(9):e1003821.
-
(2013)
PLoS Genet
, vol.9
, Issue.9
, pp. e1003821
-
-
Huang, V.1
-
14
-
-
33646130414
-
Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: Comprehensive profiles by representational difference analysis, microarrays and proteomics
-
Nagaraja GM, et al. (2006) Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: Comprehensive profiles by representational difference analysis, microarrays and proteomics. Oncogene 25(16):2328-2338.
-
(2006)
Oncogene
, vol.25
, Issue.16
, pp. 2328-2338
-
-
Nagaraja, G.M.1
-
15
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst J, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345):43-49.
-
(2011)
Nature
, vol.473
, Issue.7345
, pp. 43-49
-
-
Ernst, J.1
-
16
-
-
66249108936
-
Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells
-
Hawkins PG, Santoso S, Adams C, Anest V, Morris KV (2009) Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells. Nucleic Acids Res 37(9):2984-2995.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.9
, pp. 2984-2995
-
-
Hawkins, P.G.1
Santoso, S.2
Adams, C.3
Anest, V.4
Morris, K.V.5
-
17
-
-
33748368912
-
Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells
-
Kim DH, Villeneuve LM, Morris KV, Rossi JJ (2006) Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat Struct Mol Biol 13(9):793-797.
-
(2006)
Nat Struct Mol Biol
, vol.13
, Issue.9
, pp. 793-797
-
-
Kim, D.H.1
Villeneuve, L.M.2
Morris, K.V.3
Rossi, J.J.4
-
18
-
-
84879695128
-
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
-
Li W, et al. (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498(7455):516-520.
-
(2013)
Nature
, vol.498
, Issue.7455
, pp. 516-520
-
-
Li, W.1
-
19
-
-
84856239091
-
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
-
Bonn S, et al. (2012) Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44(2):148-156.
-
(2012)
Nat Genet
, vol.44
, Issue.2
, pp. 148-156
-
-
Bonn, S.1
-
20
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias A, et al. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470(7333):279-283.
-
(2011)
Nature
, vol.470
, Issue.7333
, pp. 279-283
-
-
Rada-Iglesias, A.1
-
21
-
-
78650758676
-
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
-
22
-
-
35748932681
-
Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells
-
Höck J, et al. (2007) Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells. EMBO Rep 8(11):1052-1060.
-
(2007)
EMBO Rep
, vol.8
, Issue.11
, pp. 1052-1060
-
-
Höck, J.1
-
23
-
-
84882452116
-
Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation
-
Schor IE, Fiszbein A, Petrillo E, Kornblihtt AR (2013) Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation. EMBO J 32(16): 2264-2274.
-
(2013)
EMBO J
, vol.32
, Issue.16
, pp. 2264-2274
-
-
Schor, I.E.1
Fiszbein, A.2
Petrillo, E.3
Kornblihtt, A.R.4
-
24
-
-
84901188097
-
How slow RNA polymerase II elongation favors alternative exon skipping
-
Dujardin G, et al. (2014) How slow RNA polymerase II elongation favors alternative exon skipping. Mol Cell 54(4):683-690.
-
(2014)
Mol Cell
, vol.54
, Issue.4
, pp. 683-690
-
-
Dujardin, G.1
-
25
-
-
35548988487
-
The transcriptional cycle of HIV-1 in real-time and live cells
-
Boireau S, et al. (2007) The transcriptional cycle of HIV-1 in real-time and live cells. J Cell Biol 179(2):291-304.
-
(2007)
J Cell Biol
, vol.179
, Issue.2
, pp. 291-304
-
-
Boireau, S.1
-
26
-
-
34548507690
-
In vivo dynamics of RNA polymerase II transcription
-
Darzacq X, et al. (2007) In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 14(9):796-806.
-
(2007)
Nat Struct Mol Biol
, vol.14
, Issue.9
, pp. 796-806
-
-
Darzacq, X.1
-
27
-
-
79952266577
-
Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation
-
Ip JY, et al. (2011) Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res 21(3):390-401.
-
(2011)
Genome Res
, vol.21
, Issue.3
, pp. 390-401
-
-
Ip, J.Y.1
-
28
-
-
0141888375
-
A slow RNA polymerase II affects alternative splicing in vivo
-
de la Mata M, et al. (2003) A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12(2):525-532.
-
(2003)
Mol Cell
, vol.12
, Issue.2
, pp. 525-532
-
-
De La Mata, M.1
-
29
-
-
78549288104
-
Cotranscriptional exon skipping in the genotoxic stress response
-
Dutertre M, et al. (2010) Cotranscriptional exon skipping in the genotoxic stress response. Nat Struct Mol Biol 17(11):1358-1366.
-
(2010)
Nat Struct Mol Biol
, vol.17
, Issue.11
, pp. 1358-1366
-
-
Dutertre, M.1
-
30
-
-
70449953975
-
The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs
-
Jacquier A (2009) The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10(12):833-844.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.12
, pp. 833-844
-
-
Jacquier, A.1
-
31
-
-
78751477191
-
Gene silencing by microRNAs: Contributions of translational repression and mRNA decay
-
Huntzinger E, Izaurralde E (2011) Gene silencing by microRNAs: Contributions of translational repression and mRNA decay. Nat Rev Genet 12(2):99-110.
-
(2011)
Nat Rev Genet
, vol.12
, Issue.2
, pp. 99-110
-
-
Huntzinger, E.1
Izaurralde, E.2
-
32
-
-
84872533627
-
RNA interference in the nucleus: Roles for small RNAs in transcription, epigenetics and beyond
-
Castel SE, Martienssen RA (2013) RNA interference in the nucleus: Roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 14(2):100-112.
-
(2013)
Nat Rev Genet
, vol.14
, Issue.2
, pp. 100-112
-
-
Castel, S.E.1
Martienssen, R.A.2
-
33
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel DP (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116(2):281-297.
-
(2004)
Cell
, vol.116
, Issue.2
, pp. 281-297
-
-
Bartel, D.P.1
-
34
-
-
4344705410
-
Small interfering RNA-induced transcriptional gene silencing in human cells
-
Morris KV, Chan SW, Jacobsen SE, Looney DJ (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305(5688):1289-1292.
-
(2004)
Science
, vol.305
, Issue.5688
, pp. 1289-1292
-
-
Morris, K.V.1
Chan, S.W.2
Jacobsen, S.E.3
Looney, D.J.4
-
35
-
-
53149132028
-
Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region
-
Suzuki K, et al. (2008) Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J Biol Chem 283(34):23353-23363.
-
(2008)
J Biol Chem
, vol.283
, Issue.34
, pp. 23353-23363
-
-
Suzuki, K.1
-
36
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim T-K, et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465(7295):182-187.
-
(2010)
Nature
, vol.465
, Issue.7295
, pp. 182-187
-
-
Kim, T.-K.1
-
37
-
-
84874368349
-
Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
-
Lai F, et al. (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494(7438):497-501.
-
(2013)
Nature
, vol.494
, Issue.7438
, pp. 497-501
-
-
Lai, F.1
-
38
-
-
84862778066
-
Intragenic enhancers act as alternative promoters
-
Kowalczyk MS, et al. (2012) Intragenic enhancers act as alternative promoters. Mol Cell 45(4):447-458.
-
(2012)
Mol Cell
, vol.45
, Issue.4
, pp. 447-458
-
-
Kowalczyk, M.S.1
-
39
-
-
84891945420
-
Widespread misinterpretable ChIPseq bias in yeast
-
Park D, Lee Y, Bhupindersingh G, Iyer VR (2013) Widespread misinterpretable ChIPseq bias in yeast. PLoS ONE 8(12):e83506.
-
(2013)
PLoS ONE
, vol.8
, Issue.12
, pp. e83506
-
-
Park, D.1
Lee, Y.2
Bhupindersingh, G.3
Iyer, V.R.4
-
40
-
-
84887478181
-
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
-
Teytelman L, Thurtle DM, Rine J, van Oudenaarden A (2013) Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci USA 110(46):18602-18607.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.46
, pp. 18602-18607
-
-
Teytelman, L.1
Thurtle, D.M.2
Rine, J.3
Van Oudenaarden, A.4
-
41
-
-
84895072244
-
High-resolution mapping of transcription factor binding sites on native chromatin
-
Kasinathan S, Orsi GA, Zentner GE, Ahmad K, Henikoff S (2014) High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods 11(2):203-209.
-
(2014)
Nat Methods
, vol.11
, Issue.2
, pp. 203-209
-
-
Kasinathan, S.1
Orsi, G.A.2
Zentner, G.E.3
Ahmad, K.4
Henikoff, S.5
-
42
-
-
84902736247
-
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
-
Ward LD, Wang J, Bussemaker HJ (2014) Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. BMC Genomics 15:494-510.
-
(2014)
BMC Genomics
, vol.15
, pp. 494-510
-
-
Ward, L.D.1
Wang, J.2
Bussemaker, H.J.3
-
43
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen X, et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6):1106-1117.
-
(2008)
Cell
, vol.133
, Issue.6
, pp. 1106-1117
-
-
Chen, X.1
-
44
-
-
33747072322
-
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
-
Moorman C, et al. (2006) Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci USA 103(32):12027-12032.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.32
, pp. 12027-12032
-
-
Moorman, C.1
-
45
-
-
83255194564
-
Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data
-
Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E (2011) Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics 27(24):3333-3340.
-
(2011)
Bioinformatics
, vol.27
, Issue.24
, pp. 3333-3340
-
-
Althammer, S.1
González-Vallinas, J.2
Ballaré, C.3
Beato, M.4
Eyras, E.5
-
46
-
-
75249095274
-
DEGseq: An R package for identifying differentially expressed genes from RNA-seq data
-
Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: An R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26(1):136-138.
-
(2010)
Bioinformatics
, vol.26
, Issue.1
, pp. 136-138
-
-
Wang, L.1
Feng, Z.2
Wang, X.3
Wang, X.4
Zhang, X.5
|