-
1
-
-
84875200257
-
Long noncoding RNAs: Cellular address codes in development and disease
-
Batista, P.J. & Chang, H.Y. Long noncoding RNAs: cellular address codes in development and disease. Cell 152, 1298-1307 (2013).
-
(2013)
Cell
, vol.152
, pp. 1298-1307
-
-
Batista, P.J.1
Chang, H.Y.2
-
2
-
-
84875177348
-
X-inactivation, imprinting, and long noncoding RNAs in health and disease
-
Lee, J.T. & Bartolomei, M.S. X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 152, 1308-1323 (2013).
-
(2013)
Cell
, vol.152
, pp. 1308-1323
-
-
Lee, J.T.1
Bartolomei, M.S.2
-
3
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
-
4
-
-
60349120914
-
Long non-coding RNAs: Insights into functions
-
Mercer, T.R., Dinger, M.E. & Mattick, J.S. Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 10, 155-159 (2009).
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 155-159
-
-
Mercer, T.R.1
Dinger, M.E.2
Mattick, J.S.3
-
5
-
-
84857066786
-
Modular regulatory principles of large non-coding RNAs
-
Guttman, M. & Rinn, J.L. Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346 (2012).
-
(2012)
Nature
, vol.482
, pp. 339-346
-
-
Guttman, M.1
Rinn, J.L.2
-
6
-
-
27944508215
-
CLIP: A method for identifying protein-RNA interaction sites in living cells
-
Ule, J., Jensen, K., Mele, A. & Darnell, R.B. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37, 376-386 (2005).
-
(2005)
Methods
, vol.37
, pp. 376-386
-
-
Ule, J.1
Jensen, K.2
Mele, A.3
Darnell, R.B.4
-
7
-
-
77950920903
-
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
-
Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141 (2010).
-
(2010)
Cell
, vol.141
, pp. 129-141
-
-
Hafner, M.1
-
8
-
-
84876935138
-
Mapping the human miRNA interactome by CLASH reveals frequent non-canonical binding
-
Helwak, A., Kudla, G., Dudnakova, T. & Tollervey, D. Mapping the human miRNA interactome by CLASH reveals frequent non-canonical binding. Cell 153, 654-665 (2013).
-
(2013)
Cell
, vol.153
, pp. 654-665
-
-
Helwak, A.1
Kudla, G.2
Dudnakova, T.3
Tollervey, D.4
-
9
-
-
80054756754
-
Genomic maps of long noncoding RNA occupancy reveals principles of RNA-chromatin interactions
-
Chu, C., Qu, K., Zhong, F.L., Artandi, S.E. & Chang, H.Y. Genomic maps of long noncoding RNA occupancy reveals principles of RNA-chromatin interactions. Mol. Cell 44, 667-678 (2011).
-
(2011)
Mol. Cell
, vol.44
, pp. 667-678
-
-
Chu, C.1
Qu, K.2
Zhong, F.L.3
Artandi, S.E.4
Chang, H.Y.5
-
10
-
-
84862908875
-
The genomic binding sites of a noncoding RNA
-
Simon, M.D. et al. The genomic binding sites of a noncoding RNA. Proc. Natl. Acad. Sci. USA 108, 20497-20502 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 20497-20502
-
-
Simon, M.D.1
-
11
-
-
84879642373
-
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome
-
Engreitz, J.M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973 (2013).
-
(2013)
Science
, vol.341
, pp. 1237973
-
-
Engreitz, J.M.1
-
12
-
-
84883132550
-
LncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs
-
Yang, L. et al. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature 500, 598-602 (2013).
-
(2013)
Nature
, vol.500
, pp. 598-602
-
-
Yang, L.1
-
13
-
-
84877336707
-
Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA
-
Rossetto, C.C., Tarrant-Elorza, M., Verma, S., Purushothaman, P. & Pari, G.S. Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA. J. Virol. 87, 5540-5553 (2013).
-
(2013)
J. Virol.
, vol.87
, pp. 5540-5553
-
-
Rossetto, C.C.1
Tarrant-Elorza, M.2
Verma, S.3
Purushothaman, P.4
Pari, G.S.5
-
14
-
-
84896732761
-
Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome
-
Colak, D. et al. Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome. Science 343, 1002-1005 (2014).
-
(2014)
Science
, vol.343
, pp. 1002-1005
-
-
Colak, D.1
-
15
-
-
84855940430
-
Dosage compensation in Drosophila melanogaster: Epigenetic fine-tuning of chromosome-wide transcription
-
Conrad, T. & Akhtar, A. Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription. Nat. Rev. Genet. 13, 123-134 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 123-134
-
-
Conrad, T.1
Akhtar, A.2
-
16
-
-
25844440873
-
The Drosophila MSL complex activates the transcription of target genes
-
Straub, T., Gilfillan, G., Maier, V.K. & Becker, P.B. The Drosophila MSL complex activates the transcription of target genes. Genes Dev. 19, 2284-2288 (2005).
-
(2005)
Genes Dev.
, vol.19
, pp. 2284-2288
-
-
Straub, T.1
Gilfillan, G.2
Maier, V.K.3
Becker, P.B.4
-
17
-
-
49549113199
-
A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome
-
Alekseyenko, A.A. et al. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134, 599-609 (2008).
-
(2008)
Cell
, vol.134
, pp. 599-609
-
-
Alekseyenko, A.A.1
-
18
-
-
84880429542
-
Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila
-
Ilik, I.A. et al. Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol. Cell 51, 156-173 (2013).
-
(2013)
Mol. Cell
, vol.51
, pp. 156-173
-
-
Ilik, I.A.1
-
19
-
-
43949085073
-
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila
-
Kind, J. et al. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 133, 813-828 (2008).
-
(2008)
Cell
, vol.133
, pp. 813-828
-
-
Kind, J.1
-
20
-
-
84880445591
-
The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation
-
Soruco, M.M.L. et al. The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev. 27, 1551-1556 (2013).
-
(2013)
Genes Dev.
, vol.27
, pp. 1551-1556
-
-
Soruco, M.M.L.1
-
21
-
-
0036500632
-
The roX genes encode redundant Male-Specific-Lethal transcripts required for targeting of the MSL complex
-
Meller, V.H. & Rattner, B.P. The roX genes encode redundant Male-Specific-Lethal transcripts required for targeting of the MSL complex. EMBO J. 21, 1084-1091 (2002).
-
(2002)
EMBO J.
, vol.21
, pp. 1084-1091
-
-
Meller, V.H.1
Rattner, B.P.2
-
22
-
-
37249042122
-
An evolutionarily conserved domain of roX2 RNA is sufficient for induction of H4-Lys19 acetylation on the Drosophila X chromosome
-
Park, S.W. et al. An evolutionarily conserved domain of roX2 RNA is sufficient for induction of H4-Lys19 acetylation on the Drosophila X chromosome. Genetics 177, 1429-1437 (2007).
-
(2007)
Genetics
, vol.177
, pp. 1429-1437
-
-
Park, S.W.1
-
23
-
-
0042208405
-
Functional redundancy within roX1, a noncoding RNA involved in dosage compensation in Drosophila melanogaster
-
Stuckenholz, C., Meller, V.H. & Kuroda, M.I. Functional redundancy within roX1, a noncoding RNA involved in dosage compensation in Drosophila melanogaster. Genetics 164, 1003-1014 (2003).
-
(2003)
Genetics
, vol.164
, pp. 1003-1014
-
-
Stuckenholz, C.1
Meller, V.H.2
Kuroda, M.I.3
-
24
-
-
55249112898
-
Transcription rate of noncoding roX1 RNA controls local spreading of the Drosophila MSL chromatin remodeling complex
-
Kelley, R.L., Lee, O.K. & Shim, Y.K. Transcription rate of noncoding roX1 RNA controls local spreading of the Drosophila MSL chromatin remodeling complex. Mech. Dev. 125, 1009-1019 (2008).
-
(2008)
Mech. Dev.
, vol.125
, pp. 1009-1019
-
-
Kelley, R.L.1
Lee, O.K.2
Shim, Y.K.3
-
25
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
-
26
-
-
84880421665
-
ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteins
-
Maenner, S., Müller, M., Fröhlich, J., Langer, D. & Becker, P.B. ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteins. Mol. Cell 51, 174-184 (2013).
-
(2013)
Mol. Cell
, vol.51
, pp. 174-184
-
-
Maenner, S.1
Müller, M.2
Fröhlich, J.3
Langer, D.4
Becker, P.B.5
-
27
-
-
84856747483
-
Three-dimensional folding and functional organization principles of the Drosophila genome
-
Sexton, T. et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458-472 (2012).
-
(2012)
Cell
, vol.148
, pp. 458-472
-
-
Sexton, T.1
-
28
-
-
70350629982
-
The dosage compensation complex shapes the conformation of the X chromosome in Drosophila
-
Grimaud, C. & Becker, P.B. The dosage compensation complex shapes the conformation of the X chromosome in Drosophila. Genes Dev. 23, 2490-2495 (2009).
-
(2009)
Genes Dev.
, vol.23
, pp. 2490-2495
-
-
Grimaud, C.1
Becker, P.B.2
-
29
-
-
84890549512
-
High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation
-
Simon, M.D. et al. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504, 465-469 (2013).
-
(2013)
Nature
, vol.504
, pp. 465-469
-
-
Simon, M.D.1
-
30
-
-
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
-
31
-
-
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
-
32
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
33
-
-
84863741439
-
Chromatin isolation by RNA purification (ChIRP)
-
Chu, C., Quinn, J.J. & Chang, H.Y. Chromatin isolation by RNA purification (ChIRP). J. Vis. Exp. 61, e3912 (2012).
-
(2012)
J. Vis. Exp.
, vol.61
, pp. e3912
-
-
Chu, C.1
Quinn, J.J.2
Chang, H.Y.3
-
34
-
-
77951118936
-
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
-
Gupta, R.A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076 (2010).
-
(2010)
Nature
, vol.464
, pp. 1071-1076
-
-
Gupta, R.A.1
-
35
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
-
(2008)
Genome Biol.
, vol.9
, pp. R137
-
-
Zhang, Y.1
-
36
-
-
79960614727
-
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
-
Rashid, N.U., Giresi, P.G., Ibrahim, J.G., Sun, W. & Lieb, J.D. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol. 12, R67 (2011).
-
(2011)
Genome Biol.
, vol.12
, pp. R67
-
-
Rashid, N.U.1
Giresi, P.G.2
Ibrahim, J.G.3
Sun, W.4
Lieb, J.D.5
-
37
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005).
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
38
-
-
2442458847
-
Construction of transgenic Drosophila by using the site-specific integrase from phage PhiC31
-
Groth, A.C., Fish, M., Nusse, R. & Calos, M.P. Construction of transgenic Drosophila by using the site-specific integrase from phage PhiC31. Genetics 166, 1775-1782 (2004).
-
(2004)
Genetics
, vol.166
, pp. 1775-1782
-
-
Groth, A.C.1
Fish, M.2
Nusse, R.3
Calos, M.P.4
|