-
1
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227
-
(2009)
Nature
, vol.458
, pp. 223-227
-
-
Guttman, M.1
-
2
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
DOI 10.1038/nature05874, PII NATURE05874
-
Birney E et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816 (Pubitemid 46920138)
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
Kuehn, M.S.11
Taylor, C.M.12
Neph, S.13
-
3
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
DOI 10.1126/science.1103388
-
Bertone P et al (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246 (Pubitemid 40024458)
-
(2004)
Science
, vol.306
, Issue.5705
, pp. 2242-2246
-
-
Bertone, P.1
Stolc, V.2
Royce, T.E.3
Rozowsky, J.S.4
Urban, A.E.5
Zhu, X.6
Rinn, J.L.7
Tongprasit, W.8
Samanta, M.9
Weissman, S.10
Gerstein, M.11
Snyder, M.12
-
4
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
DOI 10.1126/science.1138341
-
Kapranov P et al (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484-1488 (Pubitemid 46906616)
-
(2007)
Science
, vol.316
, Issue.5830
, pp. 1484-1488
-
-
Kapranov, P.1
Cheng, J.2
Dike, S.3
Nix, D.A.4
Duttagupta, R.5
Willingham, A.T.6
Stadler, P.F.7
Hertel, J.8
Hackermuller, J.9
Hofacker, I.L.10
Bell, I.11
Cheung, E.12
Drenkow, J.13
Dumais, E.14
Patel, S.15
Helt, G.16
Ganesh, M.17
Ghosh, S.18
Piccolboni, A.19
Sementchenko, V.20
Tammana, H.21
Gingeras, T.R.22
more..
-
5
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
DOI 10.1038/ng1789, PII N1789
-
Carninci P et al (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635 (Pubitemid 43927303)
-
(2006)
Nature Genetics
, vol.38
, Issue.6
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
Semple, C.A.M.7
Taylor, M.S.8
Engstrom, P.G.9
Frith, M.C.10
Forrest, A.R.R.11
Alkema, W.B.12
Tan, S.L.13
Plessy, C.14
Kodzius, R.15
Ravasi, T.16
Kasukawa, T.17
Fukuda, S.18
Kanamori-Katayama, M.19
Kitazume, Y.20
Kawaji, H.21
Kai, C.22
Nakamura, M.23
Konno, H.24
Nakano, K.25
Mottagui-Tabar, S.26
Arner, P.27
Chesi, A.28
Gustincich, S.29
Persichetti, F.30
Suzuki, H.31
Grimmond, S.M.32
Wells, C.A.33
Orlando, V.34
Wahlestedt, C.35
Liu, E.T.36
Harbers, M.37
Kawai, J.38
Bajic, V.B.39
Hume, D.A.40
Hayashizaki, Y.41
more..
-
6
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P et al (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-1563
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
-
7
-
-
67649671961
-
Long noncoding RNAs: Functional surprises from the RNA world
-
Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23: 1494-1504
-
(2009)
Genes Dev
, vol.23
, pp. 1494-1504
-
-
Wilusz, J.E.1
Sunwoo, H.2
Spector, D.L.3
-
9
-
-
0037075032
-
The non-coding Air RNA is required for silencing autosomal imprinted genes
-
Sleutels F, Zwart R, Barlow DP (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415: 810-813 (Pubitemid 34150505)
-
(2002)
Nature
, vol.415
, Issue.6873
, pp. 810-813
-
-
Sleutels, F.1
Zwart, R.2
Barlow, D.P.3
-
10
-
-
75149163987
-
Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells
-
Sheik Mohamed J et al (2010) Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 16: 324-337
-
(2010)
RNA
, vol.16
, pp. 324-337
-
-
Sheik Mohamed, J.1
-
11
-
-
80052869283
-
LincRNAs act in the circuitry controlling pluripotency and differentiation
-
Guttman M et al (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477: 295-300
-
(2011)
Nature
, vol.477
, pp. 295-300
-
-
Guttman, M.1
-
12
-
-
77951638287
-
Noncoding RNA gas5 is a growth arrest-And starvation-Associated repressor of the glucocorticoid receptor
-
Kino T et al (2010) Noncoding RNA gas5 is a growth arrest-And starvation-Associated repressor of the glucocorticoid receptor. Sci Signal 3: ra8
-
(2010)
Sci Signal
, vol.3
-
-
Kino, T.1
-
13
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318-356
-
(1961)
J Mol Biol
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
14
-
-
0023969307
-
The structure and expression of a novel gene activated in early mouse embryogenesis
-
Pachnis V, Brannan CI, Tilghman SM (1988) The structure and expression of a novel gene activated in early mouse embryogenesis. EMBO J 7: 673-681
-
(1988)
EMBO J
, vol.7
, pp. 673-681
-
-
Pachnis, V.1
Brannan, C.I.2
Tilghman, S.M.3
-
15
-
-
0025012640
-
The product of the H19 gene may function as an RNA
-
Brannan CI et al (1990) The product of the H19 gene may function as an RNA. Mol Cell Biol 10: 28-36
-
(1990)
Mol Cell Biol
, vol.10
, pp. 28-36
-
-
Brannan, C.I.1
-
16
-
-
24644481406
-
Molecular biology: A strategy for probing the function of noncoding RNAs finds a repressor of NFAT
-
DOI 10.1126/science.1115901
-
Willingham AT et al (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309: 1570-1573 (Pubitemid 41266484)
-
(2005)
Science
, vol.309
, Issue.5740
, pp. 1570-1573
-
-
Willingham, A.T.1
Orth, A.P.2
Batalov, S.3
Peters, E.C.4
Wen, B.G.5
Aza-Blanc, P.6
Hogenesch, J.B.7
Schultz, P.G.8
-
18
-
-
57149107578
-
Differentiating protein-coding and noncoding RNA: Challenges and ambiguities
-
Dinger ME et al (2008) Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol 4: e1000176
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Dinger, M.E.1
-
19
-
-
51049102332
-
Ripples from neighbouring transcription
-
Ebisuya M et al (2008) Ripples from neighbouring transcription. Nat Cell Biol 10: 1106-1113
-
(2008)
Nat Cell Biol
, vol.10
, pp. 1106-1113
-
-
Ebisuya, M.1
-
20
-
-
33846984935
-
Transcriptional noise and the fidelity of initiation by RNA polymerase II
-
Struhl K (2007) Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 14: 103-105
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 103-105
-
-
Struhl, K.1
-
21
-
-
77952908743
-
A large fraction of extragenic RNA pol II transcription sites overlap enhancers
-
De Santa F et al (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8: e1000384
-
(2010)
PLoS Biol
, vol.8
-
-
De Santa, F.1
-
22
-
-
34249021370
-
Peptides encoded by short ORFs control development and define a new eukaryotic gene family
-
Galindo MI et al (2007) Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol 5: e106
-
(2007)
PLoS Biol
, vol.5
-
-
Galindo, M.I.1
-
23
-
-
81055155799
-
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
-
Ingolia NT, Lareau L F, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147: 789-802
-
(2011)
Cell
, vol.147
, pp. 789-802
-
-
Ingolia, N.T.1
Lareau, L.F.2
Weissman, J.S.3
-
24
-
-
34249088350
-
Genome-wide transcription and the implications for genomic organization
-
DOI 10.1038/nrg2083, PII NRG2083
-
Kapranov P, Willingham AT, Gingeras TR (2007) Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8: 413-423 (Pubitemid 46789245)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.6
, pp. 413-423
-
-
Kapranov, P.1
Willingham, A.T.2
Gingeras, T.R.3
-
25
-
-
69949159297
-
Pervasive transcription constitutes a new level of eukaryotic genome regulation
-
Berretta J, Morillon A (2009) Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep 10: 973-982
-
(2009)
EMBO Rep
, vol.10
, pp. 973-982
-
-
Berretta, J.1
Morillon, A.2
-
26
-
-
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: 833-844
-
(2009)
Nat Rev Genet
, vol.10
, pp. 833-844
-
-
Jacquier, A.1
-
27
-
-
34548432104
-
Raising the estimate of functional human sequences
-
DOI 10.1101/gr.6406307
-
Pheasant M, Mattick JS (2007) Raising the estimate of functional human sequences. Genome Res 17: 1245-1253 (Pubitemid 47360899)
-
(2007)
Genome Research
, vol.17
, Issue.9
, pp. 1245-1253
-
-
Pheasant, M.1
Mattick, J.S.2
-
28
-
-
34248162440
-
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
-
DOI 10.1101/gr.6036807
-
Ponjavic J, Ponting C P, Lunter G (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17: 556-565 (Pubitemid 46715505)
-
(2007)
Genome Research
, vol.17
, Issue.5
, pp. 556-565
-
-
Ponjavic, J.1
Ponting, C.P.2
Lunter, G.3
-
29
-
-
19344368188
-
Genomic analysis of mouse retinal development
-
Blackshaw S et al (2004) Genomic analysis of mouse retinal development. PLoS Biol 2: E247
-
(2004)
PLoS Biol
, vol.2
-
-
Blackshaw, S.1
-
30
-
-
0026456701
-
The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
-
Brown CJ et al (1992) The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71: 527-542
-
(1992)
Cell
, vol.71
, pp. 527-542
-
-
Brown, C.J.1
-
31
-
-
56549111129
-
The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin
-
Nagano T et al (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322: 1717-1720
-
(2008)
Science
, vol.322
, pp. 1717-1720
-
-
Nagano, T.1
-
32
-
-
60149092541
-
The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing
-
Redrup L et al (2009) The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 136: 525-530
-
(2009)
Development
, vol.136
, pp. 525-530
-
-
Redrup, L.1
-
33
-
-
62449319486
-
MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles
-
Sasaki YT et al (2009) MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci USA 106: 2525-2530
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 2525-2530
-
-
Sasaki, Y.T.1
-
34
-
-
61849113891
-
MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
-
Sunwoo H et al (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359
-
(2009)
Genome Res
, vol.19
, pp. 347-359
-
-
Sunwoo, H.1
-
35
-
-
62549117314
-
An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles
-
Clemson CM et al (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 33: 717-726
-
(2009)
Mol Cell
, vol.33
, pp. 717-726
-
-
Clemson, C.M.1
-
36
-
-
30044434769
-
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
-
DOI 10.1101/gr.4200206
-
Ravasi T et al (2006) Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 16: 11-19 (Pubitemid 43048929)
-
(2006)
Genome Research
, vol.16
, Issue.1
, pp. 11-19
-
-
Ravasi, T.1
Suzuki, H.2
Pang, K.C.3
Katayama, S.4
Furuno, M.5
Okunishi, R.6
Fukuda, S.7
Ru, K.8
Frith, M.C.9
Gongora, M.M.10
Grimmond, S.M.11
Hume, D.A.12
Hayashizaki, Y.13
Mattick, J.S.14
-
37
-
-
70149123708
-
Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
-
Ponjavic J et al (2009) Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet 5: e1000617
-
(2009)
PLoS Genet
, vol.5
-
-
Ponjavic, J.1
-
38
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil AM et al (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106: 11667-11672
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
-
39
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M et al (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28: 503-510
-
(2010)
Nat Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
-
40
-
-
80052978224
-
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
-
Cabili MN et al (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927
-
(2011)
Genes Dev
, vol.25
, pp. 1915-1927
-
-
Cabili, M.N.1
-
41
-
-
79959373574
-
Transcription by RNA polymerase III: More complex than we thought
-
White RJ (2011) Transcription by RNA polymerase III: more complex than we thought. Nat Rev Genet 12: 459-463
-
(2011)
Nat Rev Genet
, vol.12
, pp. 459-463
-
-
White, R.J.1
-
42
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
Ponting C P, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641
-
(2009)
Cell
, vol.136
, pp. 629-641
-
-
Ponting, C.P.1
Oliver, P.L.2
Reik, W.3
-
43
-
-
0026489906
-
The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus
-
Brockdorff N et al (1992) The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71: 515-526
-
(1992)
Cell
, vol.71
, pp. 515-526
-
-
Brockdorff, N.1
-
44
-
-
33745125901
-
The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene
-
DOI 10.1126/science.1126316
-
Duret L et al (2006) The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312: 1653-1655 (Pubitemid 43902664)
-
(2006)
Science
, vol.312
, Issue.5780
, pp. 1653-1655
-
-
Duret, L.1
Chureau, C.2
Samain, S.3
Weissanbach, J.4
Avner, P.5
-
45
-
-
43249097469
-
Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes
-
Lin MF et al (2008) Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput Bio 4: e1000067
-
(2008)
PLoS Comput Bio
, vol.4
-
-
Lin, M.F.1
-
46
-
-
79959446962
-
PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions
-
Lin M F, Jungreis I, Kellis M (2011) PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27: i275-i282
-
(2011)
Bioinformatics
, vol.27
-
-
Lin, M.F.1
Jungreis, I.2
Kellis, M.3
-
48
-
-
62549134121
-
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
-
Ingolia NT et al (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223
-
(2009)
Science
, vol.324
, pp. 218-223
-
-
Ingolia, N.T.1
-
49
-
-
79960631283
-
Nuclear export dynamics of RNA-protein complexes
-
Grunwald D, Singer RH, Rout M (2011) Nuclear export dynamics of RNA-protein complexes. Nature 475: 333-341
-
(2011)
Nature
, vol.475
, pp. 333-341
-
-
Grunwald, D.1
Singer, R.H.2
Rout, M.3
-
50
-
-
84255160602
-
Long noncoding RNA-mediated anti-Apoptotic activity in murine erythroid terminal differentiation
-
Hu W et al (2011) Long noncoding RNA-mediated anti-Apoptotic activity in murine erythroid terminal differentiation. Genes Dev 25: 2573-2578
-
(2011)
Genes Dev
, vol.25
, pp. 2573-2578
-
-
Hu, W.1
-
51
-
-
81855212626
-
Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control
-
Lee JT (2011) Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control. Nat Rev Mol Cell Biol 12: 815-826
-
(2011)
Nat Rev Mol Cell Biol
, vol.12
, pp. 815-826
-
-
Lee, J.T.1
-
52
-
-
1842584883
-
RNA regulation: A new genetics?
-
DOI 10.1038/nrg1321
-
Mattick JS (2004) RNA regulation: a new genetics? Nat Rev Genet 5: 316-323 (Pubitemid 38435628)
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.4
, pp. 316-323
-
-
Mattick, J.S.1
-
53
-
-
56949091456
-
Noncoding RNA in development
-
Amaral PP, Mattick JS (2008) Noncoding RNA in development. Mamm Genome 19: 454-492
-
(2008)
Mamm Genome
, vol.19
, pp. 454-492
-
-
Amaral, P.P.1
Mattick, J.S.2
-
54
-
-
33847698971
-
The relationship between non-protein-coding DNA and eukaryotic complexity
-
DOI 10.1002/bies.20544
-
Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29: 288-299 (Pubitemid 46384167)
-
(2007)
BioEssays
, vol.29
, Issue.3
, pp. 288-299
-
-
Taft, R.J.1
Pheasant, M.2
Mattick, J.S.3
-
55
-
-
79957840356
-
Long noncoding RNAs and human disease
-
Wapinski O, Chang HY (2011) Long noncoding RNAs and human disease. Trends Cell Biol 21: 354-361
-
(2011)
Trends Cell Biol
, vol.21
, pp. 354-361
-
-
Wapinski, O.1
Chang, H.Y.2
-
56
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human hox loci by noncoding RNAs
-
DOI 10.1016/j.cell.2007.05.022, PII S0092867407006599
-
Rinn JL et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129: 1311-1323 (Pubitemid 46962090)
-
(2007)
Cell
, vol.129
, Issue.7
, pp. 1311-1323
-
-
Rinn, J.L.1
Kertesz, M.2
Wang, J.K.3
Squazzo, S.L.4
Xu, X.5
Brugmann, S.A.6
Goodnough, L.H.7
Helms, J.A.8
Farnham, P.J.9
Segal, E.10
Chang, H.Y.11
-
57
-
-
80052972698
-
The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin
-
Bertani S et al (2011) The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol Cell 43: 1040-1046
-
(2011)
Mol Cell
, vol.43
, pp. 1040-1046
-
-
Bertani, S.1
-
58
-
-
79953748673
-
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
-
Wang KC et al (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472: 120-124
-
(2011)
Nature
, vol.472
, pp. 120-124
-
-
Wang, K.C.1
-
59
-
-
77954572735
-
Long noncoding RNA as modular scaffold of histone modification complexes
-
Tsai MC et al (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329: 689-693
-
(2010)
Science
, vol.329
, pp. 689-693
-
-
Tsai, M.C.1
-
60
-
-
77956927823
-
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation
-
Tripathi V et al (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39: 925-938
-
(2010)
Mol Cell
, vol.39
, pp. 925-938
-
-
Tripathi, V.1
-
61
-
-
84865379361
-
LincRNA-p21 suppresses target mRNA translation
-
Yoon JH et al (2012) LincRNA-p21 suppresses target mRNA translation. Mol Cell 47: 648-655
-
(2012)
Mol Cell
, vol.47
, pp. 648-655
-
-
Yoon, J.H.1
-
62
-
-
79951495822
-
LncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements
-
Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature 470: 284-288
-
(2011)
Nature
, vol.470
, pp. 284-288
-
-
Gong, C.1
Maquat, L.E.2
-
63
-
-
80054681545
-
In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma
-
Karreth FA et al (2011) In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147: 382-395
-
(2011)
Cell
, vol.147
, pp. 382-395
-
-
Karreth, F.A.1
-
64
-
-
79961170994
-
A ceRNA hypothesis: The Rosetta Stone of a hidden RNA language?
-
Salmena L et al (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146: 353-358
-
(2011)
Cell
, vol.146
, pp. 353-358
-
-
Salmena, L.1
-
65
-
-
80054715378
-
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
-
Cesana M et al (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147: 358-369
-
(2011)
Cell
, vol.147
, pp. 358-369
-
-
Cesana, M.1
-
66
-
-
84861904178
-
Genome regulation by long noncoding RNAs
-
Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81: 145-166
-
(2012)
Annu Rev Biochem
, vol.81
, pp. 145-166
-
-
Rinn, J.L.1
Chang, H.Y.2
-
67
-
-
84857066786
-
Modular regulatory principles of large non-coding RNAs
-
Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482: 339-346
-
(2012)
Nature
, vol.482
, pp. 339-346
-
-
Guttman, M.1
Rinn, J.L.2
-
68
-
-
80053045739
-
Molecular mechanisms of long noncoding RNAs
-
Wang KC, Chang HY (2011) Molecular mechanisms of long noncoding RNAs. Mol Cell 43: 904-914
-
(2011)
Mol Cell
, vol.43
, pp. 904-914
-
-
Wang, K.C.1
Chang, H.Y.2
-
69
-
-
84865192845
-
Flowering time control: Another window to the connection between antisense RNA and chromatin
-
Ietswaart R, Wu Z, Dean C (2012) Flowering time control: another window to the connection between antisense RNA and chromatin. Trends Genet 28: 445-453
-
(2012)
Trends Genet
, vol.28
, pp. 445-453
-
-
Ietswaart, R.1
Wu, Z.2
Dean, C.3
-
70
-
-
79952660821
-
Control of the embryonic stem cell state
-
Young RA (2011) Control of the embryonic stem cell state. Cell 144: 940-954
-
(2011)
Cell
, vol.144
, pp. 940-954
-
-
Young, R.A.1
-
71
-
-
55349109963
-
Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome
-
Zhao J et al (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322: 750-756
-
(2008)
Science
, vol.322
, pp. 750-756
-
-
Zhao, J.1
-
72
-
-
79960484375
-
Gene silencing in X-chromosome inactivation: Advances in understanding facultative heterochromatin formation
-
Wutz A (2011) Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat Rev Genet 12: 542-553
-
(2011)
Nat Rev Genet
, vol.12
, pp. 542-553
-
-
Wutz, A.1
-
73
-
-
77958569435
-
Induced pluripotency: History, mechanisms, and applications
-
Stadtfeld M, Hochedlinger K (2010) Induced pluripotency: history, mechanisms, and applications. Genes Dev 24: 2239-2263
-
(2010)
Genes Dev
, vol.24
, pp. 2239-2263
-
-
Stadtfeld, M.1
Hochedlinger, K.2
-
74
-
-
78149487692
-
Pluripotency and cellular reprogramming: Facts, hypotheses, unresolved issues
-
Hanna JH, Saha K, Jaenisch R (2010) Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues. Cell 143: 508-525
-
(2010)
Cell
, vol.143
, pp. 508-525
-
-
Hanna, J.H.1
Saha, K.2
Jaenisch, R.3
-
75
-
-
78649467088
-
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells
-
Loewer S et al (2010) Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 42: 1113-1117
-
(2010)
Nat Genet
, vol.42
, pp. 1113-1117
-
-
Loewer, S.1
-
76
-
-
84863116597
-
Suppression of progenitor differentiation requires the long noncoding RNA ANCR
-
Kretz M et al (2012) Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev 26: 338-343
-
(2012)
Genes Dev
, vol.26
, pp. 338-343
-
-
Kretz, M.1
-
77
-
-
33645823589
-
A noncoding RNA is a potential marker of cell fate during mammary gland development
-
Ginger MR et al (2006) A noncoding RNA is a potential marker of cell fate during mammary gland development. Proc Natl Acad Sci USA 103: 5781-5786
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5781-5786
-
-
Ginger, M.R.1
-
78
-
-
67749143699
-
Evolution of the Hox gene complex from an evolutionary ground state
-
Gehring WJ, Kloter U, Suga H (2009) Evolution of the Hox gene complex from an evolutionary ground state. Curr Top Dev Biol 88: 35-61
-
(2009)
Curr Top Dev Biol
, vol.88
, pp. 35-61
-
-
Gehring, W.J.1
Kloter, U.2
Suga, H.3
-
79
-
-
28944438404
-
Modulating Hox gene functions during animal body patterning
-
DOI 10.1038/nrg1726
-
Pearson JC, Lemons D, McGinnis W (2005) Modulating Hox gene functions during animal body patterning. Nat Rev Genet 6: 893-904 (Pubitemid 41782157)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.12
, pp. 893-904
-
-
Pearson, J.C.1
Lemons, D.2
McGinnis, W.3
-
80
-
-
52149090746
-
MicroRNAs in the Hox network: An apparent link to posterior prevalence
-
Yekta S, Tabin CJ, Bartel DP (2008) MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nat Rev Genet 9: 789-796
-
(2008)
Nat Rev Genet
, vol.9
, pp. 789-796
-
-
Yekta, S.1
Tabin, C.J.2
Bartel, D.P.3
-
81
-
-
79955088437
-
The sequence, structure and evolutionary features of HOTAIR in mammals
-
He S, Liu S, Zhu H (2011) The sequence, structure and evolutionary features of HOTAIR in mammals. BMC Evol Biol 11: 102
-
(2011)
BMC Evol Biol
, vol.11
, pp. 102
-
-
He, S.1
Liu, S.2
Zhu, H.3
-
82
-
-
84863495094
-
The hallmarks of cancer: A long non-coding RNA point of view
-
Gutschner T, Diederichs S (2012) The hallmarks of cancer: A long non-coding RNA point of view. RNA Biol 9: 703-719
-
(2012)
RNA Biol
, vol.9
, pp. 703-719
-
-
Gutschner, T.1
Diederichs, S.2
-
83
-
-
77951118936
-
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
-
Gupta RA et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464: 1071-1076
-
(2010)
Nature
, vol.464
, pp. 1071-1076
-
-
Gupta, R.A.1
-
84
-
-
80054029971
-
Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers
-
Kogo R et al (2011) Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 71: 6320-6326
-
(2011)
Cancer Res
, vol.71
, pp. 6320-6326
-
-
Kogo, R.1
-
85
-
-
0038406789
-
Biology of hematopoietic stem cells and progenitors: Implications for clinical application
-
DOI 10.1146/annurev.immunol.21.120601.141007
-
Kondo M et al (2003) Biology of hematopoietic stem cells and progenitors: implications for clinical application. Annu Rev Immunol 21: 759-806 (Pubitemid 37174547)
-
(2003)
Annual Review of Immunology
, vol.21
, pp. 759-806
-
-
Kondo, M.1
Wagers, A.J.2
Manz, M.G.3
Prohaska, S.S.4
Scherer, D.C.5
Beilhack, G.F.6
Shizuru, J.A.7
Weissman, I.L.8
-
86
-
-
34250007153
-
EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression
-
DOI 10.1182/blood-2006-06-027987
-
Wagner LA et al (2007) EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression. Blood 109: 5191-5198 (Pubitemid 46890536)
-
(2007)
Blood
, vol.109
, Issue.12
, pp. 5191-5198
-
-
Wagner, L.A.1
Christensen, C.J.2
Dunn, D.M.3
Spangrude, G.J.4
Georgelas, A.5
Kelley, L.6
Esplin, M.S.7
Weiss, R.B.8
Gleich, G.J.9
-
87
-
-
63849156246
-
A myelopoiesis-Associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster
-
Zhang X et al (2009) A myelopoiesis-Associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood 113: 2526-2534
-
(2009)
Blood
, vol.113
, pp. 2526-2534
-
-
Zhang, X.1
-
88
-
-
74949140605
-
A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo
-
Li K et al (2010) A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo. Blood 115: 133-139
-
(2010)
Blood
, vol.115
, pp. 133-139
-
-
Li, K.1
-
89
-
-
79957485838
-
Transcriptional mechanisms regulating skeletal muscle differentiation, growth and homeostasis
-
Braun T, Gautel M (2011) Transcriptional mechanisms regulating skeletal muscle differentiation, growth and homeostasis. Nat Rev Mol Cell Biol 12: 349-361
-
(2011)
Nat Rev Mol Cell Biol
, vol.12
, pp. 349-361
-
-
Braun, T.1
Gautel, M.2
-
90
-
-
84455167606
-
CeRNAs: MiRNA target mimic mimics
-
Rubio-Somoza I et al (2011) ceRNAs: miRNA target mimic mimics. Cell 147: 1431-1432
-
(2011)
Cell
, vol.147
, pp. 1431-1432
-
-
Rubio-Somoza, I.1
-
91
-
-
58149520665
-
SMD and NMD are competitive pathways that contribute to myogenesis: Effects on PAX3 and myogenin mRNAs
-
Gong C et al (2009) SMD and NMD are competitive pathways that contribute to myogenesis: effects on PAX3 and myogenin mRNAs. Genes Dev 23: 54-66
-
(2009)
Genes Dev
, vol.23
, pp. 54-66
-
-
Gong, C.1
-
92
-
-
76649122999
-
Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
-
Mercer TR et al (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 11: 14
-
(2010)
BMC Neurosci
, vol.11
, pp. 14
-
-
Mercer, T.R.1
-
93
-
-
45449092537
-
Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation
-
Tochitani S, Hayashizaki Y (2008) Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation. Biochem Biophys Res Commun 372: 691-696
-
(2008)
Biochem Biophys Res Commun
, vol.372
, pp. 691-696
-
-
Tochitani, S.1
Hayashizaki, Y.2
-
94
-
-
33744804277
-
The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator
-
DOI 10.1101/gad.1416106
-
Feng J et al (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20: 1470-1484 (Pubitemid 43830654)
-
(2006)
Genes and Development
, vol.20
, Issue.11
, pp. 1470-1484
-
-
Feng, J.1
Bi, C.2
Clark, B.S.3
Mady, R.4
Shah, P.5
Kohtz, J.D.6
-
95
-
-
68149182666
-
Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry
-
Bond AM et al (2009) Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat Neurosci 12: 1020-1027
-
(2009)
Nat Neurosci
, vol.12
, pp. 1020-1027
-
-
Bond, A.M.1
-
96
-
-
77951945884
-
The long noncoding RNA RNCR2 directs mouse retinal cell specification
-
Rapicavoli NA, Poth EM, Blackshaw S (2010) The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 10: 49
-
(2010)
BMC Dev Biol
, vol.10
, pp. 49
-
-
Rapicavoli, N.A.1
Poth, E.M.2
Blackshaw, S.3
-
97
-
-
84055212187
-
The long noncoding RNA Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina
-
Meola N et al (2012) The long noncoding RNA Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina. RNA 18: 111-123
-
(2012)
RNA
, vol.18
, pp. 111-123
-
-
Meola, N.1
-
98
-
-
84856492490
-
Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors
-
Ng SY, Johnson R, Stanton LW (2012) Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J 31: 522-533
-
(2012)
EMBO J
, vol.31
, pp. 522-533
-
-
Ng, S.Y.1
Johnson, R.2
Stanton, L.W.3
-
99
-
-
84864326893
-
Molecular biology. Use and abuse of RNAi to study mammalian gene function
-
Kaelin WG Jr (2012) Molecular biology. Use and abuse of RNAi to study mammalian gene function. Science 337: 421-422
-
(2012)
Science
, vol.337
, pp. 421-422
-
-
Kaelin Jr., W.G.1
-
100
-
-
84864856835
-
Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains
-
Cong L et al (2012) Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun 3: 968
-
(2012)
Nat Commun
, vol.3
, pp. 968
-
-
Cong, L.1
-
101
-
-
2942560254
-
Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
-
DOI 10.1038/nature02538
-
Martens JA, Laprade L, Winston F (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429: 571-574 (Pubitemid 38737662)
-
(2004)
Nature
, vol.429
, Issue.6991
, pp. 571-574
-
-
Martens, J.A.1
Laprade, L.2
Winston, F.3
-
102
-
-
77955323879
-
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
-
Huarte M et al (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142: 409-419
-
(2010)
Cell
, vol.142
, pp. 409-419
-
-
Huarte, M.1
-
103
-
-
84864927713
-
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs
-
Moran VA, Perera RJ, Khalil AM (2012) Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res 40: 6391-6400
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 6391-6400
-
-
Moran, V.A.1
Perera, R.J.2
Khalil, A.M.3
-
104
-
-
78650253763
-
Genome-wide identification of polycomb-Associated RNAs by RIP-seq
-
Zhao J et al (2010) Genome-wide identification of polycomb-Associated RNAs by RIP-seq. Mol Cell 40: 939-953
-
(2010)
Mol Cell
, vol.40
, pp. 939-953
-
-
Zhao, J.1
-
105
-
-
78049325193
-
Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse
-
Reinius B et al (2010) Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse. BMC Genomics 11: 614
-
(2010)
BMC Genomics
, vol.11
, pp. 614
-
-
Reinius, B.1
-
106
-
-
84859211025
-
Combined RNAi and localization for functionally dissecting long noncoding RNAs
-
Chakraborty D et al (2012) Combined RNAi and localization for functionally dissecting long noncoding RNAs. Nat Methods 9: 360-362
-
(2012)
Nat Methods
, vol.9
, pp. 360-362
-
-
Chakraborty, D.1
-
107
-
-
80054756754
-
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
-
Chu C et al (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44: 667-678
-
(2011)
Mol Cell
, vol.44
, pp. 667-678
-
-
Chu, C.1
-
108
-
-
84862908875
-
The genomic binding sites of a noncoding RNA
-
Simon MD et al (2011) The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci USA 108: 20497-20502
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 20497-20502
-
-
Simon, M.D.1
-
109
-
-
77954460345
-
Increased expression of angiogenic genes in the brains of mouse meg3-null embryos
-
Gordon FE et al (2010) Increased expression of angiogenic genes in the brains of mouse meg3-null embryos. Endocrinology 151: 2443-2452
-
(2010)
Endocrinology
, vol.151
, pp. 2443-2452
-
-
Gordon, F.E.1
-
110
-
-
79955506825
-
Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice
-
Nakagawa S et al (2011) Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol 193: 31-39
-
(2011)
J Cell Biol
, vol.193
, pp. 31-39
-
-
Nakagawa, S.1
-
111
-
-
84864033675
-
Malat1 is not an essential component of nuclear speckles in mice
-
Nakagawa S et al (2012) Malat1 is not an essential component of nuclear speckles in mice. RNA 18: 1487-1499
-
(2012)
RNA
, vol.18
, pp. 1487-1499
-
-
Nakagawa, S.1
-
112
-
-
79957983437
-
Structural and functional differences in the long non-coding RNA hotair in mouse and human
-
Schorderet P, Duboule D (2011) Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet 7: e1002071
-
(2011)
PLoS Genet
, vol.7
-
-
Schorderet, P.1
Duboule, D.2
-
113
-
-
80053444842
-
Tsx produces a long noncoding RNA and has general functions in the germline, stem cells, and brain
-
Anguera MC et al (2011) Tsx produces a long noncoding RNA and has general functions in the germline, stem cells, and brain. PLoS Genet 7: e1002248
-
(2011)
PLoS Genet
, vol.7
-
-
Anguera, M.C.1
-
114
-
-
77955757309
-
Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1
-
Mohammad F et al (2010) Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 137: 2493-2499
-
(2010)
Development
, vol.137
, pp. 2493-2499
-
-
Mohammad, F.1
-
115
-
-
0030993133
-
Deletion of the H19 transcription unit reveals the existence of a putative imprinting control element
-
Ripoche MA et al (1997) Deletion of the H19 transcription unit reveals the existence of a putative imprinting control element. Genes Dev 11: 1596-1604
-
(1997)
Genes Dev
, vol.11
, pp. 1596-1604
-
-
Ma, R.1
-
116
-
-
84455206362
-
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
-
Ulitsky I et al (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147: 1537-1550
-
(2011)
Cell
, vol.147
, pp. 1537-1550
-
-
Ulitsky, I.1
-
117
-
-
84864315112
-
The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult
-
Zhang B et al (2012) The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep 2: 111-123
-
(2012)
Cell Rep
, vol.2
, pp. 111-123
-
-
Zhang, B.1
-
118
-
-
84864047695
-
Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development
-
Eissmann M et al (2012) Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. Biol RNA 9: 1076-1087
-
(2012)
Biol RNA
, vol.9
, pp. 1076-1087
-
-
Eissmann, M.1
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