-
2
-
-
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
-
3
-
-
0035966319
-
microRNAs: Tiny regulators with great potential
-
Ambros V. 2001. microRNAs: tiny regulators with great potential. Cell 107: 823-826.
-
(2001)
Cell
, vol.107
, pp. 823-826
-
-
Ambros, V.1
-
4
-
-
33745402414
-
A novel class of small RNAs bind to MILI protein in mouse testes
-
Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, et al. 2006. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442: 203-207.
-
(2006)
Nature
, vol.442
, pp. 203-207
-
-
Aravin, A.1
Gaidatzis, D.2
Pfeffer, S.3
Lagos-Quintana, M.4
Landgraf, P.5
Iovino, N.6
Morris, P.7
Brownstein, M.J.8
Kuramochi-Miyagawa, S.9
Nakano, T.10
-
5
-
-
7744223490
-
MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome
-
Bao N, LyeKW, Barton MK. 2004. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Develop Cell 7: 653-662.
-
(2004)
Develop Cell
, vol.7
, pp. 653-662
-
-
Bao, N.1
Lye, K.W.2
Barton, M.K.3
-
6
-
-
0034681490
-
Crystal structure of the ribonucleoprotein core of the signal recognition particle
-
Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA. 2000. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287: 1232-1239.
-
(2000)
Science
, vol.287
, pp. 1232-1239
-
-
Batey, R.T.1
Rambo, R.P.2
Lucast, L.3
Rha, B.4
Doudna, J.A.5
-
7
-
-
36448966082
-
Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins
-
Beisel C, Buness A, Roustan-Espinosa IM, Koch B, Schmitt S, Haas SA, Hild M, Katsuyama T, Paro R. 2007. Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins. Proc Nat Acad Sci 104: 16615-16620.
-
(2007)
Proc Nat Acad Sci
, vol.104
, pp. 16615-16620
-
-
Beisel, C.1
Buness, A.2
Roustan-Espinosa, I.M.3
Koch, B.4
Schmitt, S.5
Haas, S.A.6
Hild, M.7
Katsuyama, T.8
Paro, R.9
-
9
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, TongprasitW, Samanta M, Weissman S, et al. 2004. Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246.
-
(2004)
Science
, vol.306
, 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
-
10
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, 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
-
11
-
-
68149182666
-
Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry
-
Bond AM, Vangompel MJ, Sametsky EA, Clark MF, Savage JC, Disterhoft JF, Kohtz JD. 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
Vangompel, M.J.2
Sametsky, E.A.3
Clark, M.F.4
Savage, J.C.5
Disterhoft, J.F.6
Kohtz, J.D.7
-
12
-
-
41549129240
-
Mapping of small RNAs in the human ENCODE regions
-
Borel C, Gagnebin M, Gehrig C, Kriventseva EV, Zdobnov EM, Antonarakis SE. 2008. Mapping of small RNAs in the human ENCODE regions. Am J Human Gen 82: 971-981.
-
(2008)
Am J Human Gen
, vol.82
, pp. 971-981
-
-
Borel, C.1
Gagnebin, M.2
Gehrig, C.3
Kriventseva, E.V.4
Zdobnov, E.M.5
Antonarakis, S.E.6
-
13
-
-
0026456701
-
The human XIST gene: Analysis of a 17kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
-
Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawrence J, Willard HF. 1992. The human XIST gene: Analysis of a 17kb 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
Hendrich, B.D.2
Rupert, J.L.3
Lafreniere, R.G.4
Xing, Y.5
Lawrence, J.6
Willard, H.F.7
-
14
-
-
66449114042
-
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at theDNA sequence level
-
Bruce AW, Lopez-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, et al. 2009. Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at theDNA sequence level. Genome Research 19: 994-1005.
-
(2009)
Genome Research
, vol.19
, pp. 994-1005
-
-
Bruce, A.W.1
Lopez-Contreras, A.J.2
Flicek, P.3
Down, T.A.4
Dhami, P.5
Dillon, S.C.6
Koch, C.M.7
Langford, C.F.8
Dunham, I.9
Andrews, R.M.10
-
15
-
-
0028129989
-
Conserved structures and diversity of functions of RNA-binding proteins
-
Burd CG, Dreyfuss G. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265: 615-621.
-
(1994)
Science
, vol.265
, pp. 615-621
-
-
Burd, C.G.1
Dreyfuss, G.2
-
16
-
-
34548230885
-
Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas
-
Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik SE, et al. 2007. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12: 215-229.
-
(2007)
Cancer Cell
, vol.12
, pp. 215-229
-
-
Calin, G.A.1
Liu, C.G.2
Ferracin, M.3
Hyslop, T.4
Spizzo, R.5
Sevignani, C.6
Fabbri, M.7
Cimmino, A.8
Lee, E.J.9
Wojcik, S.E.10
-
17
-
-
33749125424
-
The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators ofMyoD and skeletal muscle differentiation
-
Caretti G, Schiltz RL, Dilworth FJ, Di Padova M, Zhao P, Ogryzko V, Fuller-Pace FV, Hoffman EP, Tapscott SJ, Sartorelli V. 2006. The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators ofMyoD and skeletal muscle differentiation. Develop Cell 11: 547-560.
-
(2006)
Develop Cell
, vol.11
, pp. 547-560
-
-
Caretti, G.1
Schiltz, R.L.2
Dilworth, F.J.3
Di Padova, M.4
Zhao, P.5
Ogryzko, V.6
Fuller-Pace, F.V.7
Hoffman, E.P.8
Tapscott, S.J.9
Sartorelli, V.10
-
18
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 1559-1563.
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
Kasukawa, T.2
Katayama, S.3
Gough, J.4
Frith, M.C.5
Maeda, N.6
Oyama, R.7
Ravasi, T.8
Lenhard, B.9
Wells, C.10
-
19
-
-
33744805985
-
Genomewide analysis of mammalian promoter architecture and evolution
-
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, et al. 2006. Genomewide analysis of mammalian promoter architecture and evolution. Nat Gen 38: 626-635.
-
(2006)
Nat Gen
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
Semple, C.A.7
Taylor, M.S.8
Engstrom, P.G.9
Frith, M.C.10
-
20
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points towidespread regulation of noncoding RNAs
-
Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points towidespread regulation of noncoding RNAs. Cell 116: 499-509.
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
Kapranov, P.4
Sekinger, E.A.5
Kampa, D.6
Piccolboni, A.7
Sementchenko, V.8
Cheng, J.9
Williams, A.J.10
-
21
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, ZhangW, Jiang J, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106-1117.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
Wong, E.7
Orlov, Y.L.8
Zhang, W.9
Jiang, J.10
-
22
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
-
(2005)
Science
, vol.308
, pp. 1149-1154
-
-
Cheng, J.1
Kapranov, P.2
Drenkow, J.3
Dike, S.4
Brubaker, S.5
Patel, S.6
Long, J.7
Stern, D.8
Tammana, H.9
Helt, G.10
-
23
-
-
62549117314
-
An architectural role for a nuclear noncodingRNA: NEAT1 RNA is essential for the structure of paraspeckles
-
Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, Lawrence JB. 2009. An architectural role for a nuclear noncodingRNA: 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
Hutchinson, J.N.2
Sara, S.A.3
Ensminger, A.W.4
Fox, A.H.5
Chess, A.6
Lawrence, J.B.7
-
24
-
-
30044451918
-
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome
-
Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM. 2006. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Gen Res 16: 1-10.
-
(2006)
Gen Res
, vol.16
, pp. 1-10
-
-
Cooper, S.J.1
Trinklein, N.D.2
Anton, E.D.3
Nguyen, L.4
Myers, R.M.5
-
25
-
-
33845474731
-
Non-coding RNAs: Lost in translation?
-
Costa FF. 2007. Non-coding RNAs: lost in translation? Gene 386: 1-10.
-
(2007)
Gene
, vol.386
, pp. 1-10
-
-
Costa, F.F.1
-
26
-
-
33644784770
-
Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae
-
Davis CA, Ares MJr., 2006. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Nat Acad Sci 103: 3262-3267.
-
(2006)
Proc Nat Acad Sci
, vol.103
, pp. 3262-3267
-
-
Davis, C.A.1
Ares Jr., M.2
-
27
-
-
7744228427
-
Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation
-
de Napoles M, Mermoud JE, Wakao R, Tang YA, Endoh M, Appanah R, Nesterova TB, Silva J, Otte AP, Vidal M, et al. 2004. Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Develop Cell 7: 663-676.
-
(2004)
Develop Cell
, vol.7
, pp. 663-676
-
-
de Napoles, M.1
Mermoud, J.E.2
Wakao, R.3
Tang, Y.A.4
Endoh, M.5
Appanah, R.6
Nesterova, T.B.7
Silva, J.8
Otte, A.P.9
Vidal, M.10
-
28
-
-
0041977096
-
Ligand-independent coactivation of ERα AF-1 by steroid receptor RNA activator (SRA) via MAPK activation
-
Deblois G, Giguere V. 2003. Ligand-independent coactivation of ERα AF-1 by steroid receptor RNA activator (SRA) via MAPK activation. J Steroid Biochem Mol Biol 85: 123-131.
-
(2003)
J Steroid Biochem Mol Biol
, vol.85
, pp. 123-131
-
-
Deblois, G.1
Giguere, V.2
-
29
-
-
4143151952
-
Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, subcellular localization
-
Dettwiler S, Aringhieri C, Cardinale S, KellerW, Barabino SM. 2004. Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, subcellular localization. J Biol Chem 279: 35788-35797.
-
(2004)
J Biol Chem
, vol.279
, pp. 35788-35797
-
-
Dettwiler, S.1
Aringhieri, C.2
Cardinale, S.3
Keller, W.4
Barabino, S.M.5
-
30
-
-
36549073601
-
The expanding RNA polymerase III transcriptome
-
Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A. 2007. The expanding RNA polymerase III transcriptome. Trends Genet 23: 614-622.
-
(2007)
Trends Genet
, vol.23
, pp. 614-622
-
-
Dieci, G.1
Fiorino, G.2
Castelnuovo, M.3
Teichmann, M.4
Pagano, A.5
-
31
-
-
50649118350
-
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
-
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, et al. 2008. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Gen Res 18: 1433-1445.
-
(2008)
Gen Res
, vol.18
, pp. 1433-1445
-
-
Dinger, M.E.1
Amaral, P.P.2
Mercer, T.R.3
Pang, K.C.4
Bruce, S.J.5
Gardiner, B.B.6
Askarian-Amiri, M.E.7
Ru, K.8
Solda, G.9
Simons, C.10
-
32
-
-
4344583992
-
B2 RNA binds directly toRNApolymerase II to repress transcript synthesis
-
Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. 2004. B2 RNA binds directly toRNApolymerase II to repress transcript synthesis. Nat Structural Mol Biol 11: 822-829.
-
(2004)
Nat Structural Mol Biol
, vol.11
, pp. 822-829
-
-
Espinoza, C.A.1
Allen, T.A.2
Hieb, A.R.3
Kugel, J.F.4
Goodrich, J.A.5
-
33
-
-
33947721021
-
Characterization of the structure, function, mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription
-
Espinoza CA, Goodrich JA, Kugel JF. 2007. Characterization of the structure, function, mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA 13: 583-596.
-
(2007)
RNA
, vol.13
, pp. 583-596
-
-
Espinoza, C.A.1
Goodrich, J.A.2
Kugel, J.F.3
-
34
-
-
33744804277
-
The Evf-2 noncodingRNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator
-
Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD. 2006. The Evf-2 noncodingRNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Develop 20: 1470-1484.
-
(2006)
Genes Develop
, vol.20
, pp. 1470-1484
-
-
Feng, J.1
Bi, C.2
Clark, B.S.3
Mady, R.4
Shah, P.5
Kohtz, J.D.6
-
35
-
-
27644541914
-
P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in anRNA-dependent manner
-
Fox AH, Bond CS, Lamond AI. 2005. P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in anRNA-dependent manner. Mol Biol Cell 16: 5304-5315.
-
(2005)
Mol Biol Cell
, vol.16
, pp. 5304-5315
-
-
Fox, A.H.1
Bond, C.S.2
Lamond, A.I.3
-
36
-
-
0037039475
-
Paraspeckles: A novel nuclear domain
-
Fox AH, LamYW, Leung AK, Lyon CE, Andersen J, Mann M, Lamond AI. 2002. Paraspeckles: A novel nuclear domain. Curr Biol 12: 13-25.
-
(2002)
Curr Biol
, vol.12
, pp. 13-25
-
-
Fox, A.H.1
Lam, Y.W.2
Leung, A.K.3
Lyon, C.E.4
Andersen, J.5
Mann, M.6
Lamond, A.I.7
-
37
-
-
33645823589
-
A noncoding RNA is a potential marker of cell fate during mammary gland development
-
Ginger MR, Shore AN, Contreras A, Rijnkels M, Miller J, Gonzalez-Rimbau MF, Rosen JM. 2006. A noncoding RNA is a potential marker of cell fate during mammary gland development. Proc Nat Acad Sci 103: 5781-5786.
-
(2006)
Proc Nat Acad Sci
, vol.103
, pp. 5781-5786
-
-
Ginger, M.R.1
Shore, A.N.2
Contreras, A.3
Rijnkels, M.4
Miller, J.5
Gonzalez-Rimbau, M.F.6
Rosen, J.M.7
-
38
-
-
33745336617
-
A germlinespecific class of smallRNAs binds mammalian Piwi proteins
-
Girard A, Sachidanandam R, Hannon GJ, Carmell MA. 2006. A germlinespecific class of smallRNAs binds mammalian Piwi proteins. Nature 442: 199-202.
-
(2006)
Nature
, vol.442
, pp. 199-202
-
-
Girard, A.1
Sachidanandam, R.2
Hannon, G.J.3
Carmell, M.A.4
-
39
-
-
0034650893
-
The coregulator exchange in transcriptional functions of nuclear receptors
-
Glass CK, Rosenfeld MG. 2000. The coregulator exchange in transcriptional functions of nuclear receptors. Genes Develop 14: 121-141.
-
(2000)
Genes Develop
, vol.14
, pp. 121-141
-
-
Glass, C.K.1
Rosenfeld, M.G.2
-
40
-
-
33748303049
-
Non-coding-RNA regulators of RNA polymerase II transcription
-
Goodrich JA, Kugel JF. 2006. Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 7: 612-616.
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 612-616
-
-
Goodrich, J.A.1
Kugel, J.F.2
-
41
-
-
0036358853
-
RNAi (Nematodes: Caenorhabditis elegans)
-
Grishok A, Mello CC. 2002. RNAi (Nematodes: Caenorhabditis elegans). Adv Gen 46: 339-360.
-
(2002)
Adv Gen
, vol.46
, pp. 339-360
-
-
Grishok, A.1
Mello, C.C.2
-
42
-
-
33745621037
-
A novel class of small RNAs in mouse spermatogenic cells
-
Grivna ST, Beyret E, Wang Z, Lin H. 2006. A novel class of small RNAs in mouse spermatogenic cells. Genes Develop 20: 1709-1714.
-
(2006)
Genes Develop
, vol.20
, pp. 1709-1714
-
-
Grivna, S.T.1
Beyret, E.2
Wang, Z.3
Lin, H.4
-
43
-
-
34447098370
-
A chromatin landmark and transcription initiation at most promoters in human cells
-
Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130: 77-88.
-
(2007)
Cell
, vol.130
, pp. 77-88
-
-
Guenther, M.G.1
Levine, S.S.2
Boyer, L.A.3
Jaenisch, R.4
Young, R.A.5
-
44
-
-
33747712023
-
The complexity of the mammalian transcriptome
-
Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P. 2006. The complexity of the mammalian transcriptome. J Physiol 575: 321-332.
-
(2006)
J Physiol
, vol.575
, pp. 321-332
-
-
Gustincich, S.1
Sandelin, A.2
Plessy, C.3
Katayama, S.4
Simone, R.5
Lazarevic, D.6
Hayashizaki, Y.7
Carninci, P.8
-
45
-
-
62249133709
-
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
-
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, 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
Amit, I.2
Garber, M.3
French, C.4
Lin, M.F.5
Feldser, D.6
Huarte, M.7
Zuk, O.8
Carey, B.W.9
Cassady, J.P.10
-
46
-
-
34447647842
-
Useful 'junk': Alu RNAs in the human transcriptome
-
Hasler J, Samuelsson T, Strub K. 2007. Useful 'junk': Alu RNAs in the human transcriptome. Cell Mol Life Sci 64: 1793-1800.
-
(2007)
Cell Mol Life Sci
, vol.64
, pp. 1793-1800
-
-
Hasler, J.1
Samuelsson, T.2
Strub, K.3
-
47
-
-
33751012428
-
Alu elements as regulators of gene expression
-
Hasler J, Strub K. 2006. Alu elements as regulators of gene expression. Nuc Acids Res 34: 5491-5497.
-
(2006)
Nuc Acids Res
, vol.34
, pp. 5491-5497
-
-
Hasler, J.1
Strub, K.2
-
48
-
-
33744541544
-
SLIRP, a small SRA binding protein, is a nuclear receptor corepressor
-
Hatchell EC, Colley SM, Beveridge DJ, Epis MR, Stuart LM, Giles KM, Redfern AD, Miles LE, Barker A, MacDonald LM, et al. 2006. SLIRP, a small SRA binding protein, is a nuclear receptor corepressor. Mol Cell 22: 657-668.
-
(2006)
Mol Cell
, vol.22
, pp. 657-668
-
-
Hatchell, E.C.1
Colley, S.M.2
Beveridge, D.J.3
Epis, M.R.4
Stuart, L.M.5
Giles, K.M.6
Redfern, A.D.7
Miles, L.E.8
Barker, A.9
McDonald, L.M.10
-
49
-
-
55549098872
-
Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
-
Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, Ohta K. 2008. Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 456: 130-134.
-
(2008)
Nature
, vol.456
, pp. 130-134
-
-
Hirota, K.1
Miyoshi, T.2
Kugou, K.3
Hoffman, C.S.4
Shibata, T.5
Ohta, K.6
-
50
-
-
33847185603
-
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains
-
Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. 2007. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8: 39.
-
(2007)
BMC Genomics
, vol.8
, pp. 39
-
-
Hutchinson, J.N.1
Ensminger, A.W.2
Clemson, C.M.3
Lynch, C.R.4
Lawrence, J.B.5
Chess, A.6
-
51
-
-
0035878329
-
CpG island of rat sphingosine kinase-1 gene: Tissue-dependent DNA methylation status and multiple alternative first exons
-
Imamura T, Ohgane J, Ito S, Ogawa T, Hattori N, Tanaka S, Shiota K. 2001. CpG island of rat sphingosine kinase-1 gene: tissue-dependent DNA methylation status and multiple alternative first exons. Genomics 76: 117-125.
-
(2001)
Genomics
, vol.76
, pp. 117-125
-
-
Imamura, T.1
Ohgane, J.2
Ito, S.3
Ogawa, T.4
Hattori, N.5
Tanaka, S.6
Shiota, K.7
-
52
-
-
6044266260
-
Non-coding RNA directed DNA demethylation of Sphk1 CpG island
-
Imamura T, Yamamoto S, Ohgane J, Hattori N, Tanaka S, Shiota K. 2004. Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochem Biophys Res Comm 322: 593-600.
-
(2004)
Biochem Biophys Res Comm
, vol.322
, pp. 593-600
-
-
Imamura, T.1
Yamamoto, S.2
Ohgane, J.3
Hattori, N.4
Tanaka, S.5
Shiota, K.6
-
53
-
-
12344291073
-
Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
-
Johnson JM, Edwards S, Shoemaker D, Schadt EE. 2005. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet 21: 93-102.
-
(2005)
Trends Genet
, vol.21
, pp. 93-102
-
-
Johnson, J.M.1
Edwards, S.2
Shoemaker, D.3
Schadt, E.E.4
-
54
-
-
58149103424
-
Regulation of neural macroRNAs by the transcriptional repressor REST
-
Johnson R, Teh CH, Jia H, Vanisri RR, Pandey T, Lu ZH, Buckley NJ, Stanton LW, Lipovich L. 2009. Regulation of neural macroRNAs by the transcriptional repressor REST. RNA 15: 85-96.
-
(2009)
RNA
, vol.15
, pp. 85-96
-
-
Johnson, R.1
Teh, C.H.2
Jia, H.3
Vanisri, R.R.4
Pandey, T.5
Lu, Z.H.6
Buckley, N.J.7
Stanton, L.W.8
Lipovich, L.9
-
55
-
-
34250160256
-
RNA maps reveal newRNAclasses and a possible function for pervasive transcription
-
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, et al. 2007. RNA maps reveal newRNAclasses and a possible function for pervasive transcription. Science 316: 1484-1488.
-
(2007)
Science
, vol.316
, 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
-
56
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. 2005. Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
-
(2005)
Science
, vol.309
, pp. 1564-1566
-
-
Katayama, S.1
Tomaru, Y.2
Kasukawa, T.3
Waki, K.4
Nakanishi, M.5
Nakamura, M.6
Nishida, H.7
Yap, C.C.8
Suzuki, M.9
Kawai, J.10
-
57
-
-
65549128370
-
The FANTOM web resource: From mammalian transcriptional landscape to its dynamic regulation
-
Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, et al. 2009. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Gen Biol 10: pR40.
-
(2009)
Gen Biol
, vol.10
-
-
Kawaji, H.1
Severin, J.2
Lizio, M.3
Waterhouse, A.4
Katayama, S.5
Irvine, K.M.6
Hume, D.A.7
Forrest, A.R.8
Suzuki, H.9
Carninci, P.10
-
58
-
-
0037271634
-
A novel steroid receptor co-activator protein (SRAP) as an alternative form of steroid receptor RNA-activator gene: Expression in prostate cancer cells and enhancement of androgen receptor activity
-
Kawashima H, Takano H, Sugita S, Takahara Y, Sugimura K, Nakatani T. 2003. A novel steroid receptor co-activator protein (SRAP) as an alternative form of steroid receptor RNA-activator gene: Expression in prostate cancer cells and enhancement of androgen receptor activity. Biochem J 369: 163-171.
-
(2003)
Biochem J
, vol.369
, pp. 163-171
-
-
Kawashima, H.1
Takano, H.2
Sugita, S.3
Takahara, Y.4
Sugimura, K.5
Nakatani, T.6
-
59
-
-
67650921949
-
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
-
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Nat Acad Sci 106: 11667-11672.
-
(2009)
Proc Nat Acad Sci
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
Rivea Morales, D.6
Thomas, K.7
Presser, A.8
Bernstein, B.E.9
van Oudenaarden, A.10
-
60
-
-
23844519339
-
A high-resolution map of active promoters in the human genome
-
Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. 2005. A high-resolution map of active promoters in the human genome. Nature 436: 876-880.
-
(2005)
Nature
, vol.436
, pp. 876-880
-
-
Kim, T.H.1
Barrera, L.O.2
Zheng, M.3
Qu, C.4
Singer, M.A.5
Richmond, T.A.6
Wu, Y.7
Green, R.D.8
Ren, B.9
-
63
-
-
0026659651
-
Silencing the type II sodium channel gene: A model for neural-specific gene regulation
-
Kraner SD, Chong JA, Tsay HJ, Mandel G. 1992. Silencing the type II sodium channel gene: A model for neural-specific gene regulation. Neuron 9: 37-44.
-
(1992)
Neuron
, vol.9
, pp. 37-44
-
-
Kraner, S.D.1
Chong, J.A.2
Tsay, H.J.3
Mandel, G.4
-
64
-
-
67650474314
-
Transcriptional regulation through noncoding RNAs and epigenetic modifications
-
Kurokawa R, Rosenfeld MG, Glass CK. 2009. Transcriptional regulation through noncoding RNAs and epigenetic modifications. RNA Biology 6: 233-236.
-
(2009)
RNA Biology
, vol.6
, pp. 233-236
-
-
Kurokawa, R.1
Rosenfeld, M.G.2
Glass, C.K.3
-
65
-
-
1642603947
-
A small modulatory dsRNA specifies the fate of adult neural stem cells
-
Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH. 2004. A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116: 779-793.
-
(2004)
Cell
, vol.116
, pp. 779-793
-
-
Kuwabara, T.1
Hsieh, J.2
Nakashima, K.3
Taira, K.4
Gage, F.H.5
-
66
-
-
0033515637
-
A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex
-
Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J, Tsai SY, Tsai MJ, O'Malley BW. 1999. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 97: 17-27.
-
(1999)
Cell
, vol.97
, pp. 17-27
-
-
Lanz, R.B.1
McKenna, N.J.2
Onate, S.A.3
Albrecht, U.4
Wong, J.5
Tsai, S.Y.6
Tsai, M.J.7
O'Malley, B.W.8
-
67
-
-
33746527679
-
Characterization of the piRNA complex from rat testes
-
Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE. 2006. Characterization of the piRNA complex from rat testes. Science 313: 363-367.
-
(2006)
Science
, vol.313
, pp. 363-367
-
-
Lau, N.C.1
Seto, A.G.2
Kim, J.3
Kuramochi-Miyagawa, S.4
Nakano, T.5
Bartel, D.P.6
Kingston, R.E.7
-
68
-
-
66149084316
-
qiRNA is a new type of small interfering RNA induced by DNA damage
-
Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, Bamford DH, Liu Y. 2009. qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459: 274-277.
-
(2009)
Nature
, vol.459
, pp. 274-277
-
-
Lee, H.C.1
Chang, S.S.2
Choudhary, S.3
Aalto, A.P.4
Maiti, M.5
Bamford, D.H.6
Liu, Y.7
-
69
-
-
8144225486
-
Micro-RNA genes are transcribed by RNA polymerase II
-
Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. 2004. Micro-RNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
-
(2004)
EMBO J
, vol.23
, pp. 4051-4060
-
-
Lee, Y.1
Kim, M.2
Han, J.3
Yeom, K.H.4
Lee, S.5
Baek, S.H.6
Kim, V.N.7
-
70
-
-
38949155481
-
Incorporation of the noncoding roX RNAs alters the chromatin-binding specificity of the Drosophila MSL1/MSL2 complex
-
Li F, Schiemann AH, Scott MJ. 2008. Incorporation of the noncoding roX RNAs alters the chromatin-binding specificity of the Drosophila MSL1/MSL2 complex. Mol Cell Biol 28: 1252-1264.
-
(2008)
Mol Cell Biol
, vol.28
, pp. 1252-1264
-
-
Li, F.1
Schiemann, A.H.2
Scott, M.J.3
-
71
-
-
0029030242
-
Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts
-
Liu WM, Chu WM, Choudary PV, Schmid CW. 1995. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res 23: 1758-1765.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 1758-1765
-
-
Liu, W.M.1
Chu, W.M.2
Choudary, P.V.3
Schmid, C.W.4
-
72
-
-
61849133411
-
Long intronic noncoding RNA transcription: Expression noise or expression choice?
-
Louro R, Smirnova AS, Verjovski-Almeida S. 2009. Long intronic noncoding RNA transcription: Expression noise or expression choice? Genomics 93: 291-298.
-
(2009)
Genomics
, vol.93
, pp. 291-298
-
-
Louro, R.1
Smirnova, A.S.2
Verjovski-Almeida, S.3
-
73
-
-
0142261186
-
Gene silencing of the p15/INK4B cell-cycle inhibitor by hypermethylation: An early or later epigenetic alteration in myelodysplastic syndromes?
-
Lubbert M. 2003. Gene silencing of the p15/INK4B cell-cycle inhibitor by hypermethylation: An early or later epigenetic alteration in myelodysplastic syndromes? Leukemia 17: 1762-1764.
-
(2003)
Leukemia
, vol.17
, pp. 1762-1764
-
-
Lubbert, M.1
-
74
-
-
34249316905
-
RNA-binding proteins: Modular design for efficient function
-
Lunde BM, Moore C, Varani G. 2007. RNA-binding proteins: Modular design for efficient function. Nat Rev Mol Cell Biol 8: 479-490.
-
(2007)
Nat Rev Mol Cell Biol
, vol.8
, pp. 479-490
-
-
Lunde, B.M.1
Moore, C.2
Varani, G.3
-
75
-
-
0027158032
-
Multiple dispersed loci produce small cytoplasmic Alu RNA
-
Maraia RJ, Driscoll CT, Bilyeu T, Hsu K, Darlington GJ. 1993. Multiple dispersed loci produce small cytoplasmic Alu RNA. Mol Cell Biol 13: 4233-4241.
-
(1993)
Mol Cell Biol
, vol.13
, pp. 4233-4241
-
-
Maraia, R.J.1
Driscoll, C.T.2
Bilyeu, T.3
Hsu, K.4
Darlington, G.J.5
-
76
-
-
39549103642
-
Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock
-
Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. 2008. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 29: 499-509.
-
(2008)
Mol Cell
, vol.29
, pp. 499-509
-
-
Mariner, P.D.1
Walters, R.D.2
Espinoza, C.A.3
Drullinger, L.F.4
Wagner, S.D.5
Kugel, J.F.6
Goodrich, J.A.7
-
77
-
-
2942560254
-
Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
-
Martens JA, Laprade L, Winston F. 2004. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429: 571-574.
-
(2004)
Nature
, vol.429
, pp. 571-574
-
-
Martens, J.A.1
Laprade, L.2
Winston, F.3
-
78
-
-
27744533201
-
Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae
-
Martens JA, Wu PY, Winston F. 2005. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Develop 19: 2695-2704.
-
(2005)
Genes Develop
, vol.19
, pp. 2695-2704
-
-
Martens, J.A.1
Wu, P.Y.2
Winston, F.3
-
79
-
-
33846930357
-
Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript
-
Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A. 2007. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445: 666-670.
-
(2007)
Nature
, vol.445
, pp. 666-670
-
-
Martianov, I.1
Ramadass, A.2
Serra Barros, A.3
Chow, N.4
Akoulitchev, A.5
-
80
-
-
0142027777
-
Distribution of NFkappaB-binding sites across human chromosome 22
-
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, et al. 2003. Distribution of NFkappaB-binding sites across human chromosome 22. Proc Nat Acad Sci 100: 12247-12252.
-
(2003)
Proc Nat Acad Sci
, vol.100
, pp. 12247-12252
-
-
Martone, R.1
Euskirchen, G.2
Bertone, P.3
Hartman, S.4
Royce, T.E.5
Luscombe, N.M.6
Rinn, J.L.7
Nelson, F.K.8
Miller, P.9
Gerstein, M.10
-
81
-
-
0028631058
-
Introns: Evolution and function
-
Mattick JS. 1994. Introns: evolution and function. Current Opinion Gen Develop 4: 823-831.
-
(1994)
Current Opinion Gen Develop
, vol.4
, pp. 823-831
-
-
Mattick, J.S.1
-
82
-
-
34249740942
-
A new paradigm for developmental biology
-
Mattick JS. 2007. A new paradigm for developmental biology. J Exp Biol 210: 1526-1547.
-
(2007)
J Exp Biol
, vol.210
, pp. 1526-1547
-
-
Mattick, J.S.1
-
83
-
-
0034882101
-
The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms
-
Mattick JS, Gagen MJ. 2001. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evolution 18: 1611-1630.
-
(2001)
Mol Biol Evolution
, vol.18
, pp. 1611-1630
-
-
Mattick, J.S.1
Gagen, M.J.2
-
85
-
-
1542328263
-
Genetic analysis of RNA-mediated transcriptional gene silencing
-
Matzke M, AufsatzW, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJ. 2004. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 1677: 129-141.
-
(2004)
Biochim Biophys Acta
, vol.1677
, pp. 129-141
-
-
Matzke, M.1
Aufsatz, W.2
Kanno, T.3
Daxinger, L.4
Papp, I.5
Mette, M.F.6
Matzke, A.J.7
-
86
-
-
0037154974
-
Combinatorial control of gene expression by nuclear receptors and coregulators
-
McKenna NJ, O'Malley BW. 2002. Combinatorial control of gene expression by nuclear receptors and coregulators. Cell 108: 465-474.
-
(2002)
Cell
, vol.108
, pp. 465-474
-
-
McKenna, N.J.1
O'Malley, B.W.2
-
87
-
-
60349120914
-
Long non-coding RNAs: Insights into functions
-
Mercer TR, Dinger ME, Mattick JS. 2009. Long non-coding RNAs: Insights into functions. Nat Rev 10: 155-159.
-
(2009)
Nat Rev
, vol.10
, pp. 155-159
-
-
Mercer, T.R.1
Dinger, M.E.2
Mattick, J.S.3
-
88
-
-
38649114329
-
Specific expression of long noncoding RNAs in the mouse brain
-
Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. 2008. Specific expression of long noncoding RNAs in the mouse brain. Proc Nat Acad Sci 105: 716-721.
-
(2008)
Proc Nat Acad Sci
, vol.105
, pp. 716-721
-
-
Mercer, T.R.1
Dinger, M.E.2
Sunkin, S.M.3
Mehler, M.F.4
Mattick, J.S.5
-
89
-
-
0031826316
-
Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression
-
Montgomery MK, Fire A. 1998. Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 14: 255-258.
-
(1998)
Trends Genet
, vol.14
, pp. 255-258
-
-
Montgomery, M.K.1
Fire, A.2
-
90
-
-
0026651523
-
A common silencer element in the SCG10 and type II Na+ channel genes binds a factor present in nonneuronal cells but not in neuronal cells
-
Mori N, Schoenherr C, Vandenbergh DJ, Anderson DJ. 1992. A common silencer element in the SCG10 and type II Na+ channel genes binds a factor present in nonneuronal cells but not in neuronal cells. Neuron 9: 45-54.
-
(1992)
Neuron
, vol.9
, pp. 45-54
-
-
Mori, N.1
Schoenherr, C.2
Vandenbergh, D.J.3
Anderson, D.J.4
-
91
-
-
56549111129
-
The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin
-
Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P. 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
Mitchell, J.A.2
Sanz, L.A.3
Pauler, F.M.4
Ferguson-Smith, A.C.5
Feil, R.6
Fraser, P.7
-
92
-
-
60549114880
-
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
-
Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A. 2009. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457: 1038-1042.
-
(2009)
Nature
, vol.457
, pp. 1038-1042
-
-
Neil, H.1
Malabat, C.2
d'Aubenton-Carafa, Y.3
Xu, Z.4
Steinmetz, L.M.5
Jacquier, A.6
-
93
-
-
0035891288
-
7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes
-
Nguyen VT, Kiss T, Michels AA, Bensaude O. 2001. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414: 322-325.
-
(2001)
Nature
, vol.414
, pp. 322-325
-
-
Nguyen, V.T.1
Kiss, T.2
Michels, A.A.3
Bensaude, O.4
-
94
-
-
0142059234
-
The canonical Wnt pathway directly regulates NRSF/RESTexpression in chick spinal cord
-
Nishihara S, Tsuda L, Ogura T. 2003. The canonical Wnt pathway directly regulates NRSF/RESTexpression in chick spinal cord. Biochem Biophys Res Commun 311: 55-63.
-
(2003)
Biochem Biophys Res Commun
, vol.311
, pp. 55-63
-
-
Nishihara, S.1
Tsuda, L.2
Ogura, T.3
-
95
-
-
34250815056
-
A new binding motif for the 7 transcriptional repressor REST uncovers large gene networks devoted to neuronal functions
-
Otto SJ, McCorkle SR, Hover J, Conaco C, Han JJ, Impey S, Yochum GS, Dunn JJ, Goodman RH, Mandel G. 2007. A new binding motif for the 7 transcriptional repressor REST uncovers large gene networks devoted to neuronal functions. J Neurosci 27: 6729-6739.
-
(2007)
J Neurosci
, vol.27
, pp. 6729-6739
-
-
Otto, S.J.1
McCorkle, S.R.2
Hover, J.3
Conaco, C.4
Han, J.J.5
Impey, S.6
Yochum, G.S.7
Dunn, J.J.8
Goodman, R.H.9
Mandel, G.10
-
96
-
-
34248547495
-
Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: Identification of ANRIL, an antisense noncoding RNAwhose expression coclusters with ARF
-
Pasmant E, Laurendeau I, Heron D, Vidaud M, Vidaud D, Bieche I. 2007. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: Identification of ANRIL, an antisense noncoding RNAwhose expression coclusters with ARF. Cancer Res 67: 3963-3969.
-
(2007)
Cancer Res
, vol.67
, pp. 3963-3969
-
-
Pasmant, E.1
Laurendeau, I.2
Heron, D.3
Vidaud, M.4
Vidaud, D.5
Bieche, I.6
-
97
-
-
67549119096
-
CTCF: Master weaver of the genome
-
Phillips JE, Corces VG. 2009. CTCF: Master weaver of the genome. Cell 137: 1194-1211.
-
(2009)
Cell
, vol.137
, pp. 1194-1211
-
-
Phillips, J.E.1
Corces, V.G.2
-
99
-
-
60149099385
-
Evolution and functions of long noncoding RNAs
-
Ponting CP, 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
-
100
-
-
57849123049
-
RNA exosome depletion reveals transcription upstream of active human promoters
-
Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH. 2008. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322: 1851-1854.
-
(2008)
Science
, vol.322
, pp. 1851-1854
-
-
Preker, P.1
Nielsen, J.2
Kammler, S.3
Lykke-Andersen, S.4
Christensen, M.S.5
Mapendano, C.K.6
Schierup, M.H.7
Jensen, T.H.8
-
101
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in humanHOX loci by noncoding RNAs
-
Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, et al. 2007. Functional demarcation of active and silent chromatin domains in humanHOX loci by noncoding RNAs. Cell 129: 1311-1323.
-
(2007)
Cell
, vol.129
, 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
-
102
-
-
13444293149
-
RNA interference: Methylation mystery
-
Ronemus M, Martienssen R. 2005. RNA interference: methylation mystery. Nature 433: 472-473.
-
(2005)
Nature
, vol.433
, pp. 472-473
-
-
Ronemus, M.1
Martienssen, R.2
-
103
-
-
0035813090
-
Coregulator codes of transcriptional regulation by nuclear receptors
-
Rosenfeld MG, Glass CK. 2001. Coregulator codes of transcriptional regulation by nuclear receptors. J Biol Chem 276: 36865-36868.
-
(2001)
J Biol Chem
, vol.276
, pp. 36865-36868
-
-
Rosenfeld, M.G.1
Glass, C.K.2
-
104
-
-
33744792310
-
Sensors and signals: A coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response
-
Rosenfeld MG, Lunyak VV, Glass CK. 2006. Sensors and signals: A coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. Genes Develop 20: 1405-1428.
-
(2006)
Genes Develop
, vol.20
, pp. 1405-1428
-
-
Rosenfeld, M.G.1
Lunyak, V.V.2
Glass, C.K.3
-
105
-
-
33644514069
-
NoncodingRNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax
-
Sanchez-Elsner T, GouD, Kremmer E, Sauer F. 2006. NoncodingRNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311: 1118-1123.
-
(2006)
Science
, vol.311
, pp. 1118-1123
-
-
Sanchez-Elsner, T.1
Gou, D.2
Kremmer, E.3
Sauer, F.4
-
106
-
-
62449319486
-
MENepsilon/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles
-
Sasaki YT, Ideue T, Sano M, Mituyama T, Hirose T. 2009. MENepsilon/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Nat Acad Sci 106: 2525-2530.
-
(2009)
Proc Nat Acad Sci
, vol.106
, pp. 2525-2530
-
-
Sasaki, Y.T.1
Ideue, T.2
Sano, M.3
Mituyama, T.4
Hirose, T.5
-
107
-
-
33746407708
-
Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing
-
Schoeftner S, Sengupta AK, Kubicek S, Mechtler K, Spahn L, Koseki H, Jenuwein T, Wutz A. 2006. Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J 25: 3110-3122.
-
(2006)
EMBO J
, vol.25
, pp. 3110-3122
-
-
Schoeftner, S.1
Sengupta, A.K.2
Kubicek, S.3
Mechtler, K.4
Spahn, L.5
Koseki, H.6
Jenuwein, T.7
Wutz, A.8
-
108
-
-
33847084602
-
Genome regulation by polycomb and trithorax proteins
-
Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G. 2007. Genome regulation by polycomb and trithorax proteins. Cell 128: 735-745.
-
(2007)
Cell
, vol.128
, pp. 735-745
-
-
Schuettengruber, B.1
Chourrout, D.2
Vervoort, M.3
Leblanc, B.4
Cavalli, G.5
-
109
-
-
42549167638
-
How do ncRNAs guide chromatin-modifying complexes to specific locations within the nucleus?
-
Scott MJ, Li F. 2008. How do ncRNAs guide chromatin-modifying complexes to specific locations within the nucleus? RNA Biol 5: 13-16.
-
(2008)
RNA Biol
, vol.5
, pp. 13-16
-
-
Scott, M.J.1
Li, F.2
-
110
-
-
33645324024
-
RNAmediated response to heat shock in mammalian cells
-
Shamovsky I, Ivannikov M, Kandel ES, GershonD, Nudler E. 2006. RNAmediated response to heat shock in mammalian cells. Nature 440: 556-560.
-
(2006)
Nature
, vol.440
, pp. 556-560
-
-
Shamovsky, I.1
Ivannikov, M.2
Kandel, E.S.3
Gershon, D.4
Nudler, E.5
-
111
-
-
0035339146
-
Sharp, an inducible cofactor that integrates nuclear receptor repression and activation
-
Shi Y, Downes M, Xie W, Kao HY, Ordentlich P, Tsai CC, Hon M, Evans RM. 2001. Sharp, an inducible cofactor that integrates nuclear receptor repression and activation. Genes Develop 15: 1140-1151.
-
(2001)
Genes Develop
, vol.15
, pp. 1140-1151
-
-
Shi, Y.1
Downes, M.2
Xie, W.3
Kao, H.Y.4
Ordentlich, P.5
Tsai, C.C.6
Hon, M.7
Evans, R.M.8
-
112
-
-
24944535335
-
Regulation of LSD1 histone demethylase activity by its associated factors
-
Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y. 2005. Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell 19: 857-864.
-
(2005)
Mol Cell
, vol.19
, pp. 857-864
-
-
Shi, Y.J.1
Matson, C.2
Lan, F.3
Iwase, S.4
Baba, T.5
Shi, Y.6
-
113
-
-
44649139771
-
Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation
-
Shilatifard A. 2008. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Current Opinion Cell Biol 20: 341-348.
-
(2008)
Current Opinion Cell Biol
, vol.20
, pp. 341-348
-
-
Shilatifard, A.1
-
114
-
-
36049020719
-
Noncoding RNAs: Couplers of analog and digital information in nervous system function?
-
St Laurent G, 3rd, Wahlestedt C. 2007. Noncoding RNAs: couplers of analog and digital information in nervous system function? Trends Neurosci 30: 612-621.
-
(2007)
Trends Neurosci
, vol.30
, pp. 612-621
-
-
St Laurent 3rd, G.1
Wahlestedt, C.2
-
115
-
-
0037123632
-
An expanding universe of noncoding RNAs
-
Storz G. 2002. An expanding universe of noncoding RNAs. Science 296: 1260-1263.
-
(2002)
Science
, vol.296
, pp. 1260-1263
-
-
Storz, G.1
-
116
-
-
61849113891
-
MEN epsilon/β nuclear-retained non-coding RNAs are upregulated upon muscle differentiation and are essential components of paraspeckles
-
Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. 2009. MEN epsilon/β nuclear-retained non-coding RNAs are upregulated upon muscle differentiation and are essential components of paraspeckles. Gen Res 19: 347-359.
-
(2009)
Gen Res
, vol.19
, pp. 347-359
-
-
Sunwoo, H.1
Dinger, M.E.2
Wilusz, J.E.3
Amaral, P.P.4
Mattick, J.S.5
Spector, D.L.6
-
117
-
-
33847698971
-
The relationship between nonproteincoding DNA and eukaryotic complexity
-
Taft RJ, Pheasant M, Mattick JS. 2007. The relationship between nonproteincoding DNA and eukaryotic complexity. Bioessays 29: 288-299.
-
(2007)
Bioessays
, vol.29
, pp. 288-299
-
-
Taft, R.J.1
Pheasant, M.2
Mattick, J.S.3
-
118
-
-
0038664127
-
Identification and functional analysis of human transcriptional promoters
-
Trinklein ND, Aldred SJ, Saldanha AJ, Myers RM. 2003. Identification and functional analysis of human transcriptional promoters. Gen Res 13: 308-312.
-
(2003)
Gen Res
, vol.13
, pp. 308-312
-
-
Trinklein, N.D.1
Aldred, S.J.2
Saldanha, A.J.3
Myers, R.M.4
-
119
-
-
44649152934
-
The role of long non-codingRNAs in chromatin structure and gene regulation: Variations on a theme
-
UmlaufD, Fraser P, Nagano T. 2008. The role of long non-codingRNAs in chromatin structure and gene regulation: Variations on a theme. Biol Chem 389: 323-331.
-
(2008)
Biol Chem
, vol.389
, pp. 323-331
-
-
Umlauf, D.1
Fraser, P.2
Nagano, T.3
-
120
-
-
33746502166
-
Adistinct small RNA pathway silences selfish genetic elements in the germline
-
Vagin VV, Sigova A, Li C, Seitz H, GvozdevV, Zamore PD. 2006. Adistinct small RNA pathway silences selfish genetic elements in the germline. Science 313: 320-324.
-
(2006)
Science
, vol.313
, pp. 320-324
-
-
Vagin, V.V.1
Sigova, A.2
Li, C.3
Seitz, H.4
Gvozdev, V.5
Zamore, P.D.6
-
121
-
-
0019964240
-
Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum
-
Walter P, Blobel G. 1982. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature 299: 691-698.
-
(1982)
Nature
, vol.299
, pp. 691-698
-
-
Walter, P.1
Blobel, G.2
-
122
-
-
57849138429
-
Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes
-
Wang P, Yin S, Zhang Z, Xin D, Hu L, Kong X, Hurst LD. (2008b). Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes. Gen Biol 9: R169.
-
(2008)
Gen Biol
, vol.9
-
-
Wang, P.1
Yin, S.2
Zhang, Z.3
Xin, D.4
Hu, L.5
Kong, X.6
Hurst, L.D.7
-
123
-
-
46649093597
-
Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
-
Wang X, Arai S, Song X, ReichartD, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R. (2008a). Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454: 126-130.
-
(2008)
Nature
, vol.454
, pp. 126-130
-
-
Wang, X.1
Arai, S.2
Song, X.3
Reichart, D.4
Du, K.5
Pascual, G.6
Tempst, P.7
Rosenfeld, M.G.8
Glass, C.K.9
Kurokawa, R.10
-
124
-
-
0034625237
-
6S RNA regulates E. coli RNA polymerase activity
-
Wassarman KM, Storz G. 2000. 6S RNA regulates E. coli RNA polymerase activity. Cell 101: 613-623.
-
(2000)
Cell
, vol.101
, pp. 613-623
-
-
Wassarman, K.M.1
Storz, G.2
-
125
-
-
33745599586
-
Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposonderived siRNAs in oocytes and germline small RNAs in testes
-
Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H. 2006. Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposonderived siRNAs in oocytes and germline small RNAs in testes. Genes Develop 20: 1732-1743.
-
(2006)
Genes Develop
, vol.20
, pp. 1732-1743
-
-
Watanabe, T.1
Takeda, A.2
Tsukiyama, T.3
Mise, K.4
Okuno, T.5
Sasaki, H.6
Minami, N.7
Imai, H.8
-
126
-
-
67749093008
-
Hox genes and vertebrate axial pattern
-
Wellik DM. 2009. Hox genes and vertebrate axial pattern. Current Topics Develop Biol 88: 257-278.
-
(2009)
Current Topics Develop Biol
, vol.88
, pp. 257-278
-
-
Wellik, D.M.1
-
127
-
-
15944382675
-
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
-
Wickiser JK, WinklerWC, Breaker RR, Crothers DM. 2005. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 18: 49-60.
-
(2005)
Mol Cell
, vol.18
, pp. 49-60
-
-
Wickiser, J.K.1
Winkler, W.C.2
Breaker, R.R.3
Crothers, D.M.4
-
128
-
-
33745286231
-
TUF love for "junk" DNA
-
Willingham AT, Gingeras TR. 2006. TUF love for "junk" DNA. Cell 125: 1215-1220.
-
(2006)
Cell
, vol.125
, pp. 1215-1220
-
-
Willingham, A.T.1
Gingeras, T.R.2
-
129
-
-
24644481406
-
A strategy for probing the function of noncoding RNAs finds a repressor of NFAT
-
Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG. 2005. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309: 1570-1573.
-
(2005)
Science
, vol.309
, 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
-
130
-
-
67649671961
-
Long noncoding RNAs: Functional surprises from the RNAworld
-
Wilusz JE, Sunwoo H, Spector DL. 2009. Long noncoding RNAs: functional surprises from the RNAworld. Genes Develop 23: 1494-1504.
-
(2009)
Genes Develop
, vol.23
, pp. 1494-1504
-
-
Wilusz, J.E.1
Sunwoo, H.2
Spector, D.L.3
-
131
-
-
50949090496
-
Poly A-transcripts expressed in HeLa cells
-
Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. 2008. Poly A-transcripts expressed in HeLa cells. PloS one 3: e2803.
-
(2008)
PloS one
, vol.3
-
-
Wu, Q.1
Kim, Y.C.2
Lu, J.3
Xuan, Z.4
Chen, J.5
Zheng, Y.6
Zhou, T.7
Zhang, M.Q.8
Wu, C.I.9
Wang, S.M.10
-
132
-
-
20444368036
-
Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase
-
Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, et al. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725-737.
-
(2005)
Cell
, vol.121
, pp. 725-737
-
-
Wyers, F.1
Rougemaille, M.2
Badis, G.3
Rousselle, J.C.4
Dufour, M.E.5
Boulay, J.6
Regnault, B.7
Devaux, F.8
Namane, A.9
Seraphin, B.10
-
133
-
-
4043060093
-
An RNA-binding domain in the thyroid hormone receptor enhances transcriptional activation
-
Xu B, Koenig RJ. 2004. An RNA-binding domain in the thyroid hormone receptor enhances transcriptional activation. J Biol Chem 279: 33051-33056.
-
(2004)
J Biol Chem
, vol.279
, pp. 33051-33056
-
-
Xu, B.1
Koenig, R.J.2
-
134
-
-
30044431687
-
Regulation of thyroid hormone receptor α2 RNA binding and subcellular localization by phosphorylation
-
Xu B, Koenig RJ. 2005. Regulation of thyroid hormone receptor α2 RNA binding and subcellular localization by phosphorylation. Mol Cell Endocrinology 245: 147-157.
-
(2005)
Mol Cell Endocrinology
, vol.245
, pp. 147-157
-
-
Xu, B.1
Koenig, R.J.2
-
135
-
-
60549108380
-
Bidirectional promoters generate pervasive transcription in yeast
-
Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM. 2009. Bidirectional promoters generate pervasive transcription in yeast. Nature 457: 1033-1037.
-
(2009)
Nature
, vol.457
, pp. 1033-1037
-
-
Xu, Z.1
Wei, W.2
Gagneur, J.3
Perocchi, F.4
Clauder-Munster, S.5
Camblong, J.6
Guffanti, E.7
Stutz, F.8
Huber, W.9
Steinmetz, L.M.10
-
136
-
-
65249158053
-
B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes
-
Yakovchuk P, Goodrich JA, Kugel JF. 2009. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Nat Acad Sci 106: 5569-5574.
-
(2009)
Proc Nat Acad Sci
, vol.106
, pp. 5569-5574
-
-
Yakovchuk, P.1
Goodrich, J.A.2
Kugel, J.F.3
-
137
-
-
0035891271
-
The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription
-
Yang Z, Zhu Q, Luo K, Zhou Q. 2001. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414: 317-322.
-
(2001)
Nature
, vol.414
, pp. 317-322
-
-
Yang, Z.1
Zhu, Q.2
Luo, K.3
Zhou, Q.4
-
138
-
-
12244275645
-
Widespread occurrence of antisense transcription in the human genome
-
Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, et al. 2003. Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol 21: 379-386.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 379-386
-
-
Yelin, R.1
Dahary, D.2
Sorek, R.3
Levanon, E.Y.4
Goldstein, O.5
Shoshan, A.6
Diber, A.7
Biton, S.8
Tamir, Y.9
Khosravi, R.10
-
139
-
-
38049155825
-
Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA
-
YuW, GiusD, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H. 2008. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451: 202-206.
-
(2008)
Nature
, vol.451
, pp. 202-206
-
-
Yu, W.1
Gius, D.2
Onyango, P.3
Muldoon-Jacobs, K.4
Karp, J.5
Feinberg, A.P.6
Cui, H.7
-
140
-
-
55349109963
-
Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome
-
Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. 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
Sun, B.K.2
Erwin, J.A.3
Song, J.J.4
Lee, J.T.5
-
141
-
-
4344573761
-
Regulation of nuclear receptor activity by a pseudouridine synthase through posttranscriptional modification of steroid receptor RNA activator
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Zhao X, Patton JR, Davis SL, Florence B, Ames SJ, Spanjaard RA. 2004. Regulation of nuclear receptor activity by a pseudouridine synthase through posttranscriptional modification of steroid receptor RNA activator. Mol Cell 15: 549-558.
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(2004)
Mol Cell
, vol.15
, pp. 549-558
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Zhao, X.1
Patton, J.R.2
Davis, S.L.3
Florence, B.4
Ames, S.J.5
Spanjaard, R.A.6
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