-
1
-
-
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, 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
-
2
-
-
21044431735
-
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
-
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, 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
-
3
-
-
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, 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
-
4
-
-
65649092633
-
The genetic signatures of noncoding RNAs
-
doi:10.1371/journal.pgen.1000459
-
Mattick JS, (2009) The genetic signatures of noncoding RNAs. PLoS Genet 5: e1000459 doi:10.1371/journal.pgen.1000459.
-
(2009)
PLoS Genet
, vol.5
-
-
Mattick, J.S.1
-
5
-
-
33846420626
-
Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster
-
Sessa L, Breiling A, Lavorgna G, Silvestri L, Casari G, et al. (2007) Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA 13: 223-239.
-
(2007)
RNA
, vol.13
, pp. 223-239
-
-
Sessa, L.1
Breiling, A.2
Lavorgna, G.3
Silvestri, L.4
Casari, G.5
-
6
-
-
78649807567
-
Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA
-
Kaneko S, Li G, Son J, Xu CF, Margueron R, et al. (2010) Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 24: 2615-2620.
-
(2010)
Genes Dev
, vol.24
, pp. 2615-2620
-
-
Kaneko, S.1
Li, G.2
Son, J.3
Xu, C.F.4
Margueron, R.5
-
7
-
-
56549111129
-
The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin
-
Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, 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
Mitchell, J.A.2
Sanz, L.A.3
Pauler, F.M.4
Ferguson-Smith, A.C.5
-
8
-
-
54049138948
-
Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
-
Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, et al. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32: 232-246.
-
(2008)
Mol Cell
, vol.32
, pp. 232-246
-
-
Pandey, R.R.1
Mondal, T.2
Mohammad, F.3
Enroth, S.4
Redrup, L.5
-
9
-
-
0242668706
-
Role of histone H3 lysine 27 methylation in X inactivation
-
Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, et al. (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300: 131-135.
-
(2003)
Science
, vol.300
, pp. 131-135
-
-
Plath, K.1
Fang, J.2
Mlynarczyk-Evans, S.K.3
Cao, R.4
Worringer, K.A.5
-
10
-
-
34250729138
-
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
-
Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX 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
-
11
-
-
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
-
12
-
-
0037442493
-
The transcriptional activity of human Chromosome 22
-
Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, et al. (2003) The transcriptional activity of human Chromosome 22. Genes Dev 17: 529-540.
-
(2003)
Genes Dev
, vol.17
, pp. 529-540
-
-
Rinn, J.L.1
Euskirchen, G.2
Bertone, P.3
Martone, R.4
Luscombe, N.M.5
-
13
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, 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
-
14
-
-
22244442468
-
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
-
Kapranov P, Drenkow J, Cheng J, Long J, Helt G, et al. (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res 15: 987-997.
-
(2005)
Genome Res
, vol.15
, pp. 987-997
-
-
Kapranov, P.1
Drenkow, J.2
Cheng, J.3
Long, J.4
Helt, G.5
-
15
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, 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
-
16
-
-
23044437498
-
RNA meets chromatin
-
Bernstein E, Allis CD, (2005) RNA meets chromatin. Genes Dev 19: 1635-1655.
-
(2005)
Genes Dev
, vol.19
, pp. 1635-1655
-
-
Bernstein, E.1
Allis, C.D.2
-
18
-
-
77951118936
-
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
-
Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, 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
Shah, N.2
Wang, K.C.3
Kim, J.4
Horlings, H.M.5
-
19
-
-
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, et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 11667-11672
-
-
Khalil, A.M.1
Guttman, M.2
Huarte, M.3
Garber, M.4
Raj, A.5
-
20
-
-
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
-
21
-
-
77954572735
-
Long noncoding RNA as modular scaffold of histone modification complexes
-
Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, 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
Manor, O.2
Wan, Y.3
Mosammaparast, N.4
Wang, J.K.5
-
22
-
-
74549147547
-
Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium
-
Soshnikova N, Duboule D, (2009) Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium. Epigenetics 4: 537-540.
-
(2009)
Epigenetics
, vol.4
, pp. 537-540
-
-
Soshnikova, N.1
Duboule, D.2
-
23
-
-
3242888285
-
RVISTA 2.0: evolutionary analysis of transcription factor binding sites
-
Loots GG, Ovcharenko I, (2004) rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Res 32: W217-221.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 217-221
-
-
Loots, G.G.1
Ovcharenko, I.2
-
24
-
-
33646473694
-
Complex Loci in human and mouse genomes
-
doi:10.1371/journal.pgen.0020047
-
Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, et al. (2006) Complex Loci in human and mouse genomes. PLoS Genet 2: e47 doi:10.1371/journal.pgen.0020047.
-
(2006)
PLoS Genet
, vol.2
-
-
Engstrom, P.G.1
Suzuki, H.2
Ninomiya, N.3
Akalin, A.4
Sessa, L.5
-
25
-
-
0038115063
-
Organizing axes in time and space; 25 years of colinear tinkering
-
Kmita M, Duboule D, (2003) Organizing axes in time and space; 25 years of colinear tinkering. Science 301: 331-333.
-
(2003)
Science
, vol.301
, pp. 331-333
-
-
Kmita, M.1
Duboule, D.2
-
26
-
-
0034656095
-
Hox C cluster genes are dispensable for overall body plan of mouse embryonic development
-
Suemori H, Noguchi S, (2000) Hox C cluster genes are dispensable for overall body plan of mouse embryonic development. Dev Biol 220: 333-342.
-
(2000)
Dev Biol
, vol.220
, pp. 333-342
-
-
Suemori, H.1
Noguchi, S.2
-
27
-
-
0038613098
-
A global control region defines a chromosomal regulatory landscape containing the HoxD cluster
-
Spitz F, Gonzalez F, Duboule D, (2003) A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113: 405-417.
-
(2003)
Cell
, vol.113
, pp. 405-417
-
-
Spitz, F.1
Gonzalez, F.2
Duboule, D.3
-
28
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
29
-
-
78651271733
-
Integrative genomics viewer
-
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24-26.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdottir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
-
30
-
-
21344455343
-
Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function
-
Kmita M, Tarchini B, Zakany J, Logan M, Tabin CJ, et al. (2005) Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function. Nature 435: 1113-1116.
-
(2005)
Nature
, vol.435
, pp. 1113-1116
-
-
Kmita, M.1
Tarchini, B.2
Zakany, J.3
Logan, M.4
Tabin, C.J.5
-
31
-
-
55549148715
-
H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment
-
Creyghton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, et al. (2008) H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 135: 649-661.
-
(2008)
Cell
, vol.135
, pp. 649-661
-
-
Creyghton, M.P.1
Markoulaki, S.2
Levine, S.S.3
Hanna, J.4
Lodato, M.A.5
-
32
-
-
0033120658
-
Hox gene expression in limbs: colinearity by opposite regulatory controls
-
Herault Y, Beckers J, Gerard M, Duboule D, (1999) Hox gene expression in limbs: colinearity by opposite regulatory controls. Dev Biol 208: 157-165.
-
(1999)
Dev Biol
, vol.208
, pp. 157-165
-
-
Herault, Y.1
Beckers, J.2
Gerard, M.3
Duboule, D.4
-
33
-
-
23044477774
-
Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes
-
Spitz F, Herkenne C, Morris MA, Duboule D, (2005) Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat Genet 37: 889-893.
-
(2005)
Nat Genet
, vol.37
, pp. 889-893
-
-
Spitz, F.1
Herkenne, C.2
Morris, M.A.3
Duboule, D.4
-
34
-
-
0029748544
-
In vivo targeted mutagenesis of a regulatory element required for positioning the Hoxd-11 and Hoxd-10 expression boundaries
-
Gerard M, Chen JY, Gronemeyer H, Chambon P, Duboule D, et al. (1996) In vivo targeted mutagenesis of a regulatory element required for positioning the Hoxd-11 and Hoxd-10 expression boundaries. Genes Dev 10: 2326-2334.
-
(1996)
Genes Dev
, vol.10
, pp. 2326-2334
-
-
Gerard, M.1
Chen, J.Y.2
Gronemeyer, H.3
Chambon, P.4
Duboule, D.5
-
35
-
-
33845925394
-
Chromatin immunoprecipitation and microarray-based analysis of protein location
-
Lee TI, Johnstone SE, Young RA, (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1: 729-748.
-
(2006)
Nat Protoc
, vol.1
, pp. 729-748
-
-
Lee, T.I.1
Johnstone, S.E.2
Young, R.A.3
|