-
1
-
-
34249098071
-
Mammalian RNA polymerase II core promoters: Insights from genome-wide studies
-
DOI 10.1038/nrg2026, PII NRG2026
-
Sandelin, A. et al. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nature Rev. Genet. 8, 424-436 (2007). (Pubitemid 46789243)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.6
, pp. 424-436
-
-
Sandelin, A.1
Carninci, P.2
Lenhard, B.3
Ponjavic, J.4
Hayashizaki, Y.5
Hume, D.A.6
-
2
-
-
80054081798
-
Genomic and chromatin signals underlying transcription start-site selection
-
Valen, E. & Sandelin, A. Genomic and chromatin signals underlying transcription start-site selection. Trends Genet. 27, 475-485 (2011).
-
(2011)
Trends Genet.
, vol.27
, pp. 475-485
-
-
Valen, E.1
Sandelin, A.2
-
3
-
-
33750352462
-
Transcriptional regulatory elements in the human genome
-
DOI 10.1146/annurev.genom.7.080505.115623
-
Maston, G. A., Evans, S. K. & Green, M. R. Transcriptional regulatory elements in the human genome. Annu. Rev. Genomics Hum. Genet. 7, 29-59 (2006). (Pubitemid 44627921)
-
(2006)
Annual Review of Genomics and Human Genetics
, vol.7
, pp. 29-59
-
-
Maston, G.A.1
Evans, S.K.2
Green, M.R.3
-
4
-
-
79952114792
-
Regulatory regions in DNA: Promoters, enhancers, silencers, and insulators
-
Riethoven, J.-J. M. Regulatory regions in DNA: promoters, enhancers, silencers, and insulators. Methods Mol. Biol. 674, 33-42 (2010).
-
(2010)
Methods Mol. Biol.
, vol.674
, pp. 33-42
-
-
Riethoven, J.-J.M.1
-
5
-
-
73649105501
-
Promoting developmental transcription
-
Ohler, U. & Wassarman, D. A. Promoting developmental transcription. Development 137, 15-26 (2010).
-
(2010)
Development
, vol.137
, pp. 15-26
-
-
Ohler, U.1
Wassarman, D.A.2
-
6
-
-
79956330964
-
CpG islands and the regulation of transcription
-
Deaton, A. M. & Bird, A. CpG islands and the regulation of transcription. Genes Dev. 25, 1010-1022 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 1010-1022
-
-
Deaton, A.M.1
Bird, A.2
-
7
-
-
84858444088
-
Perspectives on the RNA polymerase II core promoter
-
Kadonaga, J. T. Perspectives on the RNA polymerase II core promoter. WIREs Dev. Biol. 1, 40-51 (2012).
-
(2012)
WIREs Dev. Biol.
, vol.1
, pp. 40-51
-
-
Kadonaga, J.T.1
-
8
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
DOI 10.1038/ng1789, PII N1789
-
Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genet. 38, 626-635 (2006). (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..
-
9
-
-
19344368143
-
Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity
-
DOI 10.1016/j.gene.2005.01.012, PII S0378111905000405
-
Yamashita, R., Suzuki, Y., Sugano, S. & Nakai, K. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350, 129-136 (2005). (Pubitemid 40719057)
-
(2005)
Gene
, vol.350
, Issue.2
, pp. 129-136
-
-
Yamashita, R.1
Suzuki, Y.2
Sugano, S.3
Nakai, K.4
-
10
-
-
0025776409
-
The cystic fibrosis gene has a "housekeeping"-type promoter and is expressed at low levels in cells of epithelial origin
-
Yoshimura, K. et al. The cystic fibrosis gene has a " housekeeping"-type promoter and is expressed at low levels in cells of epithelial origin. J. Biol. Chem. 266, 9140-9144 (1991). (Pubitemid 21906629)
-
(1991)
Journal of Biological Chemistry
, vol.266
, Issue.14
, pp. 9140-9144
-
-
Yoshimura, K.1
Nakamura, H.2
Trapnell, B.C.3
Dalemans, W.4
Pavirani, A.5
Lecocq, J.-P.6
Crystal, R.G.7
-
11
-
-
33749128065
-
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters
-
Ponjavic, J. et al. Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biol. 7, R78 (2006).
-
(2006)
Genome Biol.
, vol.7
-
-
Ponjavic, J.1
-
12
-
-
84857857538
-
Promoter architecture of mouse olfactory receptor genes
-
22 Dec doi:10.1101/gr.126201.111
-
Plessy, C. et al. Promoter architecture of mouse olfactory receptor genes. Genome Res. 22 Dec 2011 (doi:10.1101/gr.126201.111).
-
(2011)
Genome Res.
-
-
Plessy, C.1
-
13
-
-
79851485916
-
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
-
Rach, E. A. et al. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet. 7, e1001274 (2011).
-
(2011)
PLoS Genet.
, vol.7
-
-
Rach, E.A.1
-
14
-
-
33747299885
-
Comparative genomics of Drosophila and human core promoters
-
FitzGerald, P. C., Sturgill, D., Shyakhtenko, A., Oliver, B. & Vinson, C. Comparative genomics of Drosophila and human core promoters. Genome Biol. 7, R53 (2006).
-
(2006)
Genome Biol.
, vol.7
-
-
Fitzgerald, P.C.1
Sturgill, D.2
Shyakhtenko, A.3
Oliver, B.4
Vinson, C.5
-
15
-
-
33845622415
-
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
-
DOI 10.1093/nar/gkl608
-
Ohler, U. Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res. 34, 5943-5950 (2006). (Pubitemid 44941173)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.20
, pp. 5943-5950
-
-
Ohler, U.1
-
16
-
-
38849112675
-
Genomic regulatory blocks underlie extensive microsynteny conservation in insects
-
DOI 10.1101/gr.6669607
-
Engstrom, P. G., Ho Sui, S. J., Drivenes, O., Becker, T. S. & Lenhard, B. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 17, 1898-1908 (2007). (Pubitemid 351360012)
-
(2007)
Genome Research
, vol.17
, Issue.12
, pp. 1898-1908
-
-
Engstrom, P.G.1
Sui, S.J.H.2
Drivenes, O.3
Becker, T.S.4
Lenhard, B.5
-
17
-
-
65149092197
-
Transcriptional features of genomic regulatory blocks
-
Akalin, A. et al. Transcriptional features of genomic regulatory blocks. Genome Biol. 10, R38 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Akalin, A.1
-
18
-
-
68049107475
-
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
-
Rach, E. A., Yuan, H.-Y., Majoros, W. H., Tomancak, P. & Ohler, U. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol. 10, R73 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Rach, E.A.1
Yuan, H.-Y.2
Majoros, W.H.3
Tomancak, P.4
Ohler, U.5
-
19
-
-
79551610291
-
Genome-wide analysis of promoter architecture in Drosophila melanogaster
-
Hoskins, R. A. et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 21, 182-185 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 182-185
-
-
Hoskins, R.A.1
-
20
-
-
45549093494
-
Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
-
DOI 10.1073/pnas.0802406105
-
Hendrix, D. A., Hong, J.-W., Zeitlinger, J., Rokhsar, D. S. & Levine, M. S. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc. Natl Acad. Sci. USA 105, 7762-7767 (2008). (Pubitemid 351872712)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.22
, pp. 7762-7767
-
-
Hendrix, D.A.1
Hong, J.-W.2
Zeitlinger, J.3
Rokhsar, D.S.4
Levine, M.S.5
-
21
-
-
79952257234
-
Nucleotide composition-linked divergence of vertebrate core promoter architecture
-
van Heeringen, S. J. et al. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Res. 21, 410-421 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 410-421
-
-
Van Heeringen, S.J.1
-
22
-
-
79955567707
-
Core promoter T-blocks correlate with gene expression levels in C. elegans
-
Grishkevich, V., Hashimshony, T. & Yanai, I. Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Res. 21, 707-717 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 707-717
-
-
Grishkevich, V.1
Hashimshony, T.2
Yanai, I.3
-
23
-
-
77956842987
-
The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery
-
Parry, T. J. et al. The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes Dev. 24, 2013-2018 (2010).
-
(2010)
Genes Dev.
, vol.24
, pp. 2013-2018
-
-
Parry, T.J.1
-
24
-
-
80053625750
-
Translational coregulation of 5′TOP mRNAs by TIA-1 and TIAR
-
Damgaard, C. K. & Lykke-Andersen, J. Translational coregulation of 5′TOP mRNAs by TIA-1 and TIAR. Genes Dev. 25, 2057-2068 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 2057-2068
-
-
Damgaard, C.K.1
Lykke-Andersen, J.2
-
25
-
-
17544380551
-
The architecture of mammalian ribosomal protein promoters
-
Perry, R. P. The architecture of mammalian ribosomal protein promoters. BMC Evol. Biol. 5, 15 (2005).
-
(2005)
BMC Evol. Biol.
, vol.5
, pp. 15
-
-
Perry, R.P.1
-
26
-
-
78650747491
-
Discovery and characterization of chromatin states for systematic annotation of the human genome
-
Ernst, J. & Kellis, M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotech. 28, 817-825 (2010).
-
(2010)
Nature Biotech.
, vol.28
, pp. 817-825
-
-
Ernst, J.1
Kellis, M.2
-
27
-
-
36549013619
-
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
-
DOI 10.1038/ng.2007.26, PII NG200726
-
Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512-1516 (2007). (Pubitemid 350191345)
-
(2007)
Nature Genetics
, vol.39
, Issue.12
, pp. 1512-1516
-
-
Zeitlinger, J.1
Stark, A.2
Kellis, M.3
Hong, J.-W.4
Nechaev, S.5
Adelman, K.6
Levine, M.7
Young, R.A.8
-
28
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
-
29
-
-
76749164914
-
Alternative epigenetic chromatin states of Polycomb target genes
-
Schwartz, Y. B. et al. Alternative epigenetic chromatin states of Polycomb target genes. PLoS Genet. 6, e1000805 (2010).
-
(2010)
PLoS Genet.
, vol.6
-
-
Schwartz, Y.B.1
-
30
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
31
-
-
79953060951
-
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
-
Kharchenko, P. V. et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471, 480-485 (2011).
-
(2011)
Nature
, vol.471
, pp. 480-485
-
-
Kharchenko, P.V.1
-
32
-
-
79954993409
-
Chatting histone modifications in mammals
-
Izzo, A. & Schneider, R. Chatting histone modifications in mammals. Brief Funct. Genomics 9, 429-443 (2010).
-
(2010)
Brief Funct. Genomics
, vol.9
, pp. 429-443
-
-
Izzo, A.1
Schneider, R.2
-
33
-
-
77956153243
-
The language of histone crosstalk
-
Lee, J.-S., Smith, E. & Shilatifard, A. The language of histone crosstalk. Cell 142, 682-685 (2010).
-
(2010)
Cell
, vol.142
, pp. 682-685
-
-
Lee, J.-S.1
Smith, E.2
Shilatifard, A.3
-
34
-
-
80051614661
-
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification
-
Nozaki, T. et al. Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC Genomics 12, 416 (2011).
-
(2011)
BMC Genomics
, vol.12
, pp. 416
-
-
Nozaki, T.1
-
35
-
-
60349089645
-
Nucleosome positioning and gene regulation: Advances through genomics
-
Jiang, C. & Pugh, B. Nucleosome positioning and gene regulation: advances through genomics. Nature Rev. Genet. 10, 161-172 (2009).
-
(2009)
Nature Rev. Genet.
, vol.10
, pp. 161-172
-
-
Jiang, C.1
Pugh, B.2
-
36
-
-
80555125013
-
Variety of genomic DNA patterns for nucleosome positioning
-
Ioshikhes, I., Hosid, S. & Pugh, F. Variety of genomic DNA patterns for nucleosome positioning. Genome Res. 21, 1863-1871 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1863-1871
-
-
Ioshikhes, I.1
Hosid, S.2
Pugh, F.3
-
37
-
-
77649217817
-
Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast
-
Radman-Livaja, M., Liu, C. L., Friedman, N., Schreiber, S. L. & Rando, O. J. Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast. PLoS Genet. 6, e1000837 (2010).
-
(2010)
PLoS Genet.
, vol.6
-
-
Radman-Livaja, M.1
Liu, C.L.2
Friedman, N.3
Schreiber, S.L.4
Rando, O.J.5
-
38
-
-
67649669255
-
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
-
Ramirez-Carrozzi, V. R. et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138, 114-128 (2009).
-
(2009)
Cell
, vol.138
, pp. 114-128
-
-
Ramirez-Carrozzi, V.R.1
-
39
-
-
77957243147
-
BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo
-
Subtil-Rodríguez, A. & Reyes, J. C. BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo. EMBO Rep. 11, 751-757 (2010).
-
(2010)
EMBO Rep.
, vol.11
, pp. 751-757
-
-
Subtil-Rodríguez, A.1
Reyes, J.C.2
-
40
-
-
67649648237
-
Control of inducible gene expression by signal-dependent transcriptional elongation
-
Hargreaves, D. C., Horng, T. & Medzhitov, R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 138, 129-145 (2009).
-
(2009)
Cell
, vol.138
, pp. 129-145
-
-
Hargreaves, D.C.1
Horng, T.2
Medzhitov, R.3
-
41
-
-
48249153426
-
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome
-
Fu, Y., Sinha, M., Peterson, C. L., Weng, Z. & van Steensel, B. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4, e1000138 (2008).
-
(2008)
PLoS Genet.
, vol.4
-
-
Fu, Y.1
Sinha, M.2
Peterson, C.L.3
Weng, Z.4
Van Steensel, B.5
-
42
-
-
34248153777
-
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
-
DOI 10.1101/gr.6086307
-
Kikuta, H. et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17, 545-555 (2007). (Pubitemid 46715504)
-
(2007)
Genome Research
, vol.17
, Issue.5
, pp. 545-555
-
-
Kikuta, H.1
Laplante, M.2
Navratilova, P.3
Komisarczuk, A.Z.4
Engstrom, P.G.5
Fredman, D.6
Akalin, A.7
Caccamo, M.8
Sealy, I.9
Howe, K.10
Ghislain, J.11
Pezeron, G.12
Mourrain, P.13
Ellingsen, S.14
Oates, A.C.15
Thisse, C.16
Thisse, B.17
Foucher, I.18
Adolf, B.19
Geling, A.20
Lenhard, B.21
Becker, T.S.22
more..
-
43
-
-
70249088327
-
Genomic views of distant-acting enhancers
-
Visel, A., Rubin, E. M. & Pennacchio, L. A. Genomic views of distant-acting enhancers. Nature 461, 199-205 (2009).
-
(2009)
Nature
, vol.461
, pp. 199-205
-
-
Visel, A.1
Rubin, E.M.2
Pennacchio, L.A.3
-
44
-
-
77957220857
-
Comparative epigenomic analysis of murine and human adipogenesis
-
Mikkelsen, T. S. et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 143, 156-169 (2010).
-
(2010)
Cell
, vol.143
, pp. 156-169
-
-
Mikkelsen, T.S.1
-
45
-
-
71049155308
-
CpG-depleted promoters harbor tissue-specific transcription factor binding signals-implications for motif overrepresentation analyses
-
Roider, H. G., Lenhard, B., Kanhere, A., Haas, S. A. & Vingron, M. CpG-depleted promoters harbor tissue-specific transcription factor binding signals-implications for motif overrepresentation analyses. Nucleic Acids Res. 37, 6305-6315 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 6305-6315
-
-
Roider, H.G.1
Lenhard, B.2
Kanhere, A.3
Haas, S.A.4
Vingron, M.5
-
46
-
-
79251595543
-
A systems approach to analyze transcription factors in mammalian cells
-
Soler, E. et al. A systems approach to analyze transcription factors in mammalian cells. Methods 53, 151-162 (2011).
-
(2011)
Methods
, vol.53
, pp. 151-162
-
-
Soler, E.1
-
47
-
-
79954510417
-
In the loop: Long range chromatin interactions and gene regulation
-
Dean, A. In the loop: long range chromatin interactions and gene regulation. Brief Funct. Genomics 10, 3-10 (2011).
-
(2011)
Brief Funct. Genomics
, vol.10
, pp. 3-10
-
-
Dean, A.1
-
49
-
-
45149084413
-
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
-
DOI 10.1038/nature06947, PII NATURE06947
-
Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948-951 (2008). (Pubitemid 351832561)
-
(2008)
Nature
, vol.453
, Issue.7197
, pp. 948-951
-
-
Guelen, L.1
Pagie, L.2
Brasset, E.3
Meuleman, W.4
Faza, M.B.5
Talhout, W.6
Eussen, B.H.7
De Klein, A.8
Wessels, L.9
De Laat, W.10
Van Steensel, B.11
-
50
-
-
33846283384
-
Dynamic genome architecture in the nuclear space: Regulation of gene expression in three dimensions
-
DOI 10.1038/nrg2041, PII NRG2041
-
Lanctôt, C., Cheutin, T., Cremer, M., Cavalli, G. & Cremer, T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nature Rev. Genet. 8, 104-115 (2007). (Pubitemid 46122840)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.2
, pp. 104-115
-
-
Lanctot, C.1
Cheutin, T.2
Cremer, M.3
Cavalli, G.4
Cremer, T.5
-
51
-
-
77956416028
-
Gene positioning
-
Ferrai, C., de Castro, I. J., Lavitas, L., Chotalia, M. & Pombo, A. Gene positioning. Cold Spring Harb. Perspect. Biol. 2, a000588 (2010).
-
(2010)
Cold Spring Harb. Perspect. Biol.
, vol.2
-
-
Ferrai, C.1
De Castro, I.J.2
Lavitas, L.3
Chotalia, M.4
Pombo, A.5
-
52
-
-
36549061004
-
RNA polymerase is poised for activation across the genome
-
DOI 10.1038/ng.2007.21, PII NG200721
-
Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet. 39, 1507-1511 (2007). (Pubitemid 350191341)
-
(2007)
Nature Genetics
, vol.39
, Issue.12
, pp. 1507-1511
-
-
Muse, G.W.1
Gilchrist, D.A.2
Nechaev, S.3
Shah, R.4
Parker, J.S.5
Grissom, S.F.6
Zeitlinger, J.7
Adelman, K.8
-
53
-
-
34447098370
-
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells
-
DOI 10.1016/j.cell.2007.05.042, PII S0092867407006812
-
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77-88 (2007). (Pubitemid 47031323)
-
(2007)
Cell
, vol.130
, Issue.1
, pp. 77-88
-
-
Guenther, M.G.1
Levine, S.S.2
Boyer, L.A.3
Jaenisch, R.4
Young, R.A.5
-
54
-
-
78650566210
-
Pol. II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation
-
Nechaev, S. & Adelman, K. Pol. II waiting in the starting gates: regulating the transition from transcription initiation into productive elongation. Biochim. Biophys. Acta 1809, 34-45 (2011).
-
(2011)
Biochim. Biophys. Acta
, vol.1809
, pp. 34-45
-
-
Nechaev, S.1
Adelman, K.2
-
55
-
-
0022817308
-
RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells
-
Gilmour, D. S. & Lis, J. T. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol. Cell. Biol. 6, 3984-3989 (1986).
-
(1986)
Mol. Cell. Biol.
, vol.6
, pp. 3984-3989
-
-
Gilmour, D.S.1
Lis, J.T.2
-
56
-
-
57849109058
-
Nascent RNA Sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA Sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
57
-
-
70449641057
-
Progression through the RNA polymerase II CTD Cycle
-
Buratowski, S. Progression through the RNA polymerase II CTD Cycle. Mol. Cell 36, 541-546 (2009).
-
(2009)
Mol. Cell
, vol.36
, pp. 541-546
-
-
Buratowski, S.1
-
58
-
-
75749100247
-
Poised transcription factories prime silent uPA gene prior to activation
-
Ferrai, C. et al. Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol. 8, e1000270 (2010).
-
(2010)
PLoS Biol.
, vol.8
-
-
Ferrai, C.1
-
59
-
-
0346258014
-
Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
-
DOI 10.1038/nature02191
-
Shaevitz, J. W., Abbondanzieri, E. A., Landick, R. & Block, S. M. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 426, 684-687 (2003). (Pubitemid 38009379)
-
(2003)
Nature
, vol.426
, Issue.6967
, pp. 684-687
-
-
Shaevitz, J.W.1
Abbondanzieri, E.A.2
Landick, R.3
Block, S.M.4
-
60
-
-
74549132843
-
Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
-
Nechaev, S. et al. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327, 335-338 (2010).
-
(2010)
Science
, vol.327
, pp. 335-338
-
-
Nechaev, S.1
-
61
-
-
78149477660
-
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation
-
Gilchrist, D. A. et al. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 143, 540-551 (2010).
-
(2010)
Cell
, vol.143
, pp. 540-551
-
-
Gilchrist, D.A.1
-
62
-
-
67349173665
-
The regulated retrotransposon transcriptome of mammalian cells
-
Faulkner, G. J. et al. The regulated retrotransposon transcriptome of mammalian cells. Nature Genet. 41, 563-571 (2009).
-
(2009)
Nature Genet.
, vol.41
, pp. 563-571
-
-
Faulkner, G.J.1
-
63
-
-
38049020974
-
A code for transcription initiation in mammalian genomes
-
Frith, M. C. et al. A code for transcription initiation in mammalian genomes. Genome Res. 18, 1-12 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 1-12
-
-
Frith, M.C.1
-
64
-
-
70349279977
-
Altruistic functions for selfish DNA
-
Faulkner, G. J. & Carninci, P. Altruistic functions for selfish DNA. Cell Cycle 8, 2895-2900 (2009).
-
(2009)
Cell Cycle
, vol.8
, pp. 2895-2900
-
-
Faulkner, G.J.1
Carninci, P.2
-
65
-
-
77954738647
-
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
-
Plessy, C. et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods 7, 528-534 (2010).
-
(2010)
Nature Methods
, vol.7
, pp. 528-534
-
-
Plessy, C.1
-
66
-
-
70350232064
-
Endogenous retroviral LTRs as promoters for human genes: A critical assessment
-
Cohen, C. J., Lock, W. M. & Mager, D. L. Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 448, 105-114 (2009).
-
(2009)
Gene
, vol.448
, pp. 105-114
-
-
Cohen, C.J.1
Lock, W.M.2
Mager, D.L.3
-
68
-
-
80053211515
-
RNA degradome-its biogenesis and functions
-
Jackowiak, P., Nowacka, M., Strozycki, P. M. & Figlerowicz, M. RNA degradome-its biogenesis and functions. Nucleic Acids Res. 39, 7361-7370 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 7361-7370
-
-
Jackowiak, P.1
Nowacka, M.2
Strozycki, P.M.3
Figlerowicz, M.4
-
69
-
-
60549115605
-
Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
-
Fejes-Toth, K. et al. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, (2009) (1028).
-
(2009)
Nature
, vol.457
, pp. 1028
-
-
Fejes-Toth, K.1
-
70
-
-
77954716355
-
A paired-end sequencing strategy to map the complex landscape of transcription initiation
-
Ni, T. et al. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nature Methods 7, 521-527 (2010).
-
(2010)
Nature Methods
, vol.7
, pp. 521-527
-
-
Ni, T.1
-
71
-
-
78650051452
-
Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
-
Mercer, T. R. et al. Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res. 20, 1639-1650 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1639-1650
-
-
Mercer, T.R.1
-
72
-
-
4444262632
-
Gene loops juxtapose promoters and terminators in yeast
-
DOI 10.1038/ng1411
-
O'Sullivan, J. M. et al. Gene loops juxtapose promoters and terminators in yeast. Nature Genet. 36, 1014-1018 (2004). (Pubitemid 39167501)
-
(2004)
Nature Genetics
, vol.36
, Issue.9
, pp. 1014-1018
-
-
O'Sullivan, J.M.1
Tan-Wong, S.M.2
Morillon, A.3
Lee, B.4
Coles, J.5
Mellor, J.6
Proudfoot, N.J.7
-
73
-
-
69949173145
-
Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries
-
Kaderi, El, B., Medler, S., Raghunayakula, S. & Ansari, A. Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries. J. Biol. Chem. 284, 25015-25025 (2009).
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 25015-25025
-
-
Kaderi El, B.1
Medler, S.2
Raghunayakula, S.3
Ansari, A.4
-
74
-
-
38149020517
-
Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNA processing signals
-
Perkins, K. J., Lusic, M., Mitar, I., Giacca, M. & Proudfoot, N. J. Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNA processing signals. Mol. Cell 29, 56-68 (2008).
-
(2008)
Mol. Cell
, vol.29
, pp. 56-68
-
-
Perkins, K.J.1
Lusic, M.2
Mitar, I.3
Giacca, M.4
Proudfoot, N.J.5
-
75
-
-
42449140588
-
Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene
-
DOI 10.1073/pnas.0801048105
-
Tan-Wong, S. M., French, J. D., Proudfoot, N. J. & Brown, M. A. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc. Natl Acad. Sci. USA 105, 5160-5165 (2008). (Pubitemid 351738527)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.13
, pp. 5160-5165
-
-
Tan-Wong, S.M.1
French, J.D.2
Proudfoot, N.J.3
Brown, M.A.4
-
76
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
DOI 10.1126/science.1138341
-
Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484-1488 (2007). (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..
-
77
-
-
80051764912
-
PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters
-
Preker, P. et al. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Res. 39, 7179-7193 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 7179-7193
-
-
Preker, P.1
-
78
-
-
77951115595
-
RNA dust: Where are the genes?
-
Carninci, P. RNA dust: where are the genes? DNA Res. 17, 51-59 (2010).
-
(2010)
DNA Res.
, vol.17
, pp. 51-59
-
-
Carninci, P.1
-
79
-
-
70449953975
-
The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs
-
Jacquier, A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nature Rev. Genet. 10, 833-844 (2009).
-
(2009)
Nature Rev. Genet.
, vol.10
, pp. 833-844
-
-
Jacquier, A.1
-
80
-
-
68449095847
-
Biogenesis and function of promoter-associated RNAs
-
Taft, R. J., Kaplan, C. D., Simons, C. & Mattick, J. S. Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle 8, 2332-2338 (2009).
-
(2009)
Cell Cycle
, vol.8
, pp. 2332-2338
-
-
Taft, R.J.1
Kaplan, C.D.2
Simons, C.3
Evolution S., M.J.4
-
81
-
-
80052458531
-
Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
-
Valen, E. et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nature Struct. Mol. Biol. 18, 1075-1082 (2011).
-
(2011)
Nature Struct. Mol. Biol.
, vol.18
, pp. 1075-1082
-
-
Valen, E.1
-
82
-
-
83555164884
-
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila
-
Cernilogar, F. M. et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 480, 391-395 (2011).
-
(2011)
Nature
, vol.480
, pp. 391-395
-
-
Cernilogar, F.M.1
-
83
-
-
1542328960
-
Identification and distinct regulation of yeast TATA box-containing genes
-
DOI 10.1016/S0092-8674(04)00205-3, PII S0092867404002053
-
Basehoar, A. D., Zanton, S. J. & Pugh, B. F. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709 (2004). (Pubitemid 38326728)
-
(2004)
Cell
, vol.116
, Issue.5
, pp. 699-709
-
-
Basehoar, A.D.1
Zanton, S.J.2
Pugh, B.F.3
-
84
-
-
70349847245
-
Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis
-
Yamamoto, Y. Y. et al. Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J. 60, 350-362 (2009).
-
(2009)
Plant J.
, vol.60
, pp. 350-362
-
-
Yamamoto, Y.Y.1
-
85
-
-
20044366725
-
Highly conserved non-coding sequences are associated with vertebrate development
-
Woolfe, A. et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7 (2005).
-
(2005)
PLoS Biol.
, vol.3
-
-
Woolfe, A.1
-
86
-
-
57849140661
-
Divergent transcription from active promoters
-
Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849-1851 (2008).
-
(2008)
Science
, vol.322
, pp. 1849-1851
-
-
Seila, A.C.1
-
87
-
-
67349157682
-
Tiny RNAs associated with transcription start sites in animals
-
Taft, R. J. et al. Tiny RNAs associated with transcription start sites in animals. Nature Genet. 41, 572-578 (2009).
-
(2009)
Nature Genet.
, vol.41
, pp. 572-578
-
-
Taft, R.J.1
-
88
-
-
77955419755
-
Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans
-
Taft, R. J. et al. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Struct. Mol. Biol. 17, 1030-1034 (2010).
-
(2010)
Nature Struct. Mol. Biol.
, vol.17
, pp. 1030-1034
-
-
Taft, R.J.1
-
89
-
-
0027163013
-
The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes
-
Izban, M. G. & Luse, D. S. The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes. J. Biol. Chem. 268, 12874-12885 (1993). (Pubitemid 23182459)
-
(1993)
Journal of Biological Chemistry
, vol.268
, Issue.17
, pp. 12874-12885
-
-
Izban, M.G.1
Luse, D.S.2
-
90
-
-
2442681755
-
Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II
-
DOI 10.1073/pnas.0401493101
-
Mandal, S. S. et al. Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc. Natl Acad. Sci. USA 101, 7572-7577 (2004). (Pubitemid 38658070)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.20
, pp. 7572-7577
-
-
Mandal, S.S.1
Chu, C.2
Wada, T.3
Handa, H.4
Shatkin, A.J.5
Reinberg, D.6
-
91
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
DOI 10.1038/nrg1315
-
Wasserman, W. W. & Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nature Rev. Genet. 5, 276-287 (2004). (Pubitemid 38435623)
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.4
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
-
92
-
-
59949103704
-
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
-
Valen, E. et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 19, 255-265 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 255-265
-
-
Valen, E.1
-
93
-
-
79959916374
-
Unamplified cap analysis of gene expression on a single-molecule sequencer
-
Kanamori-Katayama, M. et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 21, 1150-1159 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1150-1159
-
-
Kanamori-Katayama, M.1
-
94
-
-
60549115605
-
Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
-
Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project
-
Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, 1028-1032 (2009).
-
(2009)
Nature
, vol.457
, pp. 1028-1032
-
-
-
95
-
-
4444308856
-
5′-end SAGE for the analysis of transcriptional start sites
-
DOI 10.1038/nbt998
-
Hashimoto, S.-I. et al. 5′-end SAGE for the analysis of transcriptional start sites. Nature Biotech. 22, 1146-1149 (2004). (Pubitemid 39166853)
-
(2004)
Nature Biotechnology
, vol.22
, Issue.9
, pp. 1146-1149
-
-
Hashimoto, S.-I.1
Suzuki, Y.2
Kasai, Y.3
Morohoshi, K.4
Yamada, T.5
Sese, J.6
Morishita, S.7
Sugano, S.8
Matsushima, K.9
-
96
-
-
20844463584
-
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
-
DOI 10.1038/nmeth733
-
Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2, 105-111 (2005). (Pubitemid 41131031)
-
(2005)
Nature Methods
, vol.2
, Issue.2
, pp. 105-111
-
-
Ng, P.1
Wei, C.-L.2
Sung, W.-K.3
Chiu, K.P.4
Lipovich, L.5
Ang, C.C.6
Gupta, S.7
Shahab, A.8
Ridwan, A.9
Wong, C.H.10
Liu, E.T.11
Ruan, Y.12
-
97
-
-
79952109548
-
Construction of small RNA cDNA libraries for deep sequencing
-
Thomas, M. F. & Ansel, K. M. Construction of small RNA cDNA libraries for deep sequencing. Methods Mol. Biol. 667, 93-111 (2010).
-
(2010)
Methods Mol. Biol.
, vol.667
, pp. 93-111
-
-
Thomas, M.F.1
Ansel, K.M.2
-
98
-
-
42949132235
-
Hidden layers of human small RNAs
-
Kawaji, H. et al. Hidden layers of human small RNAs. BMC Genomics 9, 157 (2008).
-
(2008)
BMC Genomics
, vol.9
, pp. 157
-
-
Kawaji, H.1
-
99
-
-
34250877841
-
A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing
-
DOI 10.1016/j.cell.2007.04.040, PII S0092867407006046
-
Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414 (2007). (Pubitemid 46970709)
-
(2007)
Cell
, vol.129
, Issue.7
, pp. 1401-1414
-
-
Landgraf, P.1
Rusu, M.2
Sheridan, R.3
Sewer, A.4
Iovino, N.5
Aravin, A.6
Pfeffer, S.7
Rice, A.8
Kamphorst, A.O.9
Landthaler, M.10
Lin, C.11
Socci, N.D.12
Hermida, L.13
Fulci, V.14
Chiaretti, S.15
Foa, R.16
Schliwka, J.17
Fuchs, U.18
Novosel, A.19
Muller, R.-U.20
Schermer, B.21
Bissels, U.22
Inman, J.23
Phan, Q.24
Chien, M.25
Weir, D.B.26
Choksi, R.27
De Vita, G.28
Frezzetti, D.29
Trompeter, H.-I.30
Hornung, V.31
Teng, G.32
Hartmann, G.33
Palkovits, M.34
Di Lauro, R.35
Wernet, P.36
Macino, G.37
Rogler, C.E.38
Nagle, J.W.39
Ju, J.40
Papavasiliou, F.N.41
Benzing, T.42
Lichter, P.43
Tam, W.44
Brownstein, M.J.45
Bosio, A.46
Borkhardt, A.47
Russo, J.J.48
Sander, C.49
Zavolan, M.50
Tuschl, T.51
more..
-
100
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
The ENCODE Project Consortium.
-
The ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046 (2011).
-
(2011)
PLoS Biol.
, vol.9
-
-
-
101
-
-
47549090254
-
NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly
-
DOI 10.1101/gad.1643208
-
Gilchrist, D. A. et al. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev. 22, 1921-1933 (2008). (Pubitemid 352008640)
-
(2008)
Genes and Development
, vol.22
, Issue.14
, pp. 1921-1933
-
-
Gilchrist, D.A.1
Nechaev, S.2
Lee, C.3
Ghosh, S.K.B.4
Collins, J.B.5
Li, L.6
Gilmour, D.S.7
Adelman, K.8
-
102
-
-
77952622899
-
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex
-
Gries, T. J., Kontur, W. S., Capp, M. W., Saecker, R. M. & Record, M. T. One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex. Proc. Natl Acad. Sci. USA 107, 10418-10423 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 10418-10423
-
-
Gries, T.J.1
Kontur, W.S.2
Capp, M.W.3
Saecker, R.M.4
Record, M.T.5
|