-
1
-
-
34250160256
-
RNA maps reveal new RNA classes and a possible function for pervasive transcription
-
Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484-1488 (2007).
-
(2007)
Science
, vol.316
, pp. 1484-1488
-
-
Kapranov, P.1
-
2
-
-
67349157682
-
Tiny RNAs associated with transcription start sites in animals
-
Taft, R.J. et al. Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 41, 572-578 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 572-578
-
-
Taft, R.J.1
-
3
-
-
57849123049
-
RNA exosome depletion reveals transcription upstream of active human promoters
-
Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851-1854 (2008).
-
(2008)
Science
, vol.322
, pp. 1851-1854
-
-
Preker, P.1
-
4
-
-
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
-
5
-
-
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
-
6
-
-
84874248583
-
Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells
-
Sigova, A.A. et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl. Acad. Sci. USA 110, 2876-2881 (2013).
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 2876-2881
-
-
Sigova, A.A.1
-
7
-
-
84881474625
-
Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality
-
Ntini, E. et al. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat. Struct. Mol. Biol. 20, 923-928 (2013).
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 923-928
-
-
Ntini, E.1
-
8
-
-
84880510553
-
Promoter directionality is controlled by U1 snRNP and polyadenylation signals
-
Almada, A.E., Wu, X., Kriz, A.J., Burge, C.B. & Sharp, P.A. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499, 360-363 (2013).
-
(2013)
Nature
, vol.499
, pp. 360-363
-
-
Almada, A.E.1
Wu, X.2
Kriz, A.J.3
Burge, C.B.4
Sharp, P.A.5
-
9
-
-
84927559450
-
Analysis of nascent RNA identifes a unifed architecture of initiation regions at mammalian promoters and enhancers
-
Core, L.J. et al. Analysis of nascent RNA identifes a unifed architecture of initiation regions at mammalian promoters and enhancers. Nat. Genet. 46, 1311-1320 (2014).
-
(2014)
Nat. Genet.
, vol.46
, pp. 1311-1320
-
-
Core, L.J.1
-
10
-
-
84928397692
-
Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution
-
Mayer, A. et al. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell 161, 541-554 (2015).
-
(2015)
Cell
, vol.161
, pp. 541-554
-
-
Mayer, A.1
-
11
-
-
84928386012
-
Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing
-
Nojima, T. et al. Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing. Cell 161, 526-540 (2015).
-
(2015)
Cell
, vol.161
, pp. 526-540
-
-
Nojima, T.1
-
12
-
-
84937636770
-
Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin
-
Scruggs, B.S. et al. Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin. Mol. Cell 58, 1101-1112 (2015).
-
(2015)
Mol. Cell
, vol.58
, pp. 1101-1112
-
-
Scruggs, B.S.1
-
13
-
-
79960569959
-
Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome
-
Flynn, R.A., Almada, A.E., Zamudio, J.R. & Sharp, P.A. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc. Natl. Acad. Sci. USA 108, 10460-10465 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 10460-10465
-
-
Flynn, R.A.1
Almada, A.E.2
Zamudio, J.R.3
Sharp, P.A.4
-
14
-
-
78649847070
-
U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation
-
Kaida, D. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664-668 (2010).
-
(2010)
Nature
, vol.468
, pp. 664-668
-
-
Kaida, D.1
-
15
-
-
84923997553
-
Human promoters are intrinsically directional
-
Duttke, S.H. et al. Human promoters are intrinsically directional. Mol. Cell 57, 674-684 (2015).
-
(2015)
Mol. Cell
, vol.57
, pp. 674-684
-
-
Duttke, S.H.1
-
16
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim, T.-K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.-K.1
-
17
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455-461 (2014).
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
-
18
-
-
84920954858
-
Nuclear stability and transcriptional directionality separate functionally distinct RNA species
-
Andersson, R. et al. Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nat Commun. 5, 5336 (2014).
-
(2014)
Nat Commun.
, vol.5
, pp. 5336
-
-
Andersson, R.1
-
19
-
-
0347135948
-
An abundance of bidirectional promoters in the human genome
-
Trinklein, N.D. et al. An abundance of bidirectional promoters in the human genome. Genome Res. 14, 62-66 (2004).
-
(2004)
Genome Res.
, vol.14
, pp. 62-66
-
-
Trinklein, N.D.1
-
20
-
-
33746657720
-
Systematic analysis of head-to-head gene organization: Evolutionary conservation and potential biological relevance
-
Li, Y.-Y. et al. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput. Biol. 2, e74 (2006).
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. e74
-
-
Li, Y.-Y.1
-
21
-
-
24644472515
-
Antisense transcription in the mammalian transcriptome
-
Katayama, S. et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566 (2005).
-
(2005)
Science
, vol.309
, pp. 1564-1566
-
-
Katayama, S.1
-
22
-
-
33646473694
-
Complex loci in human and mouse genomes
-
Engström, P.G. et al. Complex loci in human and mouse genomes. PLoS Genet. 2, e47 (2006).
-
(2006)
PLoS Genet.
, vol.2
, pp. e47
-
-
Engström, P.G.1
-
23
-
-
0036468258
-
Antisense transcripts in the human genome
-
Lehner, B., Williams, G., Campbell, R.D. & Sanderson, C.M. Antisense transcripts in the human genome. Trends Genet. 18, 63-65 (2002).
-
(2002)
Trends Genet.
, vol.18
, pp. 63-65
-
-
Lehner, B.1
Williams, G.2
Campbell, R.D.3
Sanderson, C.M.4
-
24
-
-
84947727856
-
Human gene promoters are intrinsically bidirectional
-
Andersson, R. et al. Human gene promoters are intrinsically bidirectional. Mol. Cell 60, 346-347 (2015).
-
(2015)
Mol. Cell
, vol.60
, pp. 346-347
-
-
Andersson, R.1
-
26
-
-
84865760395
-
GENCODE: The reference human genome annotation for the ENCODE Project
-
Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
-
27
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
28
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
-
29
-
-
84870485829
-
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
-
Fenouil, R. et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 22, 2399-2408 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 2399-2408
-
-
Fenouil, R.1
-
30
-
-
84959421441
-
Genomic organization of human transcription initiation complexes
-
Pugh, B.F. & Venters, B.J. Genomic organization of human transcription initiation complexes. PLoS One 11, e0149339 (2016).
-
(2016)
PLoS One
, vol.11
, pp. e0149339
-
-
Pugh, B.F.1
Venters, B.J.2
-
31
-
-
84858165145
-
Genome-wide structure and organization of eukaryotic pre-initiation complexes
-
Rhee, H.S. & Pugh, B.F. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483, 295-301 (2012).
-
(2012)
Nature
, vol.483
, pp. 295-301
-
-
Rhee, H.S.1
Pugh, B.F.2
-
32
-
-
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. Nat. Struct. Mol. Biol. 18, 1075-1082 (2011).
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 1075-1082
-
-
Valen, E.1
-
33
-
-
84877574893
-
Extensive transcriptional heterogeneity revealed by isoform profling
-
Pelechano, V., Wei, W. & Steinmetz, L.M. Extensive transcriptional heterogeneity revealed by isoform profling. Nature 497, 127-131 (2013).
-
(2013)
Nature
, vol.497
, pp. 127-131
-
-
Pelechano, V.1
Wei, W.2
Steinmetz, L.M.3
-
34
-
-
80051730960
-
Interaction profling identifes the human nuclear exosome targeting complex
-
Lubas, M. et al. Interaction profling identifes the human nuclear exosome targeting complex. Mol. Cell 43, 624-637 (2011).
-
(2011)
Mol. Cell
, vol.43
, pp. 624-637
-
-
Lubas, M.1
-
35
-
-
69249217649
-
Regulatory roles of natural antisense transcripts
-
Faghihi, M.A. & Wahlestedt, C. Regulatory roles of natural antisense transcripts. Nat. Rev. Mol. Cell Biol. 10, 637-643 (2009).
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 637-643
-
-
Faghihi, M.A.1
Wahlestedt, C.2
-
36
-
-
24644519490
-
The transcriptional landscape of the mammalian genome
-
Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-1563 (2005).
-
(2005)
Science
, vol.309
, pp. 1559-1563
-
-
Carninci, P.1
-
37
-
-
84889562158
-
Divergent transcription: A driving force for new gene origination?
-
Wu, X. & Sharp, P.A. Divergent transcription: a driving force for new gene origination? Cell 155, 990-996 (2013).
-
(2013)
Cell
, vol.155
, pp. 990-996
-
-
Wu, X.1
Sharp, P.A.2
-
38
-
-
84888187077
-
Dealing with pervasive transcription
-
Jensen, T.H., Jacquier, A. & Libri, D. Dealing with pervasive transcription. Mol. Cell 52, 473-484 (2013).
-
(2013)
Mol. Cell
, vol.52
, pp. 473-484
-
-
Jensen, T.H.1
Jacquier, A.2
Libri, D.3
-
39
-
-
84865757142
-
Landscape of transcription in human cells
-
Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
-
40
-
-
84897406127
-
A promoter-level mammalian expression atlas
-
FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature 507, 462-470 (2014).
-
(2014)
Nature
, vol.507
, pp. 462-470
-
-
-
41
-
-
84891771466
-
The UCSC Genome Browser database: 2014 update
-
Karolchik, D. et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42, D764-D770 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D764-D770
-
-
Karolchik, D.1
-
42
-
-
84890145122
-
The human cap-binding complex is functionally connected to the nuclear RNA exosome
-
Andersen, P.R. et al. The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nat. Struct. Mol. Biol. 20, 1367-1376 (2013).
-
(2013)
Nat. Struct. Mol. Biol.
, vol.20
, pp. 1367-1376
-
-
Andersen, P.R.1
-
43
-
-
84988527647
-
Genome-wide identifcation of transcript start and end sites by transcript isoform sequencing
-
Pelechano, V., Wei, W., Jakob, P. & Steinmetz, L.M. Genome-wide identifcation of transcript start and end sites by transcript isoform sequencing. Nat. Protoc. 9, 1740-1759 (2014).
-
(2014)
Nat. Protoc.
, vol.9
, pp. 1740-1759
-
-
Pelechano, V.1
Wei, W.2
Jakob, P.3
Steinmetz, L.M.4
-
44
-
-
84928987900
-
HTSeq-A Python framework to work with high-throughput sequencing data
-
Anders, S., Pyl, P.T. & Huber, W. HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
45
-
-
77951820899
-
Fast and SNP-tolerant detection of complex variants and splicing in short reads
-
Wu, T.D. & Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
-
46
-
-
62349130698
-
Ultrafast and memory-effcient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-effcient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
47
-
-
46049107540
-
Asap: A framework for over-representation statistics for transcription factor binding sites
-
Marstrand, T.T. et al. Asap: a framework for over-representation statistics for transcription factor binding sites. PLoS ONE 3, e1623 (2008).
-
(2008)
PLoS ONE
, vol.3
, pp. e1623
-
-
Marstrand, T.T.1
-
48
-
-
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
-
49
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626-635 (2006).
-
(2006)
Nat. Genet.
, vol.38
, pp. 626-635
-
-
Carninci, P.1
-
50
-
-
77951770756
-
BEDTools: A fexible suite of utilities for comparing genomic features
-
Quinlan, A.R. & Hall, I.M. BEDTools: a fexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
51
-
-
78651271733
-
Integrative genomics viewer
-
Robinson, J.T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24-26 (2011).
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
|