-
1
-
-
33748933029
-
3′-End formation signals modulate the association of genes with the nuclear periphery as well as mRNP dot formation
-
DOI 10.1038/sj.emboj.7601305, PII 7601305
-
Abruzzi KC, Belostotsky DA, Chekanova JA, Dower K, Rosbash M. 2006. 3′-end formation signals modulate the association of genes with the nuclear periphery as well as mRNP dot formation. EMBO J 25: 4253-4262. (Pubitemid 44435223)
-
(2006)
EMBO Journal
, vol.25
, Issue.18
, pp. 4253-4262
-
-
Abruzzi, K.C.1
Belostotsky, D.A.2
Chekanova, J.A.3
Dower, K.4
Rosbash, M.5
-
2
-
-
78649301379
-
RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3′-end processing in Saccharomyces cerevisiae
-
Alexander RD, Barrass JD, Dichtl B, Kos M, Obtulowicz T, Robert MC, Koper M, Karkusiewicz I, Mariconti L, Tollervey D, et al. 2010a. RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3′-end processing in Saccharomyces cerevisiae. RNA 16: 2570-2580.
-
(2010)
RNA
, vol.16
, pp. 2570-2580
-
-
Alexander, R.D.1
Barrass, J.D.2
Dichtl, B.3
Kos, M.4
Obtulowicz, T.5
Robert, M.C.6
Koper, M.7
Karkusiewicz, I.8
Mariconti, L.9
Tollervey, D.10
-
4
-
-
82955232386
-
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain
-
Ameur A, Zaghlool A, Halvardson J, Wetterbom A, Gyllensten U, Cavelier L, Feuk L. 2011. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol 18: 1435-1440.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 1435-1440
-
-
Ameur, A.1
Zaghlool, A.2
Halvardson, J.3
Wetterbom, A.4
Gyllensten, U.5
Cavelier, L.6
Feuk, L.7
-
5
-
-
70350783881
-
Tracking rates of transcription and splicing in vivo
-
Ardehali MB, Lis JT. 2009. Tracking rates of transcription and splicing in vivo. Nat Struct Mol Biol 16: 1123-1124.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 1123-1124
-
-
Ardehali, M.B.1
Lis, J.T.2
-
6
-
-
0027957779
-
Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription
-
DOI 10.1016/0092-8674(94)90182-1
-
Bauren G, Wieslander L. 1994. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76: 183-192. (Pubitemid 24035291)
-
(1994)
Cell
, vol.76
, Issue.1
, pp. 183-192
-
-
Bauren, G.1
Wieslander, L.2
-
7
-
-
77952408391
-
The life of an mRNA in space and time
-
Ben-Ari Y, Brody Y, Kinor N, Mor A, Tsukamoto T, Spector DL, Singer RH, Shav-Tal Y. 2010. The life of an mRNA in space and time. J Cell Sci 123: 1761-1774.
-
(2010)
J Cell Sci
, vol.123
, pp. 1761-1774
-
-
Ben-Ari, Y.1
Brody, Y.2
Kinor, N.3
Mor, A.4
Tsukamoto, T.5
Spector, D.L.6
Singer, R.H.7
Shav-Tal, Y.8
-
8
-
-
84864251757
-
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
-
Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST. 2012. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150: 279-290.
-
(2012)
Cell
, vol.150
, pp. 279-290
-
-
Bhatt, D.M.1
Pandya-Jones, A.2
Tong, A.J.3
Barozzi, I.4
Lissner, M.M.5
Natoli, G.6
Black, D.L.7
Smale, S.T.8
-
9
-
-
28444438876
-
Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing
-
DOI 10.1016/j.molcel.2005.11.009, PII S1097276505017697
-
Bird G, Fong N, Gatlin JC, Farabaugh S, Bentley DL. 2005. Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing. Mol Cell 20: 747-758. (Pubitemid 41740696)
-
(2005)
Molecular Cell
, vol.20
, Issue.5
, pp. 747-758
-
-
Bird, G.1
Fong, N.2
Gatlin, J.C.3
Farabaugh, S.4
Bentley, D.L.5
-
10
-
-
75949108066
-
Galaxy: A web-based genome analysis tool for experimentalists
-
Chapter 19: Unit 19
-
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. 2010. Galaxy: A web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol Chapter 19: Unit 19 10 11-21.
-
(2010)
Curr Protoc Mol Biol
, vol.10
, pp. 11-21
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
Mangan, M.6
Nekrutenko, A.7
Taylor, J.8
-
11
-
-
79851472312
-
The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing
-
Brody Y, Neufeld N, Bieberstein N, Causse SZ, Bohnlein EM, Neugebauer KM, Darzacq X, Shav-Tal Y. 2011. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol 9: e1000573.
-
(2011)
PLoS Biol
, vol.9
-
-
Brody, Y.1
Neufeld, N.2
Bieberstein, N.3
Causse, S.Z.4
Bohnlein, E.M.5
Neugebauer, K.M.6
Darzacq, X.7
Shav-Tal, Y.8
-
12
-
-
22144486964
-
Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements
-
DOI 10.1534/genetics.104.039701
-
Burnette JM, Miyamoto-Sato E, Schaub MA, Conklin J, Lopez AJ. 2005. Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements. Genetics 170: 661-674. (Pubitemid 40980668)
-
(2005)
Genetics
, vol.170
, Issue.2
, pp. 661-674
-
-
Burnette, J.M.1
Miyamoto-Sato, E.2
Schaub, M.A.3
Conklin, J.4
Lopez, A.J.5
-
13
-
-
78649289872
-
Global analysis of nascent RNA reveals transcriptional pausing in terminal exons
-
Carrillo Oesterreich F, Preibisch S, Neugebauer KM. 2010. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell 40: 571-581.
-
(2010)
Mol Cell
, vol.40
, pp. 571-581
-
-
Carrillo Oesterreich, F.1
Preibisch, S.2
Neugebauer, K.M.3
-
14
-
-
84857761249
-
Pre-mRNA 3′-end processing complex assembly and function
-
Chan S, Choi EA, Shi Y. 2011. Pre-mRNA 3′-end processing complex assembly and function. Wiley Interdiscip Rev RNA 2: 321-335.
-
(2011)
Wiley Interdiscip Rev RNA
, vol.2
, pp. 321-335
-
-
Chan, S.1
Choi, E.A.2
Shi, Y.3
-
15
-
-
0031453408
-
mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain
-
Cho EJ, Takagi T, Moore CR, Buratowski S. 1997. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev 11: 3319-3326. (Pubitemid 28023956)
-
(1997)
Genes and Development
, vol.11
, Issue.24
, pp. 3319-3326
-
-
Cho, E.-J.1
Takagi, T.2
Moore, C.R.3
Buratowski, S.4
-
16
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-1848.
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
17
-
-
0041013167
-
Inefficient processing impairs release of RNA from the site of transcription
-
DOI 10.1093/emboj/18.10.2855
-
Custodio N, Carmo-Fonseca M, Geraghty F, Pereira HS, Grosveld F, Antoniou M. 1999. Inefficient processing impairs release of RNA from the site of transcription. EMBO J 18: 2855-2866. (Pubitemid 29233957)
-
(1999)
EMBO Journal
, vol.18
, Issue.10
, pp. 2855-2866
-
-
Custodio, N.1
Carmo-Fonseca, M.2
Geraghty, F.3
Pereira, H.S.4
Grosveld, F.5
Antoniou, M.6
-
18
-
-
84860378396
-
Perispeckles are major assembly sites for the exon junction core complex
-
Daguenet E, Baguet A, Degot S, Schmidt U, Alpy F, Wendling C, Spiegelhalter C, Kessler P, Rio MC, Le Hir H, et al. 2012. Perispeckles are major assembly sites for the exon junction core complex. Mol Biol Cell 23: 1765-1782.
-
(2012)
Mol Biol Cell
, vol.23
, pp. 1765-1782
-
-
Daguenet, E.1
Baguet, A.2
Degot, S.3
Schmidt, U.4
Alpy, F.5
Wendling, C.6
Spiegelhalter, C.7
Kessler, P.8
Rio, M.C.9
Le Hir, H.10
-
19
-
-
84875429298
-
Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture
-
Darnell JE Jr. 2013. Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture. RNA 19: 443-460.
-
(2013)
RNA
, vol.19
, pp. 443-460
-
-
Darnell Jr., J.E.1
-
20
-
-
34548507690
-
In vivo dynamics of RNA polymerase II transcription
-
DOI 10.1038/nsmb1280, PII NSMB1280
-
Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy SM, Phair RD, Singer RH. 2007. In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 14: 796-806. (Pubitemid 47373828)
-
(2007)
Nature Structural and Molecular Biology
, vol.14
, Issue.9
, pp. 796-806
-
-
Darzacq, X.1
Shav-Tal, Y.2
De Turris, V.3
Brody, Y.4
Shenoy, S.M.5
Phair, R.D.6
Singer, R.H.7
-
21
-
-
77951200179
-
First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal
-
de la Mata M, Lafaille C, Kornblihtt AR. 2010. First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal. RNA 16: 904-912.
-
(2010)
RNA
, vol.16
, pp. 904-912
-
-
De La Mata, M.1
Lafaille, C.2
Kornblihtt, A.R.3
-
22
-
-
70350754328
-
Jmjd3 contributes to the control of gene expression in LPS-activated macrophages
-
De Santa F, Narang V, Yap ZH, Tusi BK, Burgold T, Austenaa L, Bucci G, Caganova M, Notarbartolo S, Casola S, et al. 2009. Jmjd3 contributes to the control of gene expression in LPS-activated macrophages. EMBO J 28: 3341-3352.
-
(2009)
EMBO J
, vol.28
, pp. 3341-3352
-
-
De Santa, F.1
Narang, V.2
Yap, Z.H.3
Tusi, B.K.4
Burgold, T.5
Austenaa, L.6
Bucci, G.7
Caganova, M.8
Notarbartolo, S.9
Casola, S.10
-
23
-
-
0016318515
-
Relationship of chain transcription to poly(A) addition and processing of hnRNA in HeLa cells
-
Derman E, Darnell JE. 1974. Relationship of chain transcription to poly(A) addition and processing of hnRNA in HeLa cells. Cell 3: 255-264.
-
(1974)
Cell
, vol.3
, pp. 255-264
-
-
Derman, E.1
Darnell, J.E.2
-
24
-
-
84880317039
-
A role for TREX components in the release of spliced mRNA from nuclear speckle domains
-
Dias AP, Dufu K, Lei H, Reed R. 2010. A role for TREX components in the release of spliced mRNA from nuclear speckle domains. Nat Commun 1: 97.
-
(2010)
Nat Commun
, vol.1
, pp. 97
-
-
Dias, A.P.1
Dufu, K.2
Lei, H.3
Reed, R.4
-
25
-
-
84855286273
-
Mechanisms establishing TLR4-responsive activation states of inflammatory response genes
-
Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, et al. 2011. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet 7: e1002401.
-
(2011)
PLoS Genet
, vol.7
-
-
Escoubet-Lozach, L.1
Benner, C.2
Kaikkonen, M.U.3
Lozach, J.4
Heinz, S.5
Spann, N.J.6
Crotti, A.7
Stender, J.8
Ghisletti, S.9
Reichart, D.10
-
26
-
-
60549104588
-
Splice-site pairing is an intrinsically high fidelity process
-
Fox-Walsh KL, Hertel KJ. 2009. Splice-site pairing is an intrinsically high fidelity process. Proc Natl Acad Sci 106: 1766-1771.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 1766-1771
-
-
Fox-Walsh, K.L.1
Hertel, K.J.2
-
27
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
DOI 10.1101/gr.4086505
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, et al. 2005. Galaxy: A platform for interactive large-scale genome analysis. Genome Res 15: 1451-1455. (Pubitemid 41400913)
-
(2005)
Genome Research
, vol.15
, Issue.10
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
Miller, W.11
Kent, W.J.12
Nekrutenko, A.13
-
28
-
-
84866077515
-
Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion
-
Girard C, Will CL, Peng J, Makarov EM, Kastner B, Lemm I, Urlaub H, Hartmuth K, Luhrmann R. 2012. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nat Commun 3: 994.
-
(2012)
Nat Commun
, vol.3
, pp. 994
-
-
Girard, C.1
Will, C.L.2
Peng, J.3
Makarov, E.M.4
Kastner, B.5
Lemm, I.6
Urlaub, H.7
Hartmuth, K.8
Luhrmann, R.9
-
29
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks J, Nekrutenko A, Taylor J. 2010. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
-
(2010)
Genome Biol
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
30
-
-
77957370148
-
In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport
-
Grunwald D, Singer RH. 2010. In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Nature 467: 604-607.
-
(2010)
Nature
, vol.467
, pp. 604-607
-
-
Grunwald, D.1
Singer, R.H.2
-
31
-
-
0018385738
-
The synthesis and processing of a nuclear RNA precursor to rat pregrowth hormone messenger RNA
-
Harpold MM, Dobner PR, Evans R, Bancroft FC, Darnell JE Jr. 1979. The synthesis and processing of a nuclear RNA precursor to rat pregrowth hormone messenger RNA. Nucleic Acids Res 6: 3133-3144. (Pubitemid 9222562)
-
(1979)
Nucleic Acids Research
, vol.6
, Issue.9
, pp. 3133-3144
-
-
Harpold, M.M.1
Dobner, P.R.2
Evans, R.3
-
32
-
-
0032247577
-
Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions
-
Hatton AR, Subramaniam V, Lopez AJ. 1998. Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions. Mol Cell 2: 787-796. (Pubitemid 128378986)
-
(1998)
Molecular Cell
, vol.2
, Issue.6
, pp. 787-796
-
-
Hatton, A.R.1
Subramaniam, V.2
Lopez, A.J.3
-
33
-
-
0031990320
-
The Function of Multisite Splicing Enhancers
-
Hertel KJ, Maniatis T. 1998. The function of multisite splicing enhancers. Mol Cell 1: 449-455. (Pubitemid 128378893)
-
(1998)
Molecular Cell
, vol.1
, Issue.3
, pp. 449-455
-
-
Hertel, K.J.1
Maniatis, T.2
-
35
-
-
77950643284
-
Competing upstream 5′ splice sites enhance the rate of proximal splicing
-
Hicks MJ, Mueller WF, Shepard PJ, Hertel KJ. 2010. Competing upstream 5′ splice sites enhance the rate of proximal splicing. Mol Cell Biol 30: 1878-1886.
-
(2010)
Mol Cell Biol
, vol.30
, pp. 1878-1886
-
-
Hicks, M.J.1
Mueller, W.F.2
Shepard, P.J.3
Hertel, K.J.4
-
37
-
-
84867160564
-
The RNA polymerase II CTD coordinates transcription and RNA processing
-
Hsin JP, Manley JL. 2012. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev 26: 2119-2137.
-
(2012)
Genes Dev
, vol.26
, pp. 2119-2137
-
-
Hsin, J.P.1
Manley, J.L.2
-
38
-
-
17044427579
-
Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers
-
Ibrahim EC, Schaal TD, Hertel KJ, Reed R, Maniatis T. 2005. Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc Natl Acad Sci 102: 5002-5007.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 5002-5007
-
-
Ibrahim, E.C.1
Schaal, T.D.2
Hertel, K.J.3
Reed, R.4
Maniatis, T.5
-
39
-
-
0035022577
-
A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription
-
DOI 10.1016/S1097-2765(01)00232-5
-
Jensen TH, Patricio K, McCarthy T, Rosbash M. 2001. A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription. Mol Cell 7: 887-898. (Pubitemid 32436448)
-
(2001)
Molecular Cell
, vol.7
, Issue.4
, pp. 887-898
-
-
Jensen, T.H.1
Patricio, K.2
McCarthy, T.3
Rosbash, M.4
-
40
-
-
0030013179
-
Inhibition by SR proteins splicing of a regulated adenovirus pre-mRNA
-
DOI 10.1038/381535a0
-
Kanopka A, Muhlemann O, Akusjarvi G. 1996. Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA. Nature 381: 535-538. (Pubitemid 26170934)
-
(1996)
Nature
, vol.381
, Issue.6582
, pp. 535-538
-
-
Kanopka, A.1
Muhlemann, O.2
Akusjarvi, G.3
-
41
-
-
0027495952
-
Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA
-
Kessler O, Jiang Y, Chasin LA. 1993. Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA. Mol Cell Biol 13: 6211-6222. (Pubitemid 23292615)
-
(1993)
Molecular and Cellular Biology
, vol.13
, Issue.10
, pp. 6211-6222
-
-
Kessler, O.1
Jiang, Y.2
Chasin, L.A.3
-
42
-
-
82955247079
-
Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila
-
Khodor YL, Rodriguez J, Abruzzi KC, Tang CH, Marr MT II, Rosbash M. 2011. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev 25: 2502-2512.
-
(2011)
Genes Dev
, vol.25
, pp. 2502-2512
-
-
Khodor, Y.L.1
Rodriguez, J.2
Abruzzi, K.C.3
Tang, C.H.4
Marr II, M.T.5
Rosbash, M.6
-
43
-
-
84869859046
-
Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse
-
Khodor YL, Menet JS, Tolan M, Rosbash M. 2012. Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA 18: 2174-2186.
-
(2012)
RNA
, vol.18
, pp. 2174-2186
-
-
Khodor, Y.L.1
Menet, J.S.2
Tolan, M.3
Rosbash, M.4
-
44
-
-
33846945735
-
Processing of intronic microRNAs
-
Kim YK, Kim VN. 2007. Processing of intronic microRNAs. EMBO J 26: 775-783.
-
(2007)
EMBO J
, vol.26
, pp. 775-783
-
-
Kim, Y.K.1
Kim, V.N.2
-
45
-
-
59449100357
-
Spliceosome assembly pathways for different types of alternative splicing converge during commitment to splice site pairing in the A complex
-
Kotlajich MV, Crabb TL, Hertel KJ. 2009. Spliceosome assembly pathways for different types of alternative splicing converge during commitment to splice site pairing in the A complex. Mol Cell Biol 29: 1072-1082.
-
(2009)
Mol Cell Biol
, vol.29
, pp. 1072-1082
-
-
Kotlajich, M.V.1
Crabb, T.L.2
Hertel, K.J.3
-
46
-
-
33746630487
-
In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants
-
DOI 10.1101/gad.1434706
-
Lacadie SA, Tardiff DF, Kadener S, Rosbash M. 2006. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. Genes Dev 20: 2055-2066. (Pubitemid 44157457)
-
(2006)
Genes and Development
, vol.20
, Issue.15
, pp. 2055-2066
-
-
Lacadie, S.A.1
Tardiff, D.F.2
Kadener, S.3
Rosbash, M.4
-
47
-
-
0025169502
-
Splicing precedes polyadenylation during Drosophila E74A transcription
-
LeMaire MF, Thummel CS. 1990. Splicing precedes polyadenylation during Drosophila E74A transcription. Mol Cell Biol 10: 6059-6063.
-
(1990)
Mol Cell Biol
, vol.10
, pp. 6059-6063
-
-
LeMaire, M.F.1
Thummel, C.S.2
-
48
-
-
77956340995
-
Comprehensive comparative analysis of strand-specific RNA sequencing methods
-
Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7: 709-715.
-
(2010)
Nat Methods
, vol.7
, pp. 709-715
-
-
Levin, J.Z.1
Yassour, M.2
Adiconis, X.3
Nusbaum, C.4
Thompson, D.A.5
Friedman, N.6
Gnirke, A.7
Regev, A.8
-
49
-
-
4143078172
-
Commitment to splice site pairing coincides with a complex formation
-
DOI 10.1016/j.molcel.2004.06.025, PII S1097276504003739
-
Lim SR, Hertel KJ. 2004. Commitment to splice site pairing coincides with A complex formation. Mol Cell 15: 477-483. (Pubitemid 39092762)
-
(2004)
Molecular Cell
, vol.15
, Issue.3
, pp. 477-483
-
-
Lim, S.R.1
Hertel, K.J.2
-
50
-
-
33748351186
-
Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells
-
DOI 10.1038/nsmb1135, PII NSMB1135
-
Listerman I, Sapra AK, Neugebauer KM. 2006. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol 13: 815-822. (Pubitemid 44338776)
-
(2006)
Nature Structural and Molecular Biology
, vol.13
, Issue.9
, pp. 815-822
-
-
Listerman, I.1
Sapra, A.K.2
Neugebauer, K.M.3
-
51
-
-
10244239317
-
Consequences of regulated pre-mRNA splicing in the immune system
-
DOI 10.1038/nri1497
-
Lynch KW. 2004. Consequences of regulated pre-mRNA splicing in the immune system. Nat Rev Immunol 4: 931-940. (Pubitemid 39620068)
-
(2004)
Nature Reviews Immunology
, vol.4
, Issue.12
, pp. 931-940
-
-
Lynch, K.W.1
-
52
-
-
80455164573
-
Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes
-
Martins SB, Rino J, Carvalho T, Carvalho C, Yoshida M, Klose JM, de Almeida SF, Carmo-Fonseca M. 2011. Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes. Nat Struct Mol Biol 18: 1115-1123.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 1115-1123
-
-
Martins, S.B.1
Rino, J.2
Carvalho, T.3
Carvalho, C.4
Yoshida, M.5
Klose, J.M.6
De Almeida, S.F.7
Carmo-Fonseca, M.8
-
53
-
-
42449158952
-
Spliceosome assembly and composition
-
Matlin AJ, Moore MJ. 2007. Spliceosome assembly and composition. Adv Exp Med Biol 623: 14-35.
-
(2007)
Adv Exp Med Biol
, vol.623
, pp. 14-35
-
-
Matlin, A.J.1
Moore, M.J.2
-
54
-
-
15644372864
-
5'-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II
-
McCracken S, Fong N, Rosonina E, Yankulov K, Brothers G, Siderovski D, Hessel A, Foster S, Shuman S, Bentley DL. 1997. 5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev 11: 3306-3318. (Pubitemid 28023955)
-
(1997)
Genes and Development
, vol.11
, Issue.24
, pp. 3306-3318
-
-
McCracken, S.1
Fong, N.2
Rosonina, E.3
Yankulov, K.4
Brothers, G.5
Siderovski, D.6
Hessel, A.7
Foster, S.8
Shuman, S.9
Bentley, D.L.10
-
55
-
-
0018233483
-
+ nuclear sequences are conserved and poly(A) addition precedes splicing
-
+ nuclear sequences are conserved and poly(A) addition precedes splicing. Cell 15: 1477-1493.
-
(1978)
Cell
, vol.15
, pp. 1477-1493
-
-
Nevins, J.R.1
Darnell Jr., J.E.2
-
56
-
-
80053932983
-
Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor
-
Ninomiya K, Kataoka N, Hagiwara M. 2011. Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor. J Cell Biol 195: 27-40.
-
(2011)
J Cell Biol
, vol.195
, pp. 27-40
-
-
Ninomiya, K.1
Kataoka, N.2
Hagiwara, M.3
-
57
-
-
0022160149
-
RNP particles at splice junction sequences on Drosophila chorion transcripts
-
Osheim YN, Miller OL Jr, Beyer AL. 1985. RNP particles at splice junction sequences on Drosophila chorion transcripts. Cell 43: 143-151.
-
(1985)
Cell
, vol.43
, pp. 143-151
-
-
Osheim, Y.N.1
Miller Jr., O.L.2
Beyer, A.L.3
-
58
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
-
(2008)
Nat Genet
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
59
-
-
84857745166
-
Pre-mRNA splicing during transcription in the mammalian system
-
Pandya-Jones A. 2011. Pre-mRNA splicing during transcription in the mammalian system. Wiley Interdiscip Rev RNA 2: 700-717.
-
(2011)
Wiley Interdiscip Rev RNA
, vol.2
, pp. 700-717
-
-
Pandya-Jones, A.1
-
60
-
-
70349125488
-
Co-transcriptional splicing of constitutive and alternative exons
-
Pandya-Jones A, Black DL. 2009. Co-transcriptional splicing of constitutive and alternative exons. RNA 15: 1896-1908.
-
(2009)
RNA
, vol.15
, pp. 1896-1908
-
-
Pandya-Jones, A.1
Black, D.L.2
-
61
-
-
47549105524
-
Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production
-
DOI 10.1083/jcb.200803111
-
Pawlicki JM, Steitz JA. 2008. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. J Cell Biol 182: 61-76. (Pubitemid 352008622)
-
(2008)
Journal of Cell Biology
, vol.182
, Issue.1
, pp. 61-76
-
-
Pawlicki, J.M.1
Steitz, J.A.2
-
62
-
-
70350005395
-
"Cotranscriptionality": The transcription elongation complex as a nexus for nuclear transactions
-
Perales R, Bentley D. 2009. "Cotranscriptionality": The transcription elongation complex as a nexus for nuclear transactions. Mol Cell 36: 178-191.
-
(2009)
Mol Cell
, vol.36
, pp. 178-191
-
-
Perales, R.1
Bentley, D.2
-
63
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
64
-
-
79955768436
-
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
-
Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, et al. 2011. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol 29: 436-442.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 436-442
-
-
Rabani, M.1
Levin, J.Z.2
Fan, L.3
Adiconis, X.4
Raychowdhury, R.5
Garber, M.6
Gnirke, A.7
Nusbaum, C.8
Hacohen, N.9
Friedman, N.10
-
65
-
-
67649669255
-
A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling
-
Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. 2009. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138: 114-128.
-
(2009)
Cell
, vol.138
, pp. 114-128
-
-
Ramirez-Carrozzi, V.R.1
Braas, D.2
Bhatt, D.M.3
Cheng, C.S.4
Hong, C.5
Doty, K.R.6
Black, J.C.7
Hoffmann, A.8
Carey, M.9
Smale, S.T.10
-
66
-
-
65249151979
-
Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing
-
Rigo F, Martinson HG. 2009. Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing. RNA 15: 823-836.
-
(2009)
RNA
, vol.15
, pp. 823-836
-
-
Rigo, F.1
Martinson, H.G.2
-
67
-
-
53749089421
-
THO/Sub2p functions to coordinate 3′-end processing with gene-nuclear pore association
-
Rougemaille M, Dieppois G, Kisseleva-Romanova E, Gudipati RK, Lemoine S, Blugeon C, Boulay J, Jensen TH, Stutz F, Devaux F, et al. 2008. THO/Sub2p functions to coordinate 3′-end processing with gene-nuclear pore association. Cell 135: 308-321.
-
(2008)
Cell
, vol.135
, pp. 308-321
-
-
Rougemaille, M.1
Dieppois, G.2
Kisseleva-Romanova, E.3
Gudipati, R.K.4
Lemoine, S.5
Blugeon, C.6
Boulay, J.7
Jensen, T.H.8
Stutz, F.9
Devaux, F.10
-
68
-
-
0019058252
-
Addition of poly(A) to nuclear RNA occurs soon after RNA synthesis
-
Salditt-Georgieff M, Harpold M, Sawicki S, Nevins J, Darnell JE Jr. 1980. Addition of poly(A) to nuclear RNA occurs soon after RNA synthesis. J Cell Biol 86: 844-848.
-
(1980)
J Cell Biol
, vol.86
, pp. 844-848
-
-
Salditt-Georgieff, M.1
Harpold, M.2
Sawicki, S.3
Nevins, J.4
Darnell Jr., J.E.5
-
69
-
-
84856218082
-
Nuclear quality control of RNA polymerase II transcripts
-
Schmid M, Jensen TH. 2010. Nuclear quality control of RNA polymerase II transcripts. Wiley Interdiscip Rev RNA 1: 474-485.
-
(2010)
Wiley Interdiscip Rev RNA
, vol.1
, pp. 474-485
-
-
Schmid, M.1
Jensen, T.H.2
-
70
-
-
79959450181
-
Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: Implications for alternative splicing regulation
-
Schmidt U, Basyuk E, Robert MC, Yoshida M, Villemin JP, Auboeuf D, Aitken S, Bertrand E. 2011. Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: Implications for alternative splicing regulation. J Cell Biol 193: 819-829.
-
(2011)
J Cell Biol
, vol.193
, pp. 819-829
-
-
Schmidt, U.1
Basyuk, E.2
Robert, M.C.3
Yoshida, M.4
Villemin, J.P.5
Auboeuf, D.6
Aitken, S.7
Bertrand, E.8
-
72
-
-
70649088961
-
The peculiarities of large intron splicing in animals
-
Shepard S, McCreary M, Fedorov A. 2009. The peculiarities of large intron splicing in animals. PLoS One 4: e7853.
-
(2009)
PLoS One
, vol.4
-
-
Shepard, S.1
McCreary, M.2
Fedorov, A.3
-
73
-
-
80455176999
-
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
-
Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S. 2011. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479: 74-79.
-
(2011)
Nature
, vol.479
, pp. 74-79
-
-
Shukla, S.1
Kavak, E.2
Gregory, M.3
Imashimizu, M.4
Shutinoski, B.5
Kashlev, M.6
Oberdoerffer, P.7
Sandberg, R.8
Oberdoerffer, S.9
-
74
-
-
0035201941
-
Structure, mechanism, and evolution of the mRNA capping apparatus
-
Shuman S. 2001. Structure, mechanism, and evolution of the mRNA capping apparatus. Prog Nucleic Acid Res Mol Biol 66: 1-40.
-
(2001)
Prog Nucleic Acid Res Mol Biol
, vol.66
, pp. 1-40
-
-
Shuman, S.1
-
75
-
-
70350754211
-
Rates of in situ transcription and splicing in large human genes
-
Singh J, Padgett RA. 2009. Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 16: 1128-1133.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 1128-1133
-
-
Singh, J.1
Padgett, R.A.2
-
76
-
-
78049296915
-
Nuclear export of mRNA
-
Stewart M. 2010. Nuclear export of mRNA. Trends Biochem Sci 35: 609-617.
-
(2010)
Trends Biochem Sci
, vol.35
, pp. 609-617
-
-
Stewart, M.1
-
77
-
-
0037118052
-
TREX is a conserved complex coupling transcription with messenger RNA export
-
Strasser K, Masuda S, Mason P, Pfannstiel J, Oppizzi M, Rodriguez-Navarro S, Rondon AG, Aguilera A, Struhl K, Reed R, et al. 2002. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417: 304-308.
-
(2002)
Nature
, vol.417
, pp. 304-308
-
-
Strasser, K.1
Masuda, S.2
Mason, P.3
Pfannstiel, J.4
Oppizzi, M.5
Rodriguez-Navarro, S.6
Rondon, A.G.7
Aguilera, A.8
Struhl, K.9
Reed, R.10
-
78
-
-
0028837312
-
The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced
-
Tennyson CN, Klamut HJ, Worton RG. 1995. The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat Genet 9: 184-190.
-
(1995)
Nat Genet
, vol.9
, pp. 184-190
-
-
Tennyson, C.N.1
Klamut, H.J.2
Worton, R.G.3
-
79
-
-
84865777822
-
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly cotranscriptional in the human genome but inefficient for lncRNAs
-
Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R. 2012. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly cotranscriptional in the human genome but inefficient for lncRNAs. Genome Res 22: 1616-1625.
-
(2012)
Genome Res
, vol.22
, pp. 1616-1625
-
-
Tilgner, H.1
Knowles, D.G.2
Johnson, R.3
Davis, C.A.4
Chakrabortty, S.5
Djebali, S.6
Curado, J.7
Snyder, M.8
Gingeras, T.R.9
Guigo, R.10
-
80
-
-
33644525401
-
Differential expression of CD45 isoforms is controlled by the combined activity of basal and inducible splicing-regulatory elements in each of the variable exons
-
DOI 10.1074/jbc.M508123200
-
Tong A, Nguyen J, Lynch KW. 2005. Differential expression of CD45 isoforms is controlled by the combined activity of basal and inducible splicing-regulatory elements in each of the variable exons. J Biol Chem 280: 38297-38304. (Pubitemid 43853727)
-
(2005)
Journal of Biological Chemistry
, vol.280
, Issue.46
, pp. 38297-38304
-
-
Tong, A.1
Nguyen, J.2
Lynch, K.W.3
-
81
-
-
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
-
82
-
-
81855183655
-
Single-molecule imaging of transcriptionally coupled and uncoupled splicing
-
Vargas DY, Shah K, Batish M, Levandoski M, Sinha S, Marras SA, Schedl P, Tyagi S. 2011. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147: 1054-1065.
-
(2011)
Cell
, vol.147
, pp. 1054-1065
-
-
Vargas, D.Y.1
Shah, K.2
Batish, M.3
Levandoski, M.4
Sinha, S.5
Marras, S.A.6
Schedl, P.7
Tyagi, S.8
-
83
-
-
60349104299
-
The spliceosome: Design principles of a dynamic RNP machine
-
Wahl MC, Will CL, Luhrmann R. 2009. The spliceosome: Design principles of a dynamic RNP machine. Cell 136: 701-718.
-
(2009)
Cell
, vol.136
, pp. 701-718
-
-
Wahl, M.C.1
Will, C.L.2
Luhrmann, R.3
-
84
-
-
0018898480
-
Order of polyadenylic acid addition and splicing events in early adenovirus mRNA formation
-
Weber J, Blanchard JM, Ginsberg H, Darnell JE Jr. 1980. Order of polyadenylic acid addition and splicing events in early adenovirus mRNA formation. J Virol 33: 286-291. (Pubitemid 10157296)
-
(1980)
Journal of Virology
, vol.33
, Issue.1
, pp. 286-291
-
-
Weber, J.1
Blanchard, J.M.2
Ginsberg, H.3
Darnell Jr., J.E.4
-
85
-
-
0029902511
-
The intranuclear site of excision of each intron in Balbiani ring 3 pre- mRNA is influenced by the time remaining to transcription termination and different excision efficiencies for the various introns
-
Wetterberg I, Bauren G, Wieslander L. 1996. The intranuclear site of excision of each intron in Balbiani ring 3 pre-mRNA is influenced by the time remaining to transcription termination and different excision efficiencies for the various introns. RNA 2: 641-651. (Pubitemid 26374216)
-
(1996)
RNA
, vol.2
, Issue.7
, pp. 641-651
-
-
Wetterberg, I.1
Bauren, G.2
Wieslander, L.3
-
86
-
-
0028090567
-
Physical isolation of nascent RNA chains transcribed by RNA polymerase II: Evidence for cotranscriptional splicing
-
Wuarin J, Schibler U. 1994. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: Evidence for cotranscriptional splicing. Mol Cell Biol 14: 7219-7225. (Pubitemid 24326386)
-
(1994)
Molecular and Cellular Biology
, vol.14
, Issue.11
, pp. 7219-7225
-
-
Wuarin, J.1
Schibler, U.2
-
87
-
-
79960484375
-
Gene silencing in X-chromosome inactivation: Advances in understanding facultative heterochromatin formation
-
Wutz A. 2011. Gene silencing in X-chromosome inactivation: Advances in understanding facultative heterochromatin formation. Nat Rev Genet 12: 542-553.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 542-553
-
-
Wutz, A.1
-
88
-
-
57649231776
-
Dynamic regulation of alternative splicing by silencers that modulate 5′ splice site competition
-
Yu Y, Maroney PA, Denker JA, Zhang XH, Dybkov O, Luhrmann R, Jankowsky E, Chasin LA, Nilsen TW. 2008. Dynamic regulation of alternative splicing by silencers that modulate 5′ splice site competition. Cell 135: 1224-1236.
-
(2008)
Cell
, vol.135
, pp. 1224-1236
-
-
Yu, Y.1
Maroney, P.A.2
Denker, J.A.3
Zhang, X.H.4
Dybkov, O.5
Luhrmann, R.6
Jankowsky, E.7
Chasin, L.A.8
Nilsen, T.W.9
|