-
1
-
-
3343003673
-
Biochemical analysis of TREX complex recruitment to intronless and introncontaining yeast genes
-
Abruzzi KC, Lacadie S, Rosbash M. 2004. Biochemical analysis of TREX complex recruitment to intronless and introncontaining yeast genes. EMBO J 23: 2620-2631.
-
(2004)
EMBO J
, vol.23
, pp. 2620-2631
-
-
Abruzzi, K.C.1
Lacadie, S.2
Rosbash, M.3
-
3
-
-
0027957779
-
Splicing of balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription
-
Bauren G, Wieslander L. 1994. Splicing of balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76: 183-192.
-
(1994)
Cell
, vol.76
, pp. 183-192
-
-
Bauren, G.1
Wieslander, L.2
-
4
-
-
0024021747
-
Splice site selection, rate of splicing, and alternative splicing on nascent transcripts
-
Beyer AL, Osheim YN. 1988. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev 2: 754-765.
-
(1988)
Genes Dev
, vol.2
, pp. 754-765
-
-
Beyer, A.L.1
Osheim, Y.N.2
-
5
-
-
4744373424
-
RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 39-end formation
-
Bird G, Zorio DA, Bentley DL. 2004. RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 39-end formation. Mol Cell Biol 24: 8963-8969.
-
(2004)
Mol Cell Biol
, vol.24
, pp. 8963-8969
-
-
Bird, G.1
Zorio, D.A.2
Bentley, D.L.3
-
6
-
-
35548988487
-
The transcriptional cycle of HIV-1 in real-time and live cells
-
Boireau S, Maiuri P, Basyuk E, de la Mata M, Knezevich A, Pradet-Balade B, Backer V, Kornblihtt A, Marcello A, Bertrand E. 2007. The transcriptional cycle of HIV-1 in real-time and live cells. J Cell Biol 179: 291-304.
-
(2007)
J Cell Biol
, vol.179
, pp. 291-304
-
-
Boireau, S.1
Maiuri, P.2
Basyuk, E.3
de la Mata, M.4
Knezevich, A.5
Pradet-Balade, B.6
Backer, V.7
Kornblihtt, A.8
Marcello, A.9
Bertrand, E.10
-
7
-
-
79851472312
-
The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing
-
doi:10.1371/journal.pbio.1000573
-
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. doi:10.1371/journal.pbio.1000573.
-
(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
-
8
-
-
22144486964
-
Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements
-
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.
-
(2005)
Genetics
, vol.170
, pp. 661-674
-
-
Burnette, J.M.1
Miyamoto-Sato, E.2
Schaub, M.A.3
Conklin, J.4
Lopez, A.J.5
-
9
-
-
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
-
10
-
-
0022345860
-
A mutation in the largest subunit of RNA polymerase II alters RNA chain elongation in vitro
-
Coulter DE, Greenleaf AL. 1985. A mutation in the largest subunit of RNA polymerase II alters RNA chain elongation in vitro. J Biol Chem 260: 13190-13198.
-
(1985)
J Biol Chem
, vol.260
, pp. 13190-13198
-
-
Coulter, D.E.1
Greenleaf, A.L.2
-
11
-
-
38649096939
-
A 59 splice site enhances the recruitment of basal transcription initiation factors in vivo
-
Damgaard CK, Kahns S, Lykke-Andersen S, Nielsen AL, Jensen TH, Kjems J. 2008. A 59 splice site enhances the recruitment of basal transcription initiation factors in vivo. Mol Cell 29: 271-278.
-
(2008)
Mol Cell
, vol.29
, pp. 271-278
-
-
Damgaard, C.K.1
Kahns, S.2
Lykke-Andersen, S.3
Nielsen, A.L.4
Jensen, T.H.5
Kjems, J.6
-
12
-
-
33745132168
-
Functional coupling of RNAP II transcription to spliceosome assembly
-
Das R, Dufu K, Romney B, Feldt M, Elenko M, Reed R. 2006. Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev 20: 1100-1109.
-
(2006)
Genes Dev
, vol.20
, pp. 1100-1109
-
-
Das, R.1
Dufu, K.2
Romney, B.3
Feldt, M.4
Elenko, M.5
Reed, R.6
-
13
-
-
34250363024
-
SR proteins function in coupling RNAP II transcription to pre-mRNA splicing
-
Das R, Yu J, Zhang Z, Gygi MP, Krainer AR, Gygi SP, Reed R. 2007. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol Cell 26: 867-881.
-
(2007)
Mol Cell
, vol.26
, pp. 867-881
-
-
Das, R.1
Yu, J.2
Zhang, Z.3
Gygi, M.P.4
Krainer, A.R.5
Gygi, S.P.6
Reed, R.7
-
14
-
-
0141888375
-
A slow RNA polymerase II affects alternative splicing in vivo
-
de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, Pelisch F, Cramer P, Bentley D, Kornblihtt AR. 2003. A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 12: 525-532.
-
(2003)
Mol Cell
, vol.12
, pp. 525-532
-
-
de la Mata, M.1
Alonso, C.R.2
Kadener, S.3
Fededa, J.P.4
Blaustein, M.5
Pelisch, F.6
Cramer, P.7
Bentley, D.8
Kornblihtt, A.R.9
-
15
-
-
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
-
16
-
-
0035878112
-
Capping, splicing, and 39 processing are independently stimulated by RNA polymerase II: Different functions for different segments of the CTD
-
Fong N, Bentley DL. 2001. Capping, splicing, and 39 processing are independently stimulated by RNA polymerase II: Different functions for different segments of the CTD. Genes Dev 15: 1783-1795.
-
(2001)
Genes Dev
, vol.15
, pp. 1783-1795
-
-
Fong, N.1
Bentley, D.L.2
-
17
-
-
21244493903
-
Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex
-
Gornemann J, Kotovic KM, Hujer K, Neugebauer KM. 2005. Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 19: 53-63.
-
(2005)
Mol Cell
, vol.19
, pp. 53-63
-
-
Gornemann, J.1
Kotovic, K.M.2
Hujer, K.3
Neugebauer, K.M.4
-
18
-
-
79952266577
-
Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation
-
Ip JY, Schmidt D, Pan Q, Ramani AK, Fraser AG, Odom DT, Blencowe BJ. 2011. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res 21: 390-401.
-
(2011)
Genome Res
, vol.21
, pp. 390-401
-
-
Ip, J.Y.1
Schmidt, D.2
Pan, Q.3
Ramani, A.K.4
Fraser, A.G.5
Odom, D.T.6
Blencowe, B.J.7
-
19
-
-
0035887299
-
Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing
-
Kadener S, Cramer P, Nogues G, Cazalla D, de la Mata M, Fededa JP, Werbajh SE, Srebrow A, Kornblihtt AR. 2001. Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing. EMBO J 20: 5759-5768.
-
(2001)
EMBO J
, vol.20
, pp. 5759-5768
-
-
Kadener, S.1
Cramer, P.2
Nogues, G.3
Cazalla, D.4
de la Mata, M.5
Fededa, J.P.6
Werbajh, S.E.7
Srebrow, A.8
Kornblihtt, A.R.9
-
20
-
-
62549120015
-
Genome-wide identification of targets of the drosha-pasha/DGCR8 complex
-
Kadener S, Rodriguez J, Abruzzi KC, Khodor YL, Sugino K, Marr MT II, Nelson S, Rosbash M. 2009. Genome-wide identification of targets of the drosha-pasha/DGCR8 complex. RNA 15: 537-545.
-
(2009)
RNA
, vol.15
, pp. 537-545
-
-
Kadener, S.1
Rodriguez, J.2
Abruzzi, K.C.3
Khodor, Y.L.4
Sugino, K.5
Marr, M.T.I.I.6
Nelson, S.7
Rosbash, M.8
-
21
-
-
78649847070
-
. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation
-
Kaida D, Berg MG, Younis I, Kasim M, Singh LN, Wan L, Dreyfuss G. 2010. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468: 664-668.
-
(2010)
Nature
, vol.468
, pp. 664-668
-
-
Kaida, D.1
Berg, M.G.2
Younis, I.3
Kasim, M.4
Singh, L.N.5
Wan, L.6
Dreyfuss, G.7
-
22
-
-
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.
-
(1993)
Mol Cell Biol
, vol.13
, pp. 6211-6222
-
-
Kessler, O.1
Jiang, Y.2
Chasin, L.A.3
-
23
-
-
0028589099
-
Assembly and disassembly of spliceosomes along a specific pre-messenger RNP fiber
-
Kiseleva E, Wurtz T, Visa N, Daneholt B. 1994. Assembly and disassembly of spliceosomes along a specific pre-messenger RNP fiber. EMBO J 13: 6052-6061.
-
(1994)
EMBO J
, vol.13
, pp. 6052-6061
-
-
Kiseleva, E.1
Wurtz, T.2
Visa, N.3
Daneholt, B.4
-
24
-
-
0036829065
-
U1 snRNA associates with TFIIH and regulates transcriptional initiation
-
Kwek KY, Murphy S, Furger A, Thomas B, O'Gorman W, Kimura H, Proudfoot NJ, Akoulitchev A. 2002. U1 snRNA associates with TFIIH and regulates transcriptional initiation. Nat Struct Biol 9: 800-805.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 800-805
-
-
Kwek, K.Y.1
Murphy, S.2
Furger, A.3
Thomas, B.4
O'Gorman, W.5
Kimura, H.6
Proudfoot, N.J.7
Akoulitchev, A.8
-
25
-
-
21244469725
-
Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:59ss base pairing in yeast
-
Lacadie SA, Rosbash M. 2005. Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:59ss base pairing in yeast. Mol Cell 19: 65-75.
-
(2005)
Mol Cell
, vol.19
, pp. 65-75
-
-
Lacadie, S.A.1
Rosbash, M.2
-
26
-
-
33746630487
-
In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants
-
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.
-
(2006)
Genes Dev
, vol.20
, pp. 2055-2066
-
-
Lacadie, S.A.1
Tardiff, D.F.2
Kadener, S.3
Rosbash, M.4
-
27
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
doi:10.1186/gb-2009-10-3-r25
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi:10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
28
-
-
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
-
29
-
-
0036285707
-
Functional interaction of yeast premRNA 39 end processing factors with RNA polymerase II
-
Licatalosi DD, Geiger G, Minet M, Schroeder S, Cilli K, McNeil JB, Bentley DL. 2002. Functional interaction of yeast premRNA 39 end processing factors with RNA polymerase II. Mol Cell 9: 1101-1111.
-
(2002)
Mol Cell
, vol.9
, pp. 1101-1111
-
-
Licatalosi, D.D.1
Geiger, G.2
Minet, M.3
Schroeder, S.4
Cilli, K.5
McNeil, J.B.6
Bentley, D.L.7
-
30
-
-
33748351186
-
Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells
-
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.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 815-822
-
-
Listerman, I.1
Sapra, A.K.2
Neugebauer, K.M.3
-
31
-
-
0031037856
-
The C-terminal domain of RNA polymerase II couples mRNA processing to transcription
-
McCracken S, Fong N, Yankulov K, Ballantyne S, Pan G, Greenblatt J, Patterson SD, Wickens M, Bentley DL. 1997. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385: 357-361.
-
(1997)
Nature
, vol.385
, pp. 357-361
-
-
McCracken, S.1
Fong, N.2
Yankulov, K.3
Ballantyne, S.4
Pan, G.5
Greenblatt, J.6
Patterson, S.D.7
Wickens, M.8
Bentley, D.L.9
-
32
-
-
0034704145
-
The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II
-
Morris DP, Greenleaf AL. 2000. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 275: 39935-39943.
-
(2000)
J Biol Chem
, vol.275
, pp. 39935-39943
-
-
Morris, D.P.1
Greenleaf, A.L.2
-
33
-
-
14844327076
-
Assaying the Drosophila negative feedback loop with RNA interference in S2 cells
-
Nawathean P, Menet JS, Rosbash M. 2005. Assaying the Drosophila negative feedback loop with RNA interference in S2 cells. Methods Enzymol 393: 610-622.
-
(2005)
Methods Enzymol
, vol.393
, pp. 610-622
-
-
Nawathean, P.1
Menet, J.S.2
Rosbash, M.3
-
34
-
-
74549132843
-
Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila
-
Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. 2010. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327: 335-338.
-
(2010)
Science
, vol.327
, pp. 335-338
-
-
Nechaev, S.1
Fargo, D.C.2
dos Santos, G.3
Liu, L.4
Gao, Y.5
Adelman, K.6
-
35
-
-
0037107547
-
On the importance of being co-transcriptional
-
Neugebauer KM. 2002. On the importance of being co-transcriptional. J Cell Sci 115: 3865-3871.
-
(2002)
J Cell Sci
, vol.115
, pp. 3865-3871
-
-
Neugebauer, K.M.1
-
37
-
-
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
-
38
-
-
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
-
39
-
-
0242490558
-
Dawdling polymerases allow introns time to splice
-
Proudfoot NJ. 2003. Dawdling polymerases allow introns time to splice. Nat Struct Biol 10: 876-878.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 876-878
-
-
Proudfoot, N.J.1
-
40
-
-
0037154967
-
Integrating mRNA processing with transcription
-
Proudfoot NJ, Furger A, Dye MJ. 2002. Integrating mRNA processing with transcription. Cell 108: 501-512.
-
(2002)
Cell
, vol.108
, pp. 501-512
-
-
Proudfoot, N.J.1
Furger, A.2
Dye, M.J.3
-
41
-
-
0033365194
-
Redefinition of exon 7 in the COL1A1 gene of type I collagen by an intron 8 splicedonor- site mutation in a form of osteogenesis imperfecta: Influence of intron splice order on outcome of splice-site mutation
-
Schwarze U, Starman BJ, Byers PH. 1999. Redefinition of exon 7 in the COL1A1 gene of type I collagen by an intron 8 splicedonor- site mutation in a form of osteogenesis imperfecta: Influence of intron splice order on outcome of splice-site mutation. Am J Hum Genet 65: 336-344.
-
(1999)
Am J Hum Genet
, vol.65
, pp. 336-344
-
-
Schwarze, U.1
Starman, B.J.2
Byers, P.H.3
-
42
-
-
33845643952
-
A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional
-
Tardiff DF, Lacadie SA, Rosbash M. 2006. A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol Cell 24: 917-929.
-
(2006)
Mol Cell
, vol.24
, pp. 917-929
-
-
Tardiff, D.F.1
Lacadie, S.A.2
Rosbash, M.3
-
43
-
-
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
-
44
-
-
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.
-
(1996)
RNA
, vol.2
, pp. 641-651
-
-
Wetterberg, I.1
Bauren, G.2
Wieslander, L.3
-
45
-
-
0035873705
-
In situ transcription and splicing in the Balbiani ring 3 gene
-
Wetterberg I, Zhao J, Masich S, Wieslander L, Skoglund U. 2001. In situ transcription and splicing in the Balbiani ring 3 gene. EMBO J 20: 2564-2574.
-
(2001)
EMBO J
, vol.20
, pp. 2564-2574
-
-
Wetterberg, I.1
Zhao, J.2
Masich, S.3
Wieslander, L.4
Skoglund, U.5
-
46
-
-
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.
-
(1994)
Mol Cell Biol
, vol.14
, pp. 7219-7225
-
-
Wuarin, J.1
Schibler, U.2
|