-
1
-
-
0036468364
-
Multisubunit RNA polymerases
-
Cramer P. Multisubunit RNA polymerases. Curr. Opin. Struct. Biol. 12 (2002) 89-97
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 89-97
-
-
Cramer, P.1
-
2
-
-
4444340288
-
Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia
-
Best A.A., Morrison H.G., McArthur A.G., Sogin M.L., and Olsen G.J. Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia. Genome Res. 14 (2004) 1537-1547
-
(2004)
Genome Res.
, vol.14
, pp. 1537-1547
-
-
Best, A.A.1
Morrison, H.G.2
McArthur, A.G.3
Sogin, M.L.4
Olsen, G.J.5
-
3
-
-
34547498469
-
Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription
-
Alic N., Ayoub N., Landrieux E., Favry E., Baudouin-Cornu P., Riva M., and Carles C. Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 10400-10405
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 10400-10405
-
-
Alic, N.1
Ayoub, N.2
Landrieux, E.3
Favry, E.4
Baudouin-Cornu, P.5
Riva, M.6
Carles, C.7
-
4
-
-
37349041027
-
Functional architecture of RNA polymerase I
-
Kuhn C.D., Geiger S.R., Baumli S., Gartmann M., Gerber J., Jennebach S., Mielke T., Tschochner H., Beckmann R., and Cramer P. Functional architecture of RNA polymerase I. Cell 131 (2007) 1260-1272
-
(2007)
Cell
, vol.131
, pp. 1260-1272
-
-
Kuhn, C.D.1
Geiger, S.R.2
Baumli, S.3
Gartmann, M.4
Gerber, J.5
Jennebach, S.6
Mielke, T.7
Tschochner, H.8
Beckmann, R.9
Cramer, P.10
-
5
-
-
0026648570
-
The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′→5′ direction in the presence of elongation factor SII
-
Izban M.G., and Luse D.S. The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′→5′ direction in the presence of elongation factor SII. Genes Dev. 6 (1992) 1342-1356
-
(1992)
Genes Dev.
, vol.6
, pp. 1342-1356
-
-
Izban, M.G.1
Luse, D.S.2
-
6
-
-
0034675857
-
The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3
-
Peyroche G., Milkereit P., Bischler N., Tschochner H., Schultz P., Sentenac A., Carles C., and Riva M. The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3. EMBO J. 19 (2000) 5473-5482
-
(2000)
EMBO J.
, vol.19
, pp. 5473-5482
-
-
Peyroche, G.1
Milkereit, P.2
Bischler, N.3
Tschochner, H.4
Schultz, P.5
Sentenac, A.6
Carles, C.7
Riva, M.8
-
7
-
-
0035971082
-
Dissociable RNAPII4-RNAPII7 subassembly of RNA polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation
-
Orlicky S.M., Tran P.T., Sayre M.H., and Edwards A.M. Dissociable RNAPII4-RNAPII7 subassembly of RNA polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J. Biol. Chem. 276 (2001) 10097-10102
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 10097-10102
-
-
Orlicky, S.M.1
Tran, P.T.2
Sayre, M.H.3
Edwards, A.M.4
-
8
-
-
0037215401
-
An RNAPII4/RNAPII7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP
-
Siaut M., Zaros C., Levivier E., Ferri M.L., Court M., Werner M., Callebaut I., Thuriaux P., Sentenac A., and Conesa C. An RNAPII4/RNAPII7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Mol. Cell. Biol. 23 (2003) 195-205
-
(2003)
Mol. Cell. Biol.
, vol.23
, pp. 195-205
-
-
Siaut, M.1
Zaros, C.2
Levivier, E.3
Ferri, M.L.4
Court, M.5
Werner, M.6
Callebaut, I.7
Thuriaux, P.8
Sentenac, A.9
Conesa, C.10
-
9
-
-
30444450804
-
A subcomplex of RNA polymerase III subunits involved in transcription termination and reinitiation
-
Landrieux E., Alic N., Ducrot C., Acker J., Riva M., and Carles C. A subcomplex of RNA polymerase III subunits involved in transcription termination and reinitiation. EMBO J. 25 (2006) 118-128
-
(2006)
EMBO J.
, vol.25
, pp. 118-128
-
-
Landrieux, E.1
Alic, N.2
Ducrot, C.3
Acker, J.4
Riva, M.5
Carles, C.6
-
10
-
-
0028824921
-
Transcription termination of RNA polymerase I due to a T-rich element interacting with Reb1p
-
Lang W.H., and Reeder R.H. Transcription termination of RNA polymerase I due to a T-rich element interacting with Reb1p. Proc. Natl. Acad. Sci. U. S. A. 92 21 (1995) 9781-9785
-
(1995)
Proc. Natl. Acad. Sci. U. S. A.
, vol.92
, Issue.21
, pp. 9781-9785
-
-
Lang, W.H.1
Reeder, R.H.2
-
11
-
-
22344443368
-
CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3′-end processing factor, Pcf11
-
Zhang Z., Fu J., and Gilmour D.S. CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3′-end processing factor, Pcf11. Genes Dev. 19 (2005) 1572-1580
-
(2005)
Genes Dev.
, vol.19
, pp. 1572-1580
-
-
Zhang, Z.1
Fu, J.2
Gilmour, D.S.3
-
12
-
-
0035827346
-
Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
-
Cramer P., Bushnell D.A., and Kornberg R.D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292 (2001) 1863-1876
-
(2001)
Science
, vol.292
, pp. 1863-1876
-
-
Cramer, P.1
Bushnell, D.A.2
Kornberg, R.D.3
-
13
-
-
0035827332
-
Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution
-
Gnatt A.L., Cramer P., Fu J., Bushnell D.A., and Kornberg R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science 292 (2001) 1876-1882
-
(2001)
Science
, vol.292
, pp. 1876-1882
-
-
Gnatt, A.L.1
Cramer, P.2
Fu, J.3
Bushnell, D.A.4
Kornberg, R.D.5
-
14
-
-
0036753435
-
Swing-gate model of nucleotide entry into the RNA polymerase active center
-
Epshtein V., Mustaev A., Markovtsov V., Bereshchenko O., Nikiforov V., and Goldfarb A. Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol. Cell 10 (2002) 623-634
-
(2002)
Mol. Cell
, vol.10
, pp. 623-634
-
-
Epshtein, V.1
Mustaev, A.2
Markovtsov, V.3
Bereshchenko, O.4
Nikiforov, V.5
Goldfarb, A.6
-
15
-
-
10944232674
-
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
-
Kettenberger H., Armache K.J., and Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16 (2004) 955-965
-
(2004)
Mol. Cell
, vol.16
, pp. 955-965
-
-
Kettenberger, H.1
Armache, K.J.2
Cramer, P.3
-
16
-
-
1142310578
-
Structural basis of transcription: separation of RNA from DNA by RNA polymerase II
-
Westover K.D., Bushnell D.A., and Kornberg R.D. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303 (2004) 1014-1016
-
(2004)
Science
, vol.303
, pp. 1014-1016
-
-
Westover, K.D.1
Bushnell, D.A.2
Kornberg, R.D.3
-
17
-
-
12944324227
-
A ratchet mechanism of transcription elongation and its control
-
Bar-Nahum G., Epshtein V., Ruckenstein A.E., Rafikov R., Mustaev A., and Nudler E. A ratchet mechanism of transcription elongation and its control. Cell 120 (2005) 183-193
-
(2005)
Cell
, vol.120
, pp. 183-193
-
-
Bar-Nahum, G.1
Epshtein, V.2
Ruckenstein, A.E.3
Rafikov, R.4
Mustaev, A.5
Nudler, E.6
-
18
-
-
33645109502
-
Structure and dynamics of RNA polymerase II elongation complex
-
Suenaga A., Okimoto N., Futatsugi N., Hirano Y., Narumi T., Ohno Y., Yanai R., Hirokawa T., Ebisuzaki T., Konagaya A., and Taiji M. Structure and dynamics of RNA polymerase II elongation complex. Biochem. Biophys. Res. Commun. 343 (2006) 90-98
-
(2006)
Biochem. Biophys. Res. Commun.
, vol.343
, pp. 90-98
-
-
Suenaga, A.1
Okimoto, N.2
Futatsugi, N.3
Hirano, Y.4
Narumi, T.5
Ohno, Y.6
Yanai, R.7
Hirokawa, T.8
Ebisuzaki, T.9
Konagaya, A.10
Taiji, M.11
-
19
-
-
49449102926
-
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation
-
Brueckner F., and Cramer P. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat. Struct. Mol. Biol. 15 (2008) 811-818
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 811-818
-
-
Brueckner, F.1
Cramer, P.2
-
20
-
-
57249108333
-
Bridge helix and trigger loop perturbations generate superactive RNA polymerases
-
Tan L., Wiesler S., Trzaska D., Carney H.C., and Weinzierl R.O. Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J. Biol. 7 (2008) 40
-
(2008)
J. Biol.
, Issue.7
, pp. 40
-
-
Tan, L.1
Wiesler, S.2
Trzaska, D.3
Carney, H.C.4
Weinzierl, R.O.5
-
21
-
-
39149093390
-
Structure function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement
-
Naji S., Bertero M.G., Spitalny P., Cramer P., and Thomm M. Structure function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement. Nucleic Acids Res. 36 (2008) 676-687
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 676-687
-
-
Naji, S.1
Bertero, M.G.2
Spitalny, P.3
Cramer, P.4
Thomm, M.5
-
22
-
-
33751235874
-
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
-
Wang D., Bushnell D.A., Westover K.D., Kaplan C.D., and Kornberg R.D. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127 (2006) 941-954
-
(2006)
Cell
, vol.127
, pp. 941-954
-
-
Wang, D.1
Bushnell, D.A.2
Westover, K.D.3
Kaplan, C.D.4
Kornberg, R.D.5
-
23
-
-
0034922711
-
Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction
-
Wang Y., and Gu X. Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics 158 (2001) 1311-1320
-
(2001)
Genetics
, vol.158
, pp. 1311-1320
-
-
Wang, Y.1
Gu, X.2
-
24
-
-
0036107253
-
Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes
-
Gu J., Wang Y., and Gu X. Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes. J. Mol. Evol. 54 (2002) 725-733
-
(2002)
J. Mol. Evol.
, vol.54
, pp. 725-733
-
-
Gu, J.1
Wang, Y.2
Gu, X.3
-
25
-
-
0004232308
-
-
Upper Saddle River, NJ, Prentice Hall
-
Zar J.H. Biostatistical analysis. 4th ed (1999), Upper Saddle River, NJ, Prentice Hall 196-200
-
(1999)
Biostatistical analysis. 4th ed
, pp. 196-200
-
-
Zar, J.H.1
-
26
-
-
0037531306
-
Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I
-
De Carlo S., Carles C., Riva M., and Schultz P. Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I. J. Mol. Biol. 329 (2003) 891-902
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 891-902
-
-
De Carlo, S.1
Carles, C.2
Riva, M.3
Schultz, P.4
-
27
-
-
0036134765
-
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
-
Yang Z., and Swanson W.J. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19 (2002) 49-57
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 49-57
-
-
Yang, Z.1
Swanson, W.J.2
-
28
-
-
0041817651
-
Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases
-
Knudsen B., Miyamoto M.M., Laipis P.J., and Silverman D.N. Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases. Genetics 164 (2003) 1261-1269
-
(2003)
Genetics
, vol.164
, pp. 1261-1269
-
-
Knudsen, B.1
Miyamoto, M.M.2
Laipis, P.J.3
Silverman, D.N.4
-
29
-
-
27844439855
-
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
-
Zhang J., Nielsen R., and Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22 (2005) 2472-2479
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 2472-2479
-
-
Zhang, J.1
Nielsen, R.2
Yang, Z.3
-
30
-
-
0033578701
-
Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution
-
Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., and Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98 (1999) 811-824
-
(1999)
Cell
, vol.98
, pp. 811-824
-
-
Zhang, G.1
Campbell, E.A.2
Minakhin, L.3
Richter, C.4
Severinov, K.5
Darst, S.A.6
-
31
-
-
1142274214
-
Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 angstroms
-
Bushnell D.A., Westover K.D., Davis R.E., and Kornberg R.D. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 angstroms. Science 303 (2004) 983-988
-
(2004)
Science
, vol.303
, pp. 983-988
-
-
Bushnell, D.A.1
Westover, K.D.2
Davis, R.E.3
Kornberg, R.D.4
-
32
-
-
5444275331
-
Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC
-
Chen H.T., and Hahn S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell 119 (2004) 169-180
-
(2004)
Cell
, vol.119
, pp. 169-180
-
-
Chen, H.T.1
Hahn, S.2
-
33
-
-
0242666374
-
Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin
-
Gribaldo S., Casane D., Lopez P., and Philippe H. Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol. Biol. Evol. 20 (2003) 1754-1759
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1754-1759
-
-
Gribaldo, S.1
Casane, D.2
Lopez, P.3
Philippe, H.4
-
34
-
-
0036134757
-
Heterotachy, an important process of protein evolution
-
Lopez P., Casane D., and Philippe H. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19 (2002) 1-7
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
35
-
-
0043244876
-
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
-
Kettenberger H., Armache K.J., and Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114 (2003) 347-357
-
(2003)
Cell
, vol.114
, pp. 347-357
-
-
Kettenberger, H.1
Armache, K.J.2
Cramer, P.3
-
36
-
-
58149163281
-
Malleable machines in transcription regulation: the mediator complex
-
Tóth-Petróczy A., Oldfield C.J., Simon I., Takagi Y., Dunker A.K., Uversky V.N., and Fuxreiter M. Malleable machines in transcription regulation: the mediator complex. PLoS Comput Biol. 4 (2008) e1000251
-
(2008)
PLoS Comput Biol.
, vol.4
-
-
Tóth-Petróczy, A.1
Oldfield, C.J.2
Simon, I.3
Takagi, Y.4
Dunker, A.K.5
Uversky, V.N.6
Fuxreiter, M.7
-
37
-
-
0036671095
-
Structure of the yeast RNA polymerase II holoenzyme: mediator conformation and polymerase interaction
-
Davis J.A., Takagi Y., Kornberg R.D., and Asturias F.A. Structure of the yeast RNA polymerase II holoenzyme: mediator conformation and polymerase interaction. Mol. Cell 10 (2002) 409-415
-
(2002)
Mol. Cell
, vol.10
, pp. 409-415
-
-
Davis, J.A.1
Takagi, Y.2
Kornberg, R.D.3
Asturias, F.A.4
-
38
-
-
0034613012
-
Novel dimerization fold of RAP32/RAP74 in human TFIIF at 1.7 A resolution
-
Gaiser F., Tan S., and Richmond T.J. Novel dimerization fold of RAP32/RAP74 in human TFIIF at 1.7 A resolution. J. Mol. Biol. 302 (2000) 1119-1127
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 1119-1127
-
-
Gaiser, F.1
Tan, S.2
Richmond, T.J.3
-
39
-
-
0028921452
-
Identification of the gene (SSU71/TFG1) encoding the largest subunit of transcription factor TFIIF as a suppressor of a TFIIB mutation in Saccharomyces cerevisiae
-
Sun Z.W., and Hampsey M. Identification of the gene (SSU71/TFG1) encoding the largest subunit of transcription factor TFIIF as a suppressor of a TFIIB mutation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 3127-3131
-
(1995)
Proc. Natl. Acad. Sci. U. S. A.
, vol.92
, pp. 3127-3131
-
-
Sun, Z.W.1
Hampsey, M.2
-
40
-
-
24944549150
-
Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex
-
Freire-Picos M.A., Krishnamurthy S., Sun Z.W., and Hampsey M. Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex. Nucleic Acids Res. 33 (2005) 5045-5052
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5045-5052
-
-
Freire-Picos, M.A.1
Krishnamurthy, S.2
Sun, Z.W.3
Hampsey, M.4
-
41
-
-
0034623005
-
T-Coffee: a novel method for fast and accurate multiple sequence alignment
-
Notredame C., Higgins D.G., and Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
42
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
-
(2003)
Syst. Biol.
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
43
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
44
-
-
27144551715
-
Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
-
Cheng G., Qian B., Samudrala R., and Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res. 33 (2005) 5861-5867
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5861-5867
-
-
Cheng, G.1
Qian, B.2
Samudrala, R.3
Baker, D.4
-
45
-
-
4143051195
-
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior
-
Mayrose I., Graur D., Ben-Tal N., and Pupko T. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol. Biol. Evol. 21 (2004) 1781-1791
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1781-1791
-
-
Mayrose, I.1
Graur, D.2
Ben-Tal, N.3
Pupko, T.4
-
46
-
-
0032728408
-
Statistical methods for testing functional divergence after gene duplication
-
Gu X. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16 (1999) 1664-1674
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1664-1674
-
-
Gu, X.1
-
47
-
-
0035061686
-
Maximum-likelihood approach for gene family evolution under functional divergence
-
Gu X. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18 (2001) 453-464
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 453-464
-
-
Gu, X.1
|