-
1
-
-
45749153508
-
22 Regulation of Termination and Recoding
-
J. D. Dinman, M. J. Berry, 22 Regulation of Termination and Recoding. Cold Spring Harb. Monogr. Arch. 48, 625–654 (2007); https://cshmonographs.org/index.php/monographs/article/view/3291.
-
(2007)
Cold Spring Harb. Monogr. Arch.
, vol.48
, pp. 625-654
-
-
Dinman, J.D.1
Berry, M.J.2
-
3
-
-
84861841297
-
Translation drives mRNA quality control
-
C. J. Shoemaker, R. Green, Translation drives mRNA quality control. Nat. Struct. Mol. Biol. 19, 594–601 (2012).
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 594-601
-
-
Shoemaker, C.J.1
Green, R.2
-
4
-
-
33645277360
-
Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation
-
M. K. Doma, R. Parker, Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440, 561–564 (2006).
-
(2006)
Nature
, vol.440
, pp. 561-564
-
-
Doma, M.K.1
Parker, R.2
-
5
-
-
78649656286
-
Control of translation efficiency in yeast by codon–anticodon interactions
-
D. P. Letzring, K. M. Dean, E. J. Grayhack, Control of translation efficiency in yeast by codon–anticodon interactions. RNA 16, 2516–2528 (2010).
-
(2010)
RNA
, vol.16
, pp. 2516-2528
-
-
Letzring, D.P.1
Dean, K.M.2
Grayhack, E.J.3
-
6
-
-
66849136862
-
Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome
-
L. N. Dimitrova, K. Kuroha, T. Tatematsu, T. Inada, Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome. J. Biol. Chem. 284, 10343–10352 (2009).
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 10343-10352
-
-
Dimitrova, L.N.1
Kuroha, K.2
Tatematsu, T.3
Inada, T.4
-
7
-
-
78649472341
-
Receptor for activated C kinase 1 stimulates nascent polypeptide-dependent translation arrest
-
K. Kuroha, M. Akamatsu, L. Dimitrova, T. Ito, Y. Kato, K. Shirahige, T. Inada, Receptor for activated C kinase 1 stimulates nascent polypeptide-dependent translation arrest. EMBO Rep. 11, 956–961 (2010).
-
(2010)
EMBO Rep.
, vol.11
, pp. 956-961
-
-
Kuroha, K.1
Akamatsu, M.2
Dimitrova, L.3
Ito, T.4
Kato, Y.5
Shirahige, K.6
Inada, T.7
-
8
-
-
84871523350
-
A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress
-
O. Brandman, J. Stewart-Ornstein, D. Wong, A. Larson, C. C. Williams, G. W. Li, S. Zhou, D. King, P. S. Shen, J. Weibezahn, J. G. Dunn, S. Rouskin, T. Inada, A. Frost, J. S. Weissman, A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell 151, 1042–1054 (2012).
-
(2012)
Cell
, vol.151
, pp. 1042-1054
-
-
Brandman, O.1
Stewart-Ornstein, J.2
Wong, D.3
Larson, A.4
Williams, C.C.5
Li, G.W.6
Zhou, S.7
King, D.8
Shen, P.S.9
Weibezahn, J.10
Dunn, J.G.11
Rouskin, S.12
Inada, T.13
Frost, A.14
Weissman, J.S.15
-
9
-
-
54249096045
-
Electrostatics in the ribosomal tunnel modulate chain elongation rates
-
J. Lu, C. Deutsch, Electrostatics in the ribosomal tunnel modulate chain elongation rates. J. Mol. Biol. 384, 73–86 (2008).
-
(2008)
J. Mol. Biol.
, vol.384
, pp. 73-86
-
-
Lu, J.1
Deutsch, C.2
-
10
-
-
84925047574
-
Ribosomes slide on lysine-encoding homopolymeric A stretches
-
K. S. Koutmou, A. P. Schuller, J. L. Brunelle, A. Radhakrishnan, S. Djuranovic, R. Green, Ribosomes slide on lysine-encoding homopolymeric A stretches. eLife 4, e05534 (2015).
-
(2015)
eLife
, vol.4
, pp. e05534
-
-
Koutmou, K.S.1
Schuller, A.P.2
Brunelle, J.L.3
Radhakrishnan, A.4
Djuranovic, S.5
Green, R.6
-
11
-
-
84861456756
-
Dom34:Hbs1 plays a general role in quality-control systems by dissociation of a stalled ribosome at the 3′ end of aberrant mRNA
-
T. Tsuboi, K. Kuroha, K. Kudo, S. Makino, E. Inoue, I. Kashima, T. Inada, Dom34:Hbs1 plays a general role in quality-control systems by dissociation of a stalled ribosome at the 3′ end of aberrant mRNA. Mol. Cell 46, 518–529 (2012).
-
(2012)
Mol. Cell
, vol.46
, pp. 518-529
-
-
Tsuboi, T.1
Kuroha, K.2
Kudo, K.3
Makino, S.4
Inoue, E.5
Kashima, I.6
Inada, T.7
-
12
-
-
0037039436
-
Amino acid runs in eukaryotic proteomes and disease associations
-
S. Karlin, L. Brocchieri, A. Bergman, J. Mrazek, A. J. Gentles, Amino acid runs in eukaryotic proteomes and disease associations. Proc. Natl. Acad. Sci. U.S.A. 99, 333–338 (2002).
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 333-338
-
-
Karlin, S.1
Brocchieri, L.2
Bergman, A.3
Mrazek, J.4
Gentles, A.J.5
-
13
-
-
84859632747
-
MiRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay
-
S. Djuranovic, A. Nahvi, R. Green, miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237–240 (2012).
-
(2012)
Science
, vol.336
, pp. 237-240
-
-
Djuranovic, S.1
Nahvi, A.2
Green, R.3
-
14
-
-
0034948006
-
Polymerase slippage at vesicular stomatitis virus gene junctions to generate poly(A) is regulated by the upstream 3′-AUAC-5′ tetranucleotide: Implications for the mechanism of transcription termination
-
J. N. Barr, G. W. Wertz, Polymerase slippage at vesicular stomatitis virus gene junctions to generate poly(A) is regulated by the upstream 3′-AUAC-5′ tetranucleotide: Implications for the mechanism of transcription termination. J. Virol. 75, 6901–6913 (2001).
-
(2001)
J. Virol.
, vol.75
, pp. 6901-6913
-
-
Barr, J.N.1
Wertz, G.W.2
-
15
-
-
0017577805
-
Inhibition of translation in eukaryotic systems by harringtonine
-
M. Fresno, A. Jiménez, D. Vázquez, Inhibition of translation in eukaryotic systems by harringtonine. Eur. J. Biochem. 72, 323–330 (1977).
-
(1977)
Eur. J. Biochem.
, vol.72
, pp. 323-330
-
-
Fresno, M.1
Jiménez, A.2
Vázquez, D.3
-
16
-
-
84894318608
-
Ribosome profiling: New views of translation, from single codons to genome scale
-
N. T. Ingolia, Ribosome profiling: New views of translation, from single codons to genome scale. Nat. Rev. Genet. 15, 205–213 (2014).
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 205-213
-
-
Ingolia, N.T.1
-
17
-
-
84875465945
-
Positively charged residues are the major determinants of ribosomal velocity
-
C. A. Charneski, L. D. Hurst, Positively charged residues are the major determinants of ribosomal velocity. PLOS Biol. 11, e1001508 (2013).
-
(2013)
PLOS Biol.
, vol.11
, pp. e1001508
-
-
Charneski, C.A.1
Hurst, L.D.2
-
18
-
-
84891767394
-
RefSeq: An update on mammalian reference sequences
-
K. D. Pruitt, G. R. Brown, S. M. Hiatt, F. Thibaud-Nissen, A. Astashyn, O. Ermolaeva, C. M. Farrell, J. Hart, M. J. Landrum, K. M. McGarvey, M. R. Murphy, N. A. O’Leary, S. Pujar, B. Rajput, S. H. Rangwala, L. D. Riddick, A. Shkeda, H. Sun, P. Tamez, R. E. Tully, C. Wallin, D. Webb, J. Weber, W. Wu, M. DiCuccio, P. Kitts, D. R. Maglott, T. D. Murphy, J. M. Ostell, RefSeq: An update on mammalian reference sequences. Nucleic Acids Res. 42, D756–D763 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D756-D763
-
-
Pruitt, K.D.1
Brown, G.R.2
Hiatt, S.M.3
Thibaud-Nissen, F.4
Astashyn, A.5
Ermolaeva, O.6
Farrell, C.M.7
Hart, J.8
Landrum, M.J.9
McGarvey, K.M.10
Murphy, M.R.11
O’Leary, N.A.12
Pujar, S.13
Rajput, B.14
Rangwala, S.H.15
Riddick, L.D.16
Shkeda, A.17
Sun, H.18
Tamez, P.19
Tully, R.E.20
Wallin, C.21
Webb, D.22
Weber, J.23
Wu, W.24
DiCuccio, M.25
Kitts, P.26
Maglott, D.R.27
Murphy, T.D.28
Ostell, J.M.29
more..
-
19
-
-
84883618312
-
The RasGAP gene, RASAL2, is a tumor and metastasis suppressor
-
S. K. McLaughlin, S. N. Olsen, B. Dake, T. De Raedt, E. Lim, R. T. Bronson, R. Beroukhim, K. Polyak, M. Brown, C. Kuperwasser, K. Cichowski, The RasGAP gene, RASAL2, is a tumor and metastasis suppressor. Cancer Cell 24, 365–378 (2013).
-
(2013)
Cancer Cell
, vol.24
, pp. 365-378
-
-
McLaughlin, S.K.1
Olsen, S.N.2
Dake, B.3
De Raedt, T.4
Lim, E.5
Bronson, R.T.6
Beroukhim, R.7
Polyak, K.8
Brown, M.9
Kuperwasser, C.10
Cichowski, K.11
-
20
-
-
34047121587
-
The gateway pDEST17 expression vector encodes a −1 ribosomal frameshifting sequence
-
E. J. Belfield, R. K. Hughes, N. Tsesmetzis, M. J. Naldrett, R. Casey, The gateway pDEST17 expression vector encodes a −1 ribosomal frameshifting sequence. Nucleic Acids Res. 35, 1322–1332 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 1322-1332
-
-
Belfield, E.J.1
Hughes, R.K.2
Tsesmetzis, N.3
Naldrett, M.J.4
Casey, R.5
-
21
-
-
84906794802
-
Dynamic pathways of −1 translational frameshifting
-
J. Chen, A. Petrov, M. Johansson, A. Tsai, S. E. O’Leary, J. D. Puglisi, Dynamic pathways of −1 translational frameshifting. Nature 512, 328–332 (2014).
-
(2014)
Nature
, vol.512
, pp. 328-332
-
-
Chen, J.1
Petrov, A.2
Johansson, M.3
Tsai, A.4
O’Leary, S.E.5
Puglisi, J.D.6
-
22
-
-
84923378894
-
Ribosome excursions during mRNA translocation mediate broad branching of frameshift pathways
-
S. Yan, J. D. Wen, C. Bustamante, I. Tinoco Jr., Ribosome excursions during mRNA translocation mediate broad branching of frameshift pathways. Cell 160, 870–881 (2015).
-
(2015)
Cell
, vol.160
, pp. 870-881
-
-
Yan, S.1
Wen, J.D.2
Bustamante, C.3
Tinoco, I.4
-
23
-
-
84946040120
-
COSMIC: Exploring the world’s knowledge of somatic mutations in human cancer
-
S. A. Forbes, D. Beare, P. Gunasekaran, K. Leung, N. Bindal, H. Boutselakis, M. Ding, S. Bamford, C. Cole, S. Ward, C. Y. Kok, M. Jia, T. De, J. W. Teague, M. R. Stratton, U. McDermott, P. J. Campbell, COSMIC: Exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805–D811 (2014).
-
(2014)
Nucleic Acids Res.
, vol.43
, pp. D805-D811
-
-
Forbes, S.A.1
Beare, D.2
Gunasekaran, P.3
Leung, K.4
Bindal, N.5
Boutselakis, H.6
Ding, M.7
Bamford, S.8
Cole, C.9
Ward, S.10
Kok, C.Y.11
Jia, M.12
De, T.13
Teague, J.W.14
Stratton, M.R.15
McDermott, U.16
Campbell, P.J.17
-
24
-
-
79954611142
-
Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast
-
A. T. Belew, V. M. Advani, J. D. Dinman, Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast. Nucleic Acids Res. 39, 2799–2808 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 2799-2808
-
-
Belew, A.T.1
Advani, V.M.2
Dinman, J.D.3
-
25
-
-
84906561882
-
Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway
-
A. T. Belew, A. Meskauskas, S. Musalgaonkar, V. M. Advani, S. O. Sulima, W. K. Kasprzak, B. A. Shapiro, J. D. Dinman, Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway. Nature 512, 265–269 (2014).
-
(2014)
Nature
, vol.512
, pp. 265-269
-
-
Belew, A.T.1
Meskauskas, A.2
Musalgaonkar, S.3
Advani, V.M.4
Sulima, S.O.5
Kasprzak, W.K.6
Shapiro, B.A.7
Dinman, J.D.8
-
26
-
-
0034704201
-
Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon
-
J. Lykke-Andersen, M. D. Shu, J. A. Steitz, Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103, 1121–1131 (2000).
-
(2000)
Cell
, vol.103
, pp. 1121-1131
-
-
Lykke-Andersen, J.1
Shu, M.D.2
Steitz, J.A.3
-
27
-
-
0035801373
-
The exon–exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay
-
H. Le Hir, D. Gatfield, E. Izaurralde, M. J. Moore, The exon–exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20, 4987–4997 (2001).
-
(2001)
EMBO J.
, vol.20
, pp. 4987-4997
-
-
Le Hir, H.1
Gatfield, D.2
Izaurralde, E.3
Moore, M.J.4
-
29
-
-
84888617099
-
Organizing principles of mammalian nonsense-mediated mRNA decay
-
M. W.-L. Popp, L. E. Maquat, Organizing principles of mammalian nonsense-mediated mRNA decay. Annu. Rev. Genet. 47, 139–165 (2013).
-
(2013)
Annu. Rev. Genet.
, vol.47
, pp. 139-165
-
-
Popp, M.W.-L.1
Maquat, L.E.2
-
30
-
-
84903485906
-
Exposing synonymous mutations
-
R. C. Hunt, V. L. Simhadri, M. Iandoli, Z. E. Sauna, C. Kimchi-Sarfaty, Exposing synonymous mutations. Trends Genet. 30, 308–321 (2014).
-
(2014)
Trends Genet.
, vol.30
, pp. 308-321
-
-
Hunt, R.C.1
Simhadri, V.L.2
Iandoli, M.3
Sauna, Z.E.4
Kimchi-Sarfaty, C.5
-
31
-
-
0035173378
-
DbSNP: The NCBI database of genetic variation
-
S. T. Sherry, M. H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski, K. Sirotkin, dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.H.2
Kholodov, M.3
Baker, J.4
Phan, L.5
Smigielski, E.M.6
Sirotkin, K.7
-
32
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
G. S. Slater, E. Birney, Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.1
Birney, E.2
-
33
-
-
84905836835
-
Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors
-
C. Gonzalez, J. S. Sims, N. Hornstein, A. Mela, F. Garcia, L. Lei, D. A. Gass, B. Amendolara, J. N. Bruce, P. Canoll, P. A. Sims, Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors. J. Neurosci. 34, 10924–10936 (2014).
-
(2014)
J. Neurosci.
, vol.34
, pp. 10924-10936
-
-
Gonzalez, C.1
Sims, J.S.2
Hornstein, N.3
Mela, A.4
Garcia, F.5
Lei, L.6
Gass, D.A.7
Amendolara, B.8
Bruce, J.N.9
Canoll, P.10
Sims, P.A.11
-
34
-
-
84890231951
-
Ribosome profiling reveals features of normal and disease-associated mitochondrial translation
-
K. Rooijers, F. Loayza-Puch, L. G. Nijtmans, R. Agami, Ribosome profiling reveals features of normal and disease-associated mitochondrial translation. Nat. Commun. 4, 2886 (2013).
-
(2013)
Nat. Commun.
, vol.4
, pp. 2886
-
-
Rooijers, K.1
Loayza-Puch, F.2
Nijtmans, L.G.3
Agami, R.4
-
35
-
-
84876093209
-
P53 induces transcriptional and translational programs to suppress cell proliferation and growth
-
F. Loayza-Puch, J. Drost, K. Rooijers, R. Lopes, R. Elkon, R. Agami, p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol. 14, R32 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R32
-
-
Loayza-Puch, F.1
Drost, J.2
Rooijers, K.3
Lopes, R.4
Elkon, R.5
Agami, R.6
-
36
-
-
84864453787
-
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
-
N. T. Ingolia, G. A. Brar, S. Rouskin, A. M. McGeachy, J. S. Weissman, The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550 (2012).
-
(2012)
Nat. Protoc.
, vol.7
, pp. 1534-1550
-
-
Ingolia, N.T.1
Brar, G.A.2
Rouskin, S.3
McGeachy, A.M.4
Weissman, J.S.5
-
37
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
B. Langmead, C. Trapnell, M. Pop, S. L. Salzberg, Ultrafast and memory-efficient 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
-
38
-
-
84878496035
-
From mouse to human: Evolutionary genomics analysis of human orthologs of essential genes
-
B. Georgi, B. F. Voight, M. Bućan, From mouse to human: Evolutionary genomics analysis of human orthologs of essential genes. PLOS Genet. 9, e1003484 (2013).
-
(2013)
PLOS Genet.
, vol.9
-
-
Georgi, B.1
Voight, B.F.2
Bućan, M.3
|