-
1
-
-
60149091189
-
Regulation of translation initiation in eukaryotes: Mechanisms and biological targets
-
Sonenberg, N. and Hinnebusch, A.G. (2009) Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell, 136, 731-745.
-
(2009)
Cell
, vol.136
, pp. 731-745
-
-
Sonenberg, N.1
Hinnebusch, A.G.2
-
2
-
-
75149196287
-
The mechanism of eukaryotic translation initiation and principles of its regulation
-
Jackson, R.J., Hellen, C.U. and Pestova, T.V. (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol., 11, 113-127.
-
(2010)
Nat. Rev. Mol. Cell Biol.
, vol.11
, pp. 113-127
-
-
Jackson, R.J.1
Hellen, C.U.2
Pestova, T.V.3
-
3
-
-
0037112055
-
The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection
-
Pestova, T.V. and Kolupaeva, V.G. (2002) The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev., 16, 2906-2922.
-
(2002)
Genes Dev.
, vol.16
, pp. 2906-2922
-
-
Pestova, T.V.1
Kolupaeva, V.G.2
-
4
-
-
0033006919
-
EIF4E activity is regulated at multiple levels
-
Raught, B. and Gingras, A.C. (1999) eIF4E activity is regulated at multiple levels. Int. J. Biochem. Cell Biol., 31, 43-57.
-
(1999)
Int. J. Biochem. Cell Biol.
, vol.31
, pp. 43-57
-
-
Raught, B.1
Gingras, A.C.2
-
5
-
-
79251570260
-
Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide
-
Park, E.H., Zhang, F., Warringer, J., Sunnerhagen, P. and Hinnebusch, A.G. (2011) Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide. BMC Genomics, 12, 68.
-
(2011)
BMC Genomics
, vol.12
, pp. 68
-
-
Park, E.H.1
Zhang, F.2
Warringer, J.3
Sunnerhagen, P.4
Hinnebusch, A.G.5
-
6
-
-
77949353765
-
Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae
-
Clarkson, B.K., Gilbert, W.V. and Doudna, J.A. (2010) Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS One, 5, e9114.
-
(2010)
PLoS One
, vol.5
-
-
Clarkson, B.K.1
Gilbert, W.V.2
Doudna, J.A.3
-
7
-
-
0242669945
-
Regulation of mRNA translation by 50-and 30-UTR-binding factors
-
Wilkie, G.S., Dickson, K.S. and Gray, N.K. (2003) Regulation of mRNA translation by 50-and 30-UTR-binding factors. Trends Biochem. Sci., 28, 182-188.
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 182-188
-
-
Wilkie, G.S.1
Dickson, K.S.2
Gray, N.K.3
-
8
-
-
0036207282
-
Untranslated regions of mRNAs
-
REVIEWS0004
-
Mignone, F., Gissi, C., Liuni, S. and Pesole, G. (2002) Untranslated regions of mRNAs. Genome Biol., 3, REVIEWS0004.
-
(2002)
Genome Biol.
, vol.3
-
-
Mignone, F.1
Gissi, C.2
Liuni, S.3
Pesole, G.4
-
9
-
-
61649096857
-
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast
-
Lawless, C., Pearson, R.D., Selley, J.N., Smirnova, J.B., Grant, C.M., Ashe, M.P., Pavitt, G.D. and Hubbard, S.J. (2009) Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics, 10, 7.
-
(2009)
BMC Genomics
, vol.10
, pp. 7
-
-
Lawless, C.1
Pearson, R.D.2
Selley, J.N.3
Smirnova, J.B.4
Grant, C.M.5
Ashe, M.P.6
Pavitt, G.D.7
Hubbard, S.J.8
-
10
-
-
0028019573
-
Potential secondary structure at the translational start domain of eukaryotic and prokaryotic mRNAs
-
Ganoza, M.C. and Louis, B.G. (1994) Potential secondary structure at the translational start domain of eukaryotic and prokaryotic mRNAs. Biochimie, 76, 428-439.
-
(1994)
Biochimie
, vol.76
, pp. 428-439
-
-
Ganoza, M.C.1
Louis, B.G.2
-
11
-
-
77958493102
-
The mRNA landscape at yeast translation initiation sites
-
Robbins-Pianka, A., Rice, M.D. and Weir, M.P. (2010) The mRNA landscape at yeast translation initiation sites. Bioinformatics, 26, 2651-2655.
-
(2010)
Bioinformatics
, vol.26
, pp. 2651-2655
-
-
Robbins-Pianka, A.1
Rice, M.D.2
Weir, M.P.3
-
12
-
-
77649198142
-
A universal trend of reduced mRNA stability near the translation- initiation site in prokaryotes and eukaryotes
-
Gu, W., Zhou, T. and Wilke, C.O. (2010) A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput. Biol., 6, e1000664.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Gu, W.1
Zhou, T.2
Wilke, C.O.3
-
13
-
-
0033005239
-
The role of the 5' untranslated region of an mRNA in translation regulation during development
-
van der Velden, A.W. and Thomas, A.A. (1999) The role of the 5' untranslated region of an mRNA in translation regulation during development. Int. J. Biochem. Cell Biol., 31, 87-106.
-
(1999)
Int. J. Biochem. Cell Biol.
, vol.31
, pp. 87-106
-
-
Van Der Velden, A.W.1
Thomas, A.A.2
-
14
-
-
55449088127
-
Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast
-
Ringner, M. and Krogh, M. (2005) Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput. Biol., 1, e72.
-
(2005)
PLoS Comput. Biol.
, vol.1
-
-
Ringner, M.1
Krogh, M.2
-
15
-
-
0037311233
-
Eukaryotic translation initiation factors and regulators
-
Sonenberg, N. and Dever, T.E. (2003) Eukaryotic translation initiation factors and regulators. Curr. Opin. Struct. Biol., 13, 56-63.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 56-63
-
-
Sonenberg, N.1
Dever, T.E.2
-
16
-
-
2542506326
-
The mRNA cap-binding protein eIF4E in post-transcriptional gene expression
-
von der Haar, T., Gross, J.D., Wagner, G. and McCarthy, J.E. (2004) The mRNA cap-binding protein eIF4E in post-transcriptional gene expression. Nat. Struct. Mol. Biol., 11, 503-511.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 503-511
-
-
Von Der Haar, T.1
Gross, J.D.2
Wagner, G.3
McCarthy, J.E.4
-
17
-
-
77954373163
-
Molecular view of 43 S complex formation and start site selection in eukaryotic translation initiation
-
Lorsch, J.R. and Dever, T.E. (2010) Molecular view of 43 S complex formation and start site selection in eukaryotic translation initiation. J. Biol. Chem., 285, 21203-21207.
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 21203-21207
-
-
Lorsch, J.R.1
Dever, T.E.2
-
18
-
-
31344452991
-
Folding transitions during assembly of the eukaryotic mRNA cap-binding complex
-
von der Haar, T., Oku, Y., Ptushkina, M., Moerke, N., Wagner, G., Gross, J.D. and McCarthy, J.E. (2006) Folding transitions during assembly of the eukaryotic mRNA cap-binding complex. J. Mol. Biol., 356, 982-992.
-
(2006)
J. Mol. Biol.
, vol.356
, pp. 982-992
-
-
Von Der Haar, T.1
Oku, Y.2
Ptushkina, M.3
Moerke, N.4
Wagner, G.5
Gross, J.D.6
McCarthy, J.E.7
-
19
-
-
0038719941
-
RNA-binding activity of translation initiation factor eIF4G1 from Saccharomyces cerevisiae
-
Berset, C., Zurbriggen, A., Djafarzadeh, S., Altmann, M. and Trachsel, H. (2003) RNA-binding activity of translation initiation factor eIF4G1 from Saccharomyces cerevisiae. RNA, 9, 871-880.
-
(2003)
RNA
, vol.9
, pp. 871-880
-
-
Berset, C.1
Zurbriggen, A.2
Djafarzadeh, S.3
Altmann, M.4
Trachsel, H.5
-
20
-
-
78751609906
-
Multiple elements in the eIF4G1 N-terminus promote assembly of eIF4G1*PABP mRNPs in vivo
-
Park, E.H., Walker, S.E., Lee, J.M., Rothenburg, S., Lorsch, J.R. and Hinnebusch, A.G. (2011) Multiple elements in the eIF4G1 N-terminus promote assembly of eIF4G1*PABP mRNPs in vivo. EMBO J., 30, 302-316.
-
(2011)
EMBO J.
, vol.30
, pp. 302-316
-
-
Park, E.H.1
Walker, S.E.2
Lee, J.M.3
Rothenburg, S.4
Lorsch, J.R.5
Hinnebusch, A.G.6
-
22
-
-
38549104033
-
RNA association or phosphorylation of the RS domain prevents aggregation of RS domain-containing proteins
-
Nikolakaki, E., Drosou, V., Sanidas, I., Peidis, P., Papamarcaki, T., Iakoucheva, L.M. and Giannakouros, T. (2008) RNA association or phosphorylation of the RS domain prevents aggregation of RS domain-containing proteins. Biochim. Biophys. Acta, 1780, 214-225.
-
(2008)
Biochim. Biophys. Acta
, vol.1780
, pp. 214-225
-
-
Nikolakaki, E.1
Drosou, V.2
Sanidas, I.3
Peidis, P.4
Papamarcaki, T.5
Iakoucheva, L.M.6
Giannakouros, T.7
-
23
-
-
29244489033
-
Simulation of non-specific protein-mRNA interactions
-
Magee, J. and Warwicker, J. (2005) Simulation of non-specific protein-mRNA interactions. Nucleic Acids Res., 33, 6694-6699.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6694-6699
-
-
Magee, J.1
Warwicker, J.2
-
24
-
-
78650424915
-
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins
-
Cridge, A.G., Castelli, L.M., Smirnova, J.B., Selley, J.N., Rowe, W., Hubbard, S.J., McCarthy, J.E., Ashe, M.P., Grant, C.M. and Pavitt, G.D. (2010) Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins. Nucleic Acids Res., 38, 8039-8050.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 8039-8050
-
-
Cridge, A.G.1
Castelli, L.M.2
Smirnova, J.B.3
Selley, J.N.4
Rowe, W.5
Hubbard, S.J.6
McCarthy, J.E.7
Ashe, M.P.8
Grant, C.M.9
Pavitt, G.D.10
-
25
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz, M., Wan, Y., Mazor, E., Rinn, J.L., Nutter, R.C., Chang, H.Y. and Segal, E. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature, 467, 103-107.
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
Wan, Y.2
Mazor, E.3
Rinn, J.L.4
Nutter, R.C.5
Chang, H.Y.6
Segal, E.7
-
26
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M. and Snyder, M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
27
-
-
54949148332
-
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
-
Hogan, D.J., Riordan, D.P., Gerber, A.P., Herschlag, D. and Brown, P.O. (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol., 6, e255.
-
(2008)
PLoS Biol.
, vol.6
-
-
Hogan, D.J.1
Riordan, D.P.2
Gerber, A.P.3
Herschlag, D.4
Brown, P.O.5
-
28
-
-
79952351662
-
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
-
Riordan, D.P., Herschlag, D. and Brown, P.O. (2011) Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome. Nucleic Acids Res., 39, 1501-1509.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 1501-1509
-
-
Riordan, D.P.1
Herschlag, D.2
Brown, P.O.3
-
29
-
-
0042622240
-
GlobPlot: Exploring protein sequences for globularity and disorder
-
Linding, R., Russell, R.B., Neduva, V. and Gibson, T.J. (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res., 31, 3701-3708.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3701-3708
-
-
Linding, R.1
Russell, R.B.2
Neduva, V.3
Gibson, T.J.4
-
30
-
-
24044515001
-
FoldIndex: A simple tool to predict whether a given protein sequence is intrinsically unfolded
-
Prilusky, J., Felder, C.E., Zeev-Ben-Mordehai, T., Rydberg, E.H., Man, O., Beckmann, J.S., Silman, I. and Sussman, J.L. (2005) FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics, 21, 3435-3438.
-
(2005)
Bioinformatics
, vol.21
, pp. 3435-3438
-
-
Prilusky, J.1
Felder, C.E.2
Zeev-Ben-Mordehai, T.3
Rydberg, E.H.4
Man, O.5
Beckmann, J.S.6
Silman, I.7
Sussman, J.L.8
-
31
-
-
0032586777
-
Simplified methods for pKa and acid pH-dependent stability estimation in proteins: Removing dielectric and counterion boundaries
-
Warwicker, J. (1999) Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries. Protein Sci., 8, 418-425.
-
(1999)
Protein Sci.
, vol.8
, pp. 418-425
-
-
Warwicker, J.1
-
32
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
33
-
-
0031793928
-
Iterated profile searches with PSI-BLAST: A tool for discovery in protein databases
-
Altschul, S.F. and Koonin, E.V. (1998) Iterated profile searches with PSI-BLAST: a tool for discovery in protein databases. Trends Biochem. Sci., 23, 444-447.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 444-447
-
-
Altschul, S.F.1
Koonin, E.V.2
-
34
-
-
77954257799
-
ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy, H., Erez, E., Martz, E., Pupko, T. and Ben-Tal, N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
35
-
-
12344269924
-
GO::TermFinder: Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
-
Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M. and Sherlock, G. (2004) GO::TermFinder: open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715.
-
(2004)
Bioinformatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
Jin, H.4
Botstein, D.5
Cherry, J.M.6
Sherlock, G.7
-
36
-
-
3042668591
-
Comparative analysis of orthologous eukaryotic mRNAs: Potential hidden functional signals
-
Shabalina, S.A., Ogurtsov, A.Y., Rogozin, I.B., Koonin, E.V. and Lipman, D.J. (2004) Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res., 32, 1774-1782.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1774-1782
-
-
Shabalina, S.A.1
Ogurtsov, A.Y.2
Rogozin, I.B.3
Koonin, E.V.4
Lipman, D.J.5
-
37
-
-
18844442600
-
Ty1 copy number dynamics in Saccharomyces
-
Garfinkel, D.J., Nyswaner, K.M., Stefanisko, K.M., Chang, C. and Moore, S.P. (2005) Ty1 copy number dynamics in Saccharomyces. Genetics, 169, 1845-1857.
-
(2005)
Genetics
, vol.169
, pp. 1845-1857
-
-
Garfinkel, D.J.1
Nyswaner, K.M.2
Stefanisko, K.M.3
Chang, C.4
Moore, S.P.5
-
38
-
-
78751678071
-
Function of a retrotransposon nucleocapsid protein
-
Sandmeyer, S.B. and Clemens, K.A. (2010) Function of a retrotransposon nucleocapsid protein. RNA Biol., 7, 642-654.
-
(2010)
RNA Biol.
, vol.7
, pp. 642-654
-
-
Sandmeyer, S.B.1
Clemens, K.A.2
-
39
-
-
83855162728
-
The structure of the eukaryotic ribosome at 3.0 A resolution
-
Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G. and Yusupov, M. (2011) The structure of the eukaryotic ribosome at 3.0 A resolution. Science, 334, 1524-1529.
-
(2011)
Science
, vol.334
, pp. 1524-1529
-
-
Ben-Shem, A.1
De Garreau Loubresse, N.2
Melnikov, S.3
Jenner, L.4
Yusupova, G.5
Yusupov, M.6
-
40
-
-
34547462095
-
Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity
-
Borg, M., Mittag, T., Pawson, T., Tyers, M., Forman-Kay, J.D. and Chan, H.S. (2007) Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. Proc. Natl Acad. Sci. USA, 104, 9650-9655.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 9650-9655
-
-
Borg, M.1
Mittag, T.2
Pawson, T.3
Tyers, M.4
Forman-Kay, J.D.5
Chan, H.S.6
-
41
-
-
76649114676
-
Protein dynamics and conformational disorder in molecular recognition
-
Mittag, T., Kay, L.E. and Forman-Kay, J.D. (2010) Protein dynamics and conformational disorder in molecular recognition. J. Mol. Recognit., 23, 105-116.
-
(2010)
J. Mol. Recognit.
, vol.23
, pp. 105-116
-
-
Mittag, T.1
Kay, L.E.2
Forman-Kay, J.D.3
-
42
-
-
37649033126
-
Complex formation in systems of oppositely charged polyelectrolytes: A molecular dynamics simulation study
-
Winkler, R.G., Steinhauser, M.O. and Reineker, P. (2002) Complex formation in systems of oppositely charged polyelectrolytes: a molecular dynamics simulation study. Phys. Rev., 66, 021802.
-
(2002)
Phys. Rev.
, vol.66
, pp. 021802
-
-
Winkler, R.G.1
Steinhauser, M.O.2
Reineker, P.3
-
43
-
-
33846079666
-
Structure of polyelectrolyte complexes by Brownian dynamics simulation: Effects of the bond length asymmetry of the polyelectrolytes
-
Trejo-Ramos, M.A., Tristan, F., Menchaca, J.L., Perez, E. and Chavez-Paez, M. (2007) Structure of polyelectrolyte complexes by Brownian dynamics simulation: effects of the bond length asymmetry of the polyelectrolytes. J. Chem. Phys., 126, 014901.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014901
-
-
Trejo-Ramos, M.A.1
Tristan, F.2
Menchaca, J.L.3
Perez, E.4
Chavez-Paez, M.5
-
44
-
-
0028326761
-
New insights into the auxiliary domains of eukaryotic RNA binding proteins
-
Biamonti, G. and Riva, S. (1994) New insights into the auxiliary domains of eukaryotic RNA binding proteins. FEBS Lett., 340, 1-8.
-
(1994)
FEBS Lett.
, vol.340
, pp. 1-8
-
-
Biamonti, G.1
Riva, S.2
-
45
-
-
35548943472
-
Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement
-
Clore, G.M., Tang, C. and Iwahara, J. (2007) Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement. Curr. Opin. Struct. Biol., 17, 603-616.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 603-616
-
-
Clore, G.M.1
Tang, C.2
Iwahara, J.3
-
46
-
-
0347281686
-
Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E
-
Gross, J.D., Moerke, N.J., von der Haar, T., Lugovskoy, A.A., Sachs, A.B., McCarthy, J.E. and Wagner, G. (2003) Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell, 115, 739-750.
-
(2003)
Cell
, vol.115
, pp. 739-750
-
-
Gross, J.D.1
Moerke, N.J.2
Von Der Haar, T.3
Lugovskoy, A.A.4
Sachs, A.B.5
McCarthy, J.E.6
Wagner, G.7
|