-
1
-
-
84930691710
-
Mechanisms and regulation of alternative pre-mRNA splicing
-
Lee Y, Rio DC. Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem 2015, 84:291–323.
-
(2015)
Annu Rev Biochem
, vol.84
, pp. 291-323
-
-
Lee, Y.1
Rio, D.C.2
-
2
-
-
84937858431
-
The elaborate architecture of RNA
-
Dolgin E. The elaborate architecture of RNA. Nature 2015, 523:398–399.
-
(2015)
Nature
, vol.523
, pp. 398-399
-
-
Dolgin, E.1
-
3
-
-
58149487592
-
Structural and functional studies of the promoter element for dengue virus RNA peplication
-
Lodeiro MF, Filomatori CV, Gamarnik AV. Structural and functional studies of the promoter element for dengue virus RNA peplication. J Virol 2009, 83:993–1008.
-
(2009)
J Virol
, vol.83
, pp. 993-1008
-
-
Lodeiro, M.F.1
Filomatori, C.V.2
Gamarnik, A.V.3
-
4
-
-
78751662374
-
RNA folding in living cells
-
Zemora G, Waldsich C. RNA folding in living cells. RNA Biol 2010, 7:634–641.
-
(2010)
RNA Biol
, vol.7
, pp. 634-641
-
-
Zemora, G.1
Waldsich, C.2
-
5
-
-
77952876523
-
RNA-mediated regulation in bacteria: from natural to artificial systems
-
Lioliou E, Romilly C, Romby P, Fechter P. RNA-mediated regulation in bacteria: from natural to artificial systems. N Biotechnol 2010, 27:222–235.
-
(2010)
N Biotechnol
, vol.27
, pp. 222-235
-
-
Lioliou, E.1
Romilly, C.2
Romby, P.3
Fechter, P.4
-
7
-
-
60149112933
-
The dynamic landscapes of RNA architecture
-
Cruz JA, Westhof E. The dynamic landscapes of RNA architecture. Cell 2009, 136:604–609.
-
(2009)
Cell
, vol.136
, pp. 604-609
-
-
Cruz, J.A.1
Westhof, E.2
-
8
-
-
80051989609
-
Understanding the transcriptome through RNA structure
-
Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY. Understanding the transcriptome through RNA structure. Nat Rev Genet 2011, 12:641–655.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 641-655
-
-
Wan, Y.1
Kertesz, M.2
Spitale, R.C.3
Segal, E.4
Chang, H.Y.5
-
9
-
-
84857080591
-
Functional complexity and regulation through RNA dynamics
-
Dethoff EA, Chugh J, Mustoe AM, Al-Hashimi HM. Functional complexity and regulation through RNA dynamics. Nature 2012, 482:322–330.
-
(2012)
Nature
, vol.482
, pp. 322-330
-
-
Dethoff, E.A.1
Chugh, J.2
Mustoe, A.M.3
Al-Hashimi, H.M.4
-
10
-
-
84886034438
-
On the importance of cotranscriptional RNA structure formation
-
Lai D, Proctor JR, Meyer IM. On the importance of cotranscriptional RNA structure formation. RNA 2013, 19:1461–1473.
-
(2013)
RNA
, vol.19
, pp. 1461-1473
-
-
Lai, D.1
Proctor, J.R.2
Meyer, I.M.3
-
13
-
-
77955817276
-
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
-
DePaul AJ, Thompson EJ, Patel SS, Haldeman K, Sorin EJ. Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics. Nucleic Acids Res 2010, 38:4856–4867.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 4856-4867
-
-
DePaul, A.J.1
Thompson, E.J.2
Patel, S.S.3
Haldeman, K.4
Sorin, E.J.5
-
15
-
-
34249278470
-
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
-
Cheah MT, Wachter A, Sudarsan N, Breaker RR. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 2007, 447:497–500.
-
(2007)
Nature
, vol.447
, pp. 497-500
-
-
Cheah, M.T.1
Wachter, A.2
Sudarsan, N.3
Breaker, R.R.4
-
16
-
-
84941595614
-
Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design
-
Aboul-ela F, Huang W, Elrahman MA, Boyapati V, Li P. Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. Wiley Interdiscip Rev RNA 2015, 6:631–650.
-
(2015)
Wiley Interdiscip Rev RNA
, vol.6
, pp. 631-650
-
-
Aboul-ela, F.1
Huang, W.2
Elrahman, M.A.3
Boyapati, V.4
Li, P.5
-
18
-
-
78049445573
-
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis
-
Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang LS, Gregory BD. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet 2010, 6:e1001141.
-
(2010)
PLoS Genet
, vol.6
-
-
Zheng, Q.1
Ryvkin, P.2
Li, F.3
Dragomir, I.4
Valladares, O.5
Yang, J.6
Cao, K.7
Wang, L.S.8
Gregory, B.D.9
-
19
-
-
84871887837
-
Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome
-
Li F, Zheng Q, Vandivier LE, Willmann MR, Chen Y, Gregory BD. Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell 2012, 24:4346–4359.
-
(2012)
Plant Cell
, vol.24
, pp. 4346-4359
-
-
Li, F.1
Zheng, Q.2
Vandivier, L.E.3
Willmann, M.R.4
Chen, Y.5
Gregory, B.D.6
-
20
-
-
84932615130
-
Transcriptome-wide measurement of plant RNA secondary structure
-
Foley SW, Vandivier LE, Kuksa PP, Gregory BD. Transcriptome-wide measurement of plant RNA secondary structure. Curr Opin Plant Biol 2015, 27:36–43.
-
(2015)
Curr Opin Plant Biol
, vol.27
, pp. 36-43
-
-
Foley, S.W.1
Vandivier, L.E.2
Kuksa, P.P.3
Gregory, B.D.4
-
21
-
-
84902081933
-
The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability
-
Hamperl S, Cimprich KA. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair 2014, 19:84–94.
-
(2014)
DNA Repair
, vol.19
, pp. 84-94
-
-
Hamperl, S.1
Cimprich, K.A.2
-
22
-
-
0038475911
-
Effect of transcription on folding of the Tetrahymena ribozyme
-
Heilman-Miller SL, Woodson SA. Effect of transcription on folding of the Tetrahymena ribozyme. RNA 2003, 9:722–733.
-
(2003)
RNA
, vol.9
, pp. 722-733
-
-
Heilman-Miller, S.L.1
Woodson, S.A.2
-
23
-
-
84906091908
-
A single-stranded architecture for cotranscriptional folding of RNA nanostructures
-
Geary C, Rothemund PW, Andersen ES. A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 2014, 345:799–804.
-
(2014)
Science
, vol.345
, pp. 799-804
-
-
Geary, C.1
Rothemund, P.W.2
Andersen, E.S.3
-
24
-
-
84901676291
-
A pause sequence enriched at translation start sites drives transcription dynamics in vivo
-
Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick RW, Weissman JS. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science 2014, 344:1042–1047.
-
(2014)
Science
, vol.344
, pp. 1042-1047
-
-
Larson, M.H.1
Mooney, R.A.2
Peters, J.M.3
Windgassen, T.4
Nayak, D.5
Gross, C.A.6
Block, S.M.7
Greenleaf, W.J.8
Landick, R.W.9
Weissman, J.S.10
-
25
-
-
0032037421
-
TAP, the human homolog of mex67p, mediates CTE-dependent RNA export from the nucleus
-
Gruter P, Tabernero C, von Kobbe C, Schmitt C, Saavedra C, Bachi A, Wilm M, Felber BK, Izaurralde E. TAP, the human homolog of mex67p, mediates CTE-dependent RNA export from the nucleus. Mol Cell 1998, 1:649–659.
-
(1998)
Mol Cell
, vol.1
, pp. 649-659
-
-
Gruter, P.1
Tabernero, C.2
von Kobbe, C.3
Schmitt, C.4
Saavedra, C.5
Bachi, A.6
Wilm, M.7
Felber, B.K.8
Izaurralde, E.9
-
26
-
-
84857771826
-
Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch
-
Perdrizet GA, Artsimovitch I, Furman R, Sosnick TR, Pan T. Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci USA 2012, 109:3323–3328.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 3323-3328
-
-
Perdrizet, G.A.1
Artsimovitch, I.2
Furman, R.3
Sosnick, T.R.4
Pan, T.5
-
27
-
-
60149091561
-
A stress-responsive RNA switch regulates VEGFA expression
-
Ray PS, Jia J, Yao P, Majumder M, Hatzoglou M, Fox PL. A stress-responsive RNA switch regulates VEGFA expression. Nature 2009, 457:915–919.
-
(2009)
Nature
, vol.457
, pp. 915-919
-
-
Ray, P.S.1
Jia, J.2
Yao, P.3
Majumder, M.4
Hatzoglou, M.5
Fox, P.L.6
-
28
-
-
84880242457
-
Transient RNA structure features are evolutionarily conserved and can be computationally predicted
-
Zhu JY, Steif A, Proctor JR, Meyer IM. Transient RNA structure features are evolutionarily conserved and can be computationally predicted. Nucleic Acids Res 2013, 41:6273–6285.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 6273-6285
-
-
Zhu, J.Y.1
Steif, A.2
Proctor, J.R.3
Meyer, I.M.4
-
29
-
-
77949563362
-
Yeast pre-rRNA processing and modification occur cotranscriptionally
-
Kos M, Tollervey D. Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol Cell 2010, 37:809–820.
-
(2010)
Mol Cell
, vol.37
, pp. 809-820
-
-
Kos, M.1
Tollervey, D.2
-
30
-
-
84874431413
-
Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants
-
Silverman IM, Li F, Gregory BD. Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. Plant Sci 2013, 205–206:55–62.
-
(2013)
Plant Sci
, vol.205-206
, pp. 55-62
-
-
Silverman, I.M.1
Li, F.2
Gregory, B.D.3
-
31
-
-
84867629183
-
Direct observation of cotranscriptional folding in an adenine riboswitch
-
Frieda KL, Block SM. Direct observation of cotranscriptional folding in an adenine riboswitch. Science 2012, 338:397–400.
-
(2012)
Science
, vol.338
, pp. 397-400
-
-
Frieda, K.L.1
Block, S.M.2
-
32
-
-
84945197391
-
Novel RNA chaperone domain of RNA-binding protein La is regulated by AKT phosphorylation
-
Kuehnert J, Sommer G, Zierk AW, Fedarovich A, Brock A, Fedarovich D, Heise T. Novel RNA chaperone domain of RNA-binding protein La is regulated by AKT phosphorylation. Nucleic Acids Res 2015, 43:581–594.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 581-594
-
-
Kuehnert, J.1
Sommer, G.2
Zierk, A.W.3
Fedarovich, A.4
Brock, A.5
Fedarovich, D.6
Heise, T.7
-
33
-
-
35548989806
-
Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone
-
Bhaskaran H, Russell R. Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone. Nature 2007, 449:1014–1018.
-
(2007)
Nature
, vol.449
, pp. 1014-1018
-
-
Bhaskaran, H.1
Russell, R.2
-
34
-
-
84920467703
-
DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture
-
Pan C, Potratz JP, Cannon B, Simpson ZB, Ziehr JL, Tijerina P, Russell R. DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture. PLoS Biol 2014, 12:e1001981.
-
(2014)
PLoS Biol
, vol.12
-
-
Pan, C.1
Potratz, J.P.2
Cannon, B.3
Simpson, Z.B.4
Ziehr, J.L.5
Tijerina, P.6
Russell, R.7
-
35
-
-
84939561955
-
Division of labor in an oligomer of the DEAD-Box RNA helicase ded1p
-
Putnam AA, Gao Z, Liu F, Jia H, Yang Q, Jankowsky E. Division of labor in an oligomer of the DEAD-Box RNA helicase ded1p. Mol Cell 2015, 59:541–552.
-
(2015)
Mol Cell
, vol.59
, pp. 541-552
-
-
Putnam, A.A.1
Gao, Z.2
Liu, F.3
Jia, H.4
Yang, Q.5
Jankowsky, E.6
-
36
-
-
72749118512
-
A pH-responsive riboregulator
-
Nechooshtan G, Elgrably-Weiss M, Sheaffer A, Westhof E, Altuvia S. A pH-responsive riboregulator. Genes Dev 2009, 23:2650–2662.
-
(2009)
Genes Dev
, vol.23
, pp. 2650-2662
-
-
Nechooshtan, G.1
Elgrably-Weiss, M.2
Sheaffer, A.3
Westhof, E.4
Altuvia, S.5
-
38
-
-
58749105663
-
RNA folding: thermodynamic and molecular descriptions of the roles of ions
-
Draper DE. RNA folding: thermodynamic and molecular descriptions of the roles of ions. Biophys J 2008, 95:5489–5495.
-
(2008)
Biophys J
, vol.95
, pp. 5489-5495
-
-
Draper, D.E.1
-
39
-
-
84941299991
-
De novo design of heat-repressible RNA thermosensors in E. coli
-
Hoynes-O'Connor A, Hinman K, Kirchner L, Moon TS. De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res 2015, 43:6166–6179.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 6166-6179
-
-
Hoynes-O'Connor, A.1
Hinman, K.2
Kirchner, L.3
Moon, T.S.4
-
40
-
-
84891776041
-
Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element
-
Nechooshtan G, Elgrably-Weiss M, Altuvia S. Changes in transcriptional pausing modify the folding dynamics of the pH-responsive RNA element. Nucleic Acids Res 2014, 42:622–630.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 622-630
-
-
Nechooshtan, G.1
Elgrably-Weiss, M.2
Altuvia, S.3
-
41
-
-
84894318075
-
Coupling mRNA processing with transcription in time and space
-
Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet 2014, 15:163–175.
-
(2014)
Nat Rev Genet
, vol.15
, pp. 163-175
-
-
Bentley, D.L.1
-
42
-
-
84936136220
-
Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics
-
Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE. Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc Natl Acad Sci USA 2015, 112:E3485–E3494.
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, pp. E3485-E3494
-
-
Liberman, J.A.1
Suddala, K.C.2
Aytenfisu, A.3
Chan, D.4
Belashov, I.A.5
Salim, M.6
Mathews, D.H.7
Spitale, R.C.8
Walter, N.G.9
Wedekind, J.E.10
-
43
-
-
84922797318
-
Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context
-
Marcano-Velázquez JG, Batey RT. Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context. J Biol Chem 2015, 290:4464–4475.
-
(2015)
J Biol Chem
, vol.290
, pp. 4464-4475
-
-
Marcano-Velázquez, J.G.1
Batey, R.T.2
-
44
-
-
0842334528
-
Adenine riboswitches and gene activation by disruption of a transcription terminator
-
Mandal M, Breaker RR. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol 2004, 11:29–35.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 29-35
-
-
Mandal, M.1
Breaker, R.R.2
-
45
-
-
84876049606
-
The genetic code as expressed through relationships between mRNA structure and protein function
-
Mauger DM, Siegfried NA, Weeks KM. The genetic code as expressed through relationships between mRNA structure and protein function. FEBS Lett 2013, 587:1180–1188.
-
(2013)
FEBS Lett
, vol.587
, pp. 1180-1188
-
-
Mauger, D.M.1
Siegfried, N.A.2
Weeks, K.M.3
-
46
-
-
77958007950
-
G-quadruplex structures in RNA stimulate mitochondrial transcription termination and primer formation
-
Wanrooij PH, Uhler JP, Simonsson T, Falkenberg M, Gustafsson CM. G-quadruplex structures in RNA stimulate mitochondrial transcription termination and primer formation. Proc Natl Acad Sci USA 2010, 107:16072–16077.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 16072-16077
-
-
Wanrooij, P.H.1
Uhler, J.P.2
Simonsson, T.3
Falkenberg, M.4
Gustafsson, C.M.5
-
47
-
-
84921922766
-
Replication-transcription switch in human mitochondria
-
Agaronyan K, Morozov YI, Anikin M, Temiakov D. Replication-transcription switch in human mitochondria. Science 2015, 347:548–551.
-
(2015)
Science
, vol.347
, pp. 548-551
-
-
Agaronyan, K.1
Morozov, Y.I.2
Anikin, M.3
Temiakov, D.4
-
48
-
-
84923820163
-
Transcription: a mitochondrial switch between transcription and replication
-
Du Toit A. Transcription: a mitochondrial switch between transcription and replication. Nat Rev Mol Cell Biol 2015, 16:128.
-
(2015)
Nat Rev Mol Cell Biol
, vol.16
, pp. 128
-
-
Du Toit, A.1
-
49
-
-
84860338675
-
R loops: from transcription byproducts to threats to genome stability
-
Aguilera A, Garcia-Muse T. R loops: from transcription byproducts to threats to genome stability. Mol Cell 2012, 46:115–124.
-
(2012)
Mol Cell
, vol.46
, pp. 115-124
-
-
Aguilera, A.1
Garcia-Muse, T.2
-
50
-
-
84956698688
-
Nascent RNA folding mitigates transcription-associated mutagenesis
-
Chen XS, Yang JR, Zhang JZ. Nascent RNA folding mitigates transcription-associated mutagenesis. Genome Res 2015, 26:50–59.
-
(2015)
Genome Res
, vol.26
, pp. 50-59
-
-
Chen, X.S.1
Yang, J.R.2
Zhang, J.Z.3
-
51
-
-
34247564968
-
Distinct RNA elements confer specificity to flavivirus RNA cap methylation events
-
Dong H, Ray D, Ren S, Zhang B, Puig-Basagoiti F, Takagi Y, Ho CK, Li H, Shi PY. Distinct RNA elements confer specificity to flavivirus RNA cap methylation events. J Virol 2007, 81:4412–4421.
-
(2007)
J Virol
, vol.81
, pp. 4412-4421
-
-
Dong, H.1
Ray, D.2
Ren, S.3
Zhang, B.4
Puig-Basagoiti, F.5
Takagi, Y.6
Ho, C.K.7
Li, H.8
Shi, P.Y.9
-
52
-
-
84941094331
-
Flaviviral replication complex: coordination between RNA synthesis and 5′-RNA capping
-
Klema VJ, Padmanabhan R, Choi KH. Flaviviral replication complex: coordination between RNA synthesis and 5′-RNA capping. Viruses 2015, 7:4640–4656.
-
(2015)
Viruses
, vol.7
, pp. 4640-4656
-
-
Klema, V.J.1
Padmanabhan, R.2
Choi, K.H.3
-
53
-
-
84939530621
-
THZ1 reveals roles for Cdk7 in co-transcriptional capping and pausing
-
Nilson KA, Guo J, Turek ME, Brogie JE, Delaney E, Luse DS, Price DH. THZ1 reveals roles for Cdk7 in co-transcriptional capping and pausing. Mol Cell 2015, 59:576–587.
-
(2015)
Mol Cell
, vol.59
, pp. 576-587
-
-
Nilson, K.A.1
Guo, J.2
Turek, M.E.3
Brogie, J.E.4
Delaney, E.5
Luse, D.S.6
Price, D.H.7
-
54
-
-
84862526272
-
Signals for pre-mRNA cleavage and polyadenylation
-
Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA 2012, 3:385–396.
-
(2012)
Wiley Interdiscip Rev RNA
, vol.3
, pp. 385-396
-
-
Tian, B.1
Graber, J.H.2
-
55
-
-
84914154034
-
Determinants and implications of mRNA Poly(A) tail size-does this protein make my tail look big?
-
Jalkanen AL, Coleman SJ, Wilusz J. Determinants and implications of mRNA Poly(A) tail size-does this protein make my tail look big? Semin Cell Dev Biol 2014, 34:24–32.
-
(2014)
Semin Cell Dev Biol
, vol.34
, pp. 24-32
-
-
Jalkanen, A.L.1
Coleman, S.J.2
Wilusz, J.3
-
56
-
-
84884578830
-
Structural model of the complete poly (A) region of HIV-1 pre-mRNA
-
Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DМ. Structural model of the complete poly (A) region of HIV-1 pre-mRNA. J Biomol Struct Dyn 2013, 31:1044–1056.
-
(2013)
J Biomol Struct Dyn
, vol.31
, pp. 1044-1056
-
-
Zarudnaya, M.I.1
Potyahaylo, A.L.2
Kolomiets, I.M.3
Hovorun, D.М.4
-
57
-
-
0032522222
-
Inhibition of polyadenylation by stable RNA secondary structure
-
Klasens BIF, Das AT, Berkhout B. Inhibition of polyadenylation by stable RNA secondary structure. Nucleic Acids Res 1998, 26:1870–1876.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1870-1876
-
-
Klasens, B.I.F.1
Das, A.T.2
Berkhout, B.3
-
58
-
-
84914173456
-
Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG)
-
Kolomiets IN, Zarudnaya MI, Potyahaylo AL, Hovorun DM. Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG). J Biomol Struct Dyn 2015, 33:418–433.
-
(2015)
J Biomol Struct Dyn
, vol.33
, pp. 418-433
-
-
Kolomiets, I.N.1
Zarudnaya, M.I.2
Potyahaylo, A.L.3
Hovorun, D.M.4
-
59
-
-
84894131718
-
Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast
-
Geisberg JV, Moqtaderi Z, Fan X, Ozsolak F, Struhl K. Global analysis of mRNA isoform half-lives reveals stabilizing and destabilizing elements in yeast. Cell 2014, 156:812–824.
-
(2014)
Cell
, vol.156
, pp. 812-824
-
-
Geisberg, J.V.1
Moqtaderi, Z.2
Fan, X.3
Ozsolak, F.4
Struhl, K.5
-
60
-
-
84985887596
-
Secondary structures involving the poly(A) tail and other 3′ sequences are major determinants of mRNA isoform stability in yeast
-
Moqtaderi Z, Geisberg JV, Struhl K. Secondary structures involving the poly(A) tail and other 3′ sequences are major determinants of mRNA isoform stability in yeast. Microb Cell 2014, 1:137–139.
-
(2014)
Microb Cell
, vol.1
, pp. 137-139
-
-
Moqtaderi, Z.1
Geisberg, J.V.2
Struhl, K.3
-
61
-
-
69049102132
-
Modulation of alternative splicing by long-range RNA structures in Drosophila
-
Raker VA, Mironov AA, Gelfand MS, Pervouchine DD. Modulation of alternative splicing by long-range RNA structures in Drosophila. Nucleic Acids Res 2009, 37:4533–4544.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 4533-4544
-
-
Raker, V.A.1
Mironov, A.A.2
Gelfand, M.S.3
Pervouchine, D.D.4
-
62
-
-
79551653312
-
RNA secondary structure in mutually exclusive splicing
-
Yang Y, Zhan LL, Zhang WJ, Sun F, Wang WF, Tian N, Bi JP, Wang HT, Shi D, Jiang YJ, et al. RNA secondary structure in mutually exclusive splicing. Nat Struct Mol Biol 2011, 18:159–168.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 159-168
-
-
Yang, Y.1
Zhan, L.L.2
Zhang, W.J.3
Sun, F.4
Wang, W.F.5
Tian, N.6
Bi, J.P.7
Wang, H.T.8
Shi, D.9
Jiang, Y.J.10
-
63
-
-
84872543206
-
A decade of riboswitches
-
Serganov A, Nudler E. A decade of riboswitches. Cell 2013, 152:17–24.
-
(2013)
Cell
, vol.152
, pp. 17-24
-
-
Serganov, A.1
Nudler, E.2
-
64
-
-
80054769140
-
Mechanism for gene control by a natural allosteric group I ribozyme
-
Chen AG, Sudarsan N, Breaker RR. Mechanism for gene control by a natural allosteric group I ribozyme. RNA 2011, 17:1967–1972.
-
(2011)
RNA
, vol.17
, pp. 1967-1972
-
-
Chen, A.G.1
Sudarsan, N.2
Breaker, R.R.3
-
65
-
-
77953293106
-
A'-form RNA helices are required for cytoplasmic mRNA transport in Drosophila
-
Bullock SL, Ringel I, Ish-Horowicz D, Lukavsky PJ. A'-form RNA helices are required for cytoplasmic mRNA transport in Drosophila. Nat Struct Mol Biol 2010, 17:703–709.
-
(2010)
Nat Struct Mol Biol
, vol.17
, pp. 703-709
-
-
Bullock, S.L.1
Ringel, I.2
Ish-Horowicz, D.3
Lukavsky, P.J.4
-
66
-
-
84902830900
-
Insights into RNA structure and function from genome-wide studies
-
Mortimer SA, Kidwell MA, Doudna JA. Insights into RNA structure and function from genome-wide studies. Nat Rev Genet 2014, 15:469–479.
-
(2014)
Nat Rev Genet
, vol.15
, pp. 469-479
-
-
Mortimer, S.A.1
Kidwell, M.A.2
Doudna, J.A.3
-
67
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 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
-
68
-
-
84896508177
-
A stem–loop structure directs oskar mRNA to microtubule minus ends
-
Jambor H, Mueller S, Bullock SL, Ephrussi A. A stem–loop structure directs oskar mRNA to microtubule minus ends. RNA 2014, 20:429–439.
-
(2014)
RNA
, vol.20
, pp. 429-439
-
-
Jambor, H.1
Mueller, S.2
Bullock, S.L.3
Ephrussi, A.4
-
69
-
-
79959923521
-
G–quadruplex RNA structure as a signal for neurite mRNA targeting
-
Subramanian M, Rage F, Tabet R, Flatter E, Mandel JL, Moine H. G–quadruplex RNA structure as a signal for neurite mRNA targeting. EMBO Rep 2011, 12:697–704.
-
(2011)
EMBO Rep
, vol.12
, pp. 697-704
-
-
Subramanian, M.1
Rage, F.2
Tabet, R.3
Flatter, E.4
Mandel, J.L.5
Moine, H.6
-
70
-
-
60149086205
-
mRNA localization: gene expression in the spatial dimension
-
Martin KC, Ephrussi A. mRNA localization: gene expression in the spatial dimension. Cell 2009, 136:719–730.
-
(2009)
Cell
, vol.136
, pp. 719-730
-
-
Martin, K.C.1
Ephrussi, A.2
-
71
-
-
66349113529
-
The role of mRNA structure in translational control in bacteria
-
Geissmann T, Marzi S, Romby P. The role of mRNA structure in translational control in bacteria. RNA Biol 2014, 6:153–160.
-
(2014)
RNA Biol
, vol.6
, pp. 153-160
-
-
Geissmann, T.1
Marzi, S.2
Romby, P.3
-
72
-
-
79551631613
-
Alternate rRNA secondary structures as regulators of translation
-
Feng S, Li H, Zhao J, Pervushin K, Lowenhaupt K, Schwartz TU, Droge P. Alternate rRNA secondary structures as regulators of translation. Nat Struct Mol Biol 2011, 18:169–176.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 169-176
-
-
Feng, S.1
Li, H.2
Zhao, J.3
Pervushin, K.4
Lowenhaupt, K.5
Schwartz, T.U.6
Droge, P.7
-
73
-
-
0035107115
-
Role of mRNA secondary structure in translational repression of the maize transcriptional activator Lc
-
Wang LJ, Wessler SR. Role of mRNA secondary structure in translational repression of the maize transcriptional activator Lc. Plant Physiol 2001, 125:1380–1387.
-
(2001)
Plant Physiol
, vol.125
, pp. 1380-1387
-
-
Wang, L.J.1
Wessler, S.R.2
-
74
-
-
77957082956
-
A G-quadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells
-
Gomez D, Guedin A, Mergny JL, Salles B, Riou JF, Teulade-Fichou MP, Calsou P. A G-quadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells. Nucleic Acids Res 2010, 38:7187–7198.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 7187-7198
-
-
Gomez, D.1
Guedin, A.2
Mergny, J.L.3
Salles, B.4
Riou, J.F.5
Teulade-Fichou, M.P.6
Calsou, P.7
-
75
-
-
79953154960
-
Mutation of the 5′-untranslated region stem-loop structure inhibits alpha1(I) collagen expression in vivo
-
Parsons CJ, Stefanovic B, Seki E, Aoyama T, Latour AM, Marzluff WF, Rippe RA, Brenner DA. Mutation of the 5′-untranslated region stem-loop structure inhibits alpha1(I) collagen expression in vivo. J Biol Chem 2011, 286:8609–8619.
-
(2011)
J Biol Chem
, vol.286
, pp. 8609-8619
-
-
Parsons, C.J.1
Stefanovic, B.2
Seki, E.3
Aoyama, T.4
Latour, A.M.5
Marzluff, W.F.6
Rippe, R.A.7
Brenner, D.A.8
-
76
-
-
37849045636
-
Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs
-
Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 2007, 19:3437–3450.
-
(2007)
Plant Cell
, vol.19
, pp. 3437-3450
-
-
Wachter, A.1
Tunc-Ozdemir, M.2
Grove, B.C.3
Green, P.J.4
Shintani, D.K.5
Breaker, R.R.6
-
77
-
-
36248989143
-
Riboswitch-dependent gene regulation and its evolution in the plant kingdom
-
Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A. Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev 2007, 21:2874–2879.
-
(2007)
Genes Dev
, vol.21
, pp. 2874-2879
-
-
Bocobza, S.1
Adato, A.2
Mandel, T.3
Shapira, M.4
Nudler, E.5
Aharoni, A.6
-
78
-
-
45849122499
-
Widespread translational Inhibition by plant miRNAs and siRNAs
-
Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O. Widespread translational Inhibition by plant miRNAs and siRNAs. Science 2008, 320:1185–1190.
-
(2008)
Science
, vol.320
, pp. 1185-1190
-
-
Brodersen, P.1
Sakvarelidze-Achard, L.2
Bruun-Rasmussen, M.3
Dunoyer, P.4
Yamamoto, Y.Y.5
Sieburth, L.6
Voinnet, O.7
-
79
-
-
84944909591
-
MicroRNAs in control of plant development
-
Li C, Zhang BH. MicroRNAs in control of plant development. J Cell Physiol 2016, 231:303–313.
-
(2016)
J Cell Physiol
, vol.231
, pp. 303-313
-
-
Li, C.1
Zhang, B.H.2
-
80
-
-
84952673589
-
The role of small RNAs in vegetative shoot development
-
Fouracre JP, Poethig RS. The role of small RNAs in vegetative shoot development. Curr Opin Plant Biol 2016, 29:64–72.
-
(2016)
Curr Opin Plant Biol
, vol.29
, pp. 64-72
-
-
Fouracre, J.P.1
Poethig, R.S.2
-
81
-
-
84949952099
-
Unique features of long non-coding RNA biogenesis and function
-
Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet 2016, 17:47–62.
-
(2016)
Nat Rev Genet
, vol.17
, pp. 47-62
-
-
Quinn, J.J.1
Chang, H.Y.2
-
82
-
-
84891773261
-
NPInter v2.0: an updated database of ncRNA interactions
-
Yuan J, Wu W, Xie C, Zhao G, Zhao Y, Chen R. NPInter v2.0: an updated database of ncRNA interactions. Nucleic Acids Res 2014, 42:D104–D108.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D104-D108
-
-
Yuan, J.1
Wu, W.2
Xie, C.3
Zhao, G.4
Zhao, Y.5
Chen, R.6
-
83
-
-
84857066786
-
Modular regulatory principles of large non-coding RNAs
-
Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature 2012, 482:339–346.
-
(2012)
Nature
, vol.482
, pp. 339-346
-
-
Guttman, M.1
Rinn, J.L.2
-
84
-
-
84909609618
-
Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization
-
Csorba T, Questa JI, Sun QW, Dean C. Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad Sci USA 2014, 111:16160–16165.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 16160-16165
-
-
Csorba, T.1
Questa, J.I.2
Sun, Q.W.3
Dean, C.4
-
85
-
-
84935006246
-
RNA editing in plants: Machinery and flexibility of site recognition
-
Shikanai T. RNA editing in plants: Machinery and flexibility of site recognition. Biochim Biophys Acta 1847, 2015:779–785.
-
(1847)
Biochim Biophys Acta
, vol.2015
, pp. 779-785
-
-
Shikanai, T.1
-
86
-
-
84940448362
-
Long non-coding RNAs and their biological roles in plants
-
Liu X, Hao L, Li D, Zhu L, Hu S. Long non-coding RNAs and their biological roles in plants. Genomics Proteomics Bioinformatics 2015, 13:137–147.
-
(2015)
Genomics Proteomics Bioinformatics
, vol.13
, pp. 137-147
-
-
Liu, X.1
Hao, L.2
Li, D.3
Zhu, L.4
Hu, S.5
-
87
-
-
84893427735
-
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
-
Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 2014, 505:696–700.
-
(2014)
Nature
, vol.505
, pp. 696-700
-
-
Ding, Y.1
Tang, Y.2
Kwok, C.K.3
Zhang, Y.4
Bevilacqua, P.C.5
Assmann, S.M.6
-
88
-
-
84921472110
-
Global analysis of the RNA–protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
-
Gosai SJ, Foley SW, Wang D, Silverman IM, Selamoglu N, Nelson AD, Beilstein MA, Daldal F, Deal RB, Gregory BD. Global analysis of the RNA–protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus. Mol Cell 2015, 57:376–388.
-
(2015)
Mol Cell
, vol.57
, pp. 376-388
-
-
Gosai, S.J.1
Foley, S.W.2
Wang, D.3
Silverman, I.M.4
Selamoglu, N.5
Nelson, A.D.6
Beilstein, M.A.7
Daldal, F.8
Deal, R.B.9
Gregory, B.D.10
|