Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY: Understanding the transcriptome through RNA structure. Nat Rev Genet. 2011, 12 (9): 641-655. 10.1038/nrg3049.
Article
PubMed
CAS
Google Scholar
Nagalakshmi U: The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008, 320: 1344-1349. 10.1126/science.1158441.
Article
PubMed
CAS
PubMed Central
Google Scholar
Warf MB, Berglund JA: Role of RNA structure in regulating pre-mRNA splicing. Trends Biochem Sci. 2010, 35: 169-178. 10.1016/j.tibs.2009.10.004.
Article
PubMed
CAS
PubMed Central
Google Scholar
Meijer HA, Kong YW, Lu WT, Wilczynska A, Spriggs RV, Robinson SW, Godfrey JD, Willis AE, Bushell M: Translational repression and eIF4A2 activity Are critical for MicroRNA-mediated gene regulation. Science. 2013, 340 (6128): 82-85. 10.1126/science.1231197.
Article
PubMed
CAS
Google Scholar
Gu W, Wang X, Zhai C, Xie X, Zhou T: Selection on synonymous sites for increased accessibility around miRNA binding sites in plants. Mol Biol Evol. 2012, 29 (10): 3037-3044. 10.1093/molbev/mss109.
Article
PubMed
CAS
Google Scholar
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 (11): 4346-4359. 10.1105/tpc.112.104232.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gu W, Zhou T, Wilke CO: A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol. 2010, 6 (2): e1000664-10.1371/journal.pcbi.1000664.
Article
PubMed
PubMed Central
Google Scholar
Kozak M: Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene. 2005, 361: 13-37.
Article
PubMed
CAS
Google Scholar
Martin KC, Ephrussi A: mRNA localization: gene expression in the spatial dimension. Cell. 2009, 136: 719-730. 10.1016/j.cell.2009.01.044.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gonsalvez GB, Urbinati CR, Long RM: RNA localization in yeast: moving towards a mechanism. Biol Cell. 2005, 97: 75-86. 10.1042/BC20040066.
Article
PubMed
CAS
Google Scholar
Kertesz M: Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010, 467: 103-107. 10.1038/nature09322.
Article
PubMed
CAS
Google Scholar
Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Makino DL, Nutter RC, Segal E, Chang HY: Genome-wide measurement of RNA folding energies. Mol Cell. 2012, 48 (2): 169-181. 10.1016/j.molcel.2012.08.008.
Article
PubMed
PubMed Central
Google Scholar
Zheng Q, Ryvkin P, Li F, Dragomir I, Valladares O, Yang J, Cao K, Wang L-S, Gregory BD: Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet. 2010, 6 (9): e1001141-10.1371/journal.pgen.1001141.
Article
PubMed
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
Pedersen JS: Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006, 2: e33-10.1371/journal.pcbi.0020033.
Article
PubMed
CAS
PubMed Central
Google Scholar
Smith MA, Gesell T, Stadler PF, Mattick JS: Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res. 2013, 41 (17): 8220-8236. 10.1093/nar/gkt596.
Article
PubMed
CAS
PubMed Central
Google Scholar
Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF: Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007, 17 (6): 852-864. 10.1101/gr.5650707.
Article
PubMed
CAS
PubMed Central
Google Scholar
Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J: Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res. 2008, 18 (2): 242-251. 10.1101/gr.6887408.
Article
PubMed
CAS
PubMed Central
Google Scholar
Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol. 2005, 23 (11): 1383-1390. 10.1038/nbt1144.
Article
PubMed
CAS
Google Scholar
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park S-W, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007, 450 (7167): 219-232. 10.1038/nature06340.
Article
PubMed
CAS
PubMed Central
Google Scholar
Steigele S, Huber W, Stocsits C, Stadler P, Nieselt K: Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. BMC Biol. 2007, 5 (1): 25-10.1186/1741-7007-5-25.
Article
PubMed
PubMed Central
Google Scholar
Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, Makarov SS, Maixner W, Diatchenko L: Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science. 2006, 314 (5807): 1930-1933. 10.1126/science.1131262.
Article
PubMed
CAS
Google Scholar
Bartoszewski RA, Jablonsky M, Bartoszewska S, Stevenson L, Dai Q, Kappes J, Collawn JF, Bebok Z: A synonymous single nucleotide polymorphism in ΔF508 CFTR alters the secondary structure of the mRNA and the expression of the mutant protein. J Biol Chem. 2010, 285 (37): 28741-28748. 10.1074/jbc.M110.154575.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen J-M, Férec C, Cooper D: A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3′ UTR variants. Hum Genet. 2006, 120 (3): 301-333. 10.1007/s00439-006-0218-x.
Article
PubMed
CAS
Google Scholar
Naslavsky MS, Crovella S, Filho JLL, Rocha CRC: The sound of silence: human β-defensin-1 gene untranslated SNPs change the predicted mRNA secondary structure in a length-dependent manner. Immunol Lett. 2010, 129 (1): 53-55. 10.1016/j.imlet.2009.12.024.
Article
PubMed
CAS
Google Scholar
Thomas LF, Saito T, Sætrom P: Inferring causative variants in microRNA target sites. Nucleic Acids Res. 2011, 39 (16): e109-10.1093/nar/gkr414.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hurst LD: Molecular genetics: the sound of silence. Nature. 2011, 471 (7340): 582-583. 10.1038/471582a.
Article
PubMed
CAS
Google Scholar
Chursov A, Frishman D, Shneider A: Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution. Nucleic Acids Res. 2013, 41 (16): 7854-7860. 10.1093/nar/gkt507.
Article
PubMed
CAS
PubMed Central
Google Scholar
Warden CD, Kim S-H, Yi SV: Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins. PLoS One. 2008, 3 (2): e1559-10.1371/journal.pone.0001559.
Article
PubMed
PubMed Central
Google Scholar
Findeiß S, Engelhardt J, Prohaska SJ, Stadler PF: Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids. Biochimie. 2011, 93 (11): 2019-2023. 10.1016/j.biochi.2011.07.023.
Article
PubMed
Google Scholar
Meyer IM, Miklós I: Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Res. 2005, 33 (19): 6338-6348. 10.1093/nar/gki923.
Article
PubMed
CAS
PubMed Central
Google Scholar
Siepel A, Haussler D: Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 2004, 11 (2–3): 413-428.
Article
PubMed
CAS
Google Scholar
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J: RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat. 2013, 34 (4): 546-556.
PubMed
CAS
PubMed Central
Google Scholar
Mantel N, Haenszel W: Statistical aspects of the analysis of data from retrospective studies of disease. J Natl Cancer Inst. 1959, 22 (4): 719-748.
PubMed
CAS
Google Scholar
Mantel N: Chi-Square Tests with One Degree of Freedom; Extensions of the Mantel- Haenszel Procedure. J Am Stat Assoc. 1963, 58 (303): 690-700.
Google Scholar
Wright F: The ‘effective number of codons’ used in a gene. Gene. 1990, 87 (1): 23-29. 10.1016/0378-1119(90)90491-9.
Article
PubMed
CAS
Google Scholar
Fuglsang A: Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice. Mol Biol Evol. 2006, 23 (7): 1345-1347. 10.1093/molbev/msl009.
Article
PubMed
CAS
Google Scholar
Novembre JA: Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol. 2002, 19 (8): 1390-1394. 10.1093/oxfordjournals.molbev.a004201.
Article
PubMed
CAS
Google Scholar
Zhou T, Wilke CO: Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. BMC Evol Biol. 2011, 11: 59-10.1186/1471-2148-11-59.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kudla G, Murray AW, Tollervey D, Plotkin JB: Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009, 324 (5924): 255-258. 10.1126/science.1170160.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bazykin GA, Kochetov AV: Alternative translation start sites are conserved in eukaryotic genomes. Nucleic Acids Res. 2011, 39 (2): 567-577. 10.1093/nar/gkq806.
Article
PubMed
CAS
PubMed Central
Google Scholar
Akashi H: Gene expression and molecular evolution. Curr Opin Genet Dev. 2001, 11 (6): 660-666. 10.1016/S0959-437X(00)00250-1.
Article
PubMed
CAS
Google Scholar
Sharp PM, Tuohy TM, Mosurski KR: Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986, 14 (13): 5125-5143. 10.1093/nar/14.13.5125.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhou T, Weems M, Wilke CO: Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol. 2009, 26 (7): 1571-1580. 10.1093/molbev/msp070.
Article
PubMed
CAS
PubMed Central
Google Scholar
Drummond DA, Wilke CO: Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008, 134 (2): 341-352. 10.1016/j.cell.2008.05.042.
Article
PubMed
CAS
PubMed Central
Google Scholar
Duret L: Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev. 2002, 12 (6): 640-649. 10.1016/S0959-437X(02)00353-2.
Article
PubMed
CAS
Google Scholar
Zhou T, Gu W, Wilke CO: Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol. 2010, 27 (8): 1912-1922. 10.1093/molbev/msq077.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chamary JV, Hurst LD: Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol. 2005, 6 (9): R75-10.1186/gb-2005-6-9-r75.
Article
PubMed
CAS
PubMed Central
Google Scholar
Parmley JL, Chamary JV, Hurst LD: Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol. 2006, 23 (2): 301-309.
Article
PubMed
CAS
Google Scholar
Warnecke T, Hurst LD: Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster. Mol Biol Evol. 2007, 24 (12): 2755-2762. 10.1093/molbev/msm210.
Article
PubMed
CAS
Google Scholar
Komar AA, Lesnik T, Reiss C: Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett. 1999, 462 (3): 387-391. 10.1016/S0014-5793(99)01566-5.
Article
PubMed
CAS
Google Scholar
Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM: A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science. 2007, 315 (5811): 525-528. 10.1126/science.1135308.
Article
PubMed
CAS
Google Scholar
Zhang G, Hubalewska M, Ignatova Z: Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol. 2009, 16 (3): 274-280. 10.1038/nsmb.1554.
Article
PubMed
CAS
Google Scholar
Duret L, Mouchiroud D: Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 2000, 17 (1): 68-74. 10.1093/oxfordjournals.molbev.a026239.
Article
PubMed
CAS
Google Scholar
Pal C, Papp B, Hurst LD: Highly expressed genes in yeast evolve slowly. Genetics. 2001, 158 (2): 927-931.
PubMed
CAS
PubMed Central
Google Scholar
Drummond DA, Raval A, Wilke CO: A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 2006, 23 (2): 327-337.
Article
PubMed
CAS
Google Scholar
Kurland CG: Codon bias and gene expression. FEBS Lett. 1991, 285 (2): 165-169. 10.1016/0014-5793(91)80797-7.
Article
PubMed
CAS
Google Scholar
Ikemura T: Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985, 2 (1): 13-34.
PubMed
CAS
Google Scholar
Henry I, Sharp PM: Predicting gene expression level from codon usage bias. Mol Biol Evol. 2007, 24 (1): 10-12.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
Google Scholar
Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB: Rate-limiting steps in yeast protein translation. Cell. 2013, 153 (7): 1589-1601. 10.1016/j.cell.2013.05.049.
Article
PubMed
CAS
PubMed Central
Google Scholar
Goodman DB, Church GM, Kosuri S: Causes and effects of N-terminal codon bias in bacterial genes. Science. 2013, 342 (6157): 475-479. 10.1126/science.1241934.
Article
PubMed
CAS
Google Scholar
Dvir S, Velten L, Sharon E, Zeevi D, Carey LB, Weinberger A, Segal E: Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci. 2013, 110 (30): E2792-E2801. 10.1073/pnas.1222534110.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bentele K, Saffert P, Rauscher R, Ignatova Z, Bluthgen N: Efficient translation initiation dictates codon usage at gene start. Mol Syst Biol. 2013, 9: 675-
Article
PubMed
PubMed Central
Google Scholar
Kim Y, Lee G, Jeon E, Sohn E, Lee Y, Kang H, Lee D, Kim DH, Hwang I: The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana. Nucleic Acids Res. 2014, 42 (1): 485-498. 10.1093/nar/gkt864.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mokrejš M, Vopálenský V, Kolenatý O, Mašek T, Feketová Z, Sekyrová P, Skaloudová B, Kříž V, Pospíšek M: IRESite: the database of experimentally verified IRES structures. Nucleic Acids Res. 2006, 34 (1): D125-D130. http://www.iresite.org,
Article
PubMed
PubMed Central
Google Scholar
Kaempfer R: Interferon- mRNA attenuates its own translation by activating PKR: A molecular basis for the therapeutic effect of interferon- in multiple sclerosis. Cell Res. 2006, 16 (2): 148-153. 10.1038/sj.cr.7310020.
Article
PubMed
CAS
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797. 10.1093/nar/gkh340.
Article
PubMed
CAS
PubMed Central
Google Scholar
Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22 (21): 2688-2690. 10.1093/bioinformatics/btl446.
Article
PubMed
CAS
Google Scholar
Stone EA, Sidow A: Constructing a meaningful evolutionary average at the phylogenetic center of mass. BMC Bioinformatics. 2007, 8: 222-10.1186/1471-2105-8-222.
Article
PubMed
PubMed Central
Google Scholar
Siepel A, Haussler D: Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol. 2004, 21 (3): 468-488.
Article
PubMed
CAS
Google Scholar
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO: Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004, 429 (6987): 92-96. 10.1038/nature02456.
Article
PubMed
CAS
Google Scholar
Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA: Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 1998, 95 (5): 717-728. 10.1016/S0092-8674(00)81641-4.
Article
PubMed
CAS
Google Scholar
Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP: A gene expression map for the euchromatic genome of Drosophila melanogaster. Science. 2004, 306 (5696): 655-660. 10.1126/science.1101312.
Article
PubMed
CAS
Google Scholar
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004, 101 (16): 6062-6067. 10.1073/pnas.0400782101.
Article
PubMed
CAS
PubMed Central
Google Scholar