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Short Communication

Arabidopsis mRNA secondary structure correlates with protein function and domains

, , , , &
Article: e24301 | Received 09 Feb 2013, Accepted 14 Mar 2013, Published online: 19 Apr 2013

References

  • Buratti E, Baralle FE. Influence of RNA secondary structure on the pre-mRNA splicing process. Mol Cell Biol 2004; 24:10505 - 14; http://dx.doi.org/10.1128/MCB.24.24.10505-10514.2004; PMID: 15572659
  • Schroeder R, Barta A, Semrad K. Strategies for RNA folding and assembly. Nat Rev Mol Cell Biol 2004; 5:908 - 19; http://dx.doi.org/10.1038/nrm1497; PMID: 15520810
  • Trappl K, Polacek N. The ribosome: a molecular machine powered by RNA. Met Ions Life Sci 2011; 9:253 - 75; http://dx.doi.org/10.1039/9781849732512-00253; PMID: 22010275
  • Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Semin Cell Dev Biol 2011; 22:359 - 65; http://dx.doi.org/10.1016/j.semcdb.2011.02.016; PMID: 21333748
  • 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; http://dx.doi.org/10.1016/j.plantsci.2013.01.009; PMID: 23498863
  • 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 - 44; http://dx.doi.org/10.1093/nar/gkp407; PMID: 19465384
  • Warf MB, Berglund JA. Role of RNA structure in regulating pre-mRNA splicing. Trends Biochem Sci 2010; 35:169 - 78; http://dx.doi.org/10.1016/j.tibs.2009.10.004; PMID: 19959365
  • Klasens BI, Das AT, Berkhout B. Inhibition of polyadenylation by stable RNA secondary structure. Nucleic Acids Res 1998; 26:1870 - 6; http://dx.doi.org/10.1093/nar/26.8.1870; PMID: 9518478
  • Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res 2003; 31:1375 - 86; http://dx.doi.org/10.1093/nar/gkg241; PMID: 12595544
  • Kozak M. Leader length and secondary structure modulate mRNA function under conditions of stress. Mol Cell Biol 1988; 8:2737 - 44; PMID: 3405216
  • Svitkin YV, Pause A, Haghighat A, Pyronnet S, Witherell G, Belsham GJ, et al. The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure. RNA 2001; 7:382 - 94; http://dx.doi.org/10.1017/S135583820100108X; PMID: 11333019
  • Wen JD, Lancaster L, Hodges C, Zeri AC, Yoshimura SH, Noller HF, et al. Following translation by single ribosomes one codon at a time. Nature 2008; 452:598 - 603; http://dx.doi.org/10.1038/nature06716; PMID: 18327250
  • Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, et al. Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 2012; 485:264 - 8; http://dx.doi.org/10.1038/nature11013; PMID: 22495308
  • 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 - 59; http://dx.doi.org/10.1105/tpc.112.104232; PMID: 23150631
  • Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981; 9:133 - 48; http://dx.doi.org/10.1093/nar/9.1.133; PMID: 6163133
  • Leipuviene R, Theil EC. The family of iron responsive RNA structures regulated by changes in cellular iron and oxygen. Cell Mol Life Sci 2007; 64:2945 - 55; http://dx.doi.org/10.1007/s00018-007-7198-4; PMID: 17849083
  • Lai EC. RNA sensors and riboswitches: self-regulating messages. Curr Biol 2003; 13:R285 - 91; http://dx.doi.org/10.1016/S0960-9822(03)00203-3; PMID: 12676109
  • Tenenbaum SA, Christiansen J, Nielsen H. 2011. The Post-transcriptional Operon. In RNA, Vol. 703. Nielsen, H. & J. M. Walker, Eds.: 237-245. Humana Press.
  • Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW Jr., Swanstrom R, et al. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 2009; 460:711 - 6; http://dx.doi.org/10.1038/nature08237; PMID: 19661910
  • Kramer G, Boehringer D, Ban N, Bukau B. The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat Struct Mol Biol 2009; 16:589 - 97; http://dx.doi.org/10.1038/nsmb.1614; PMID: 19491936
  • Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009; 37:1 - 13; http://dx.doi.org/10.1093/nar/gkn923; PMID: 19033363
  • Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008; 4:44 - 57; http://dx.doi.org/10.1038/nprot.2008.211; PMID: 19131956

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