Genomes and Genes
Summary: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
- Deqin M, Chen Z, Nero C, Patel K, Daoud E, Cheng H, et al. Somatic deletions of the polyA tract in the 3' untranslated region of epidermal growth factor receptor are common in microsatellite instability-high endometrial and colorectal carcinomas. Arch Pathol Lab Med. 2012;136:510-6 pubmed publisher..Deletions of EGFR 3' UTR polyA are frequent in endometrial and colorectal carcinomas, are confined almost exclusively to MSI-H tumors, and do not affect KRAS and BRAF mutations. ..
- Fasken M, Stewart M, Corbett A. Functional significance of the interaction between the mRNA-binding protein, Nab2, and the nuclear pore-associated protein, Mlp1, in mRNA export. J Biol Chem. 2008;283:27130-43 pubmed publisher..These data provide in vivo evidence for a model of mRNA export in which Nab2 is important for targeting mRNAs to the nuclear pore for export. ..
- Andersen K, Jensen T, Brodersen D. Take the "A" tail--quality control of ribosomal and transfer RNA. Biochim Biophys Acta. 2008;1779:532-7 pubmed publisher..Nonetheless, our knowledge about the controlled degradation of both stable and labile RNAs is now converging into a unified picture that points to the poly(A) tail as a key discriminator of RNA quality in both bacteria and eukaryotes. ..
- Rigo F, Martinson H. Functional coupling of last-intron splicing and 3'-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage. Mol Cell Biol. 2008;28:849-62 pubmed..Finally, the chemical steps in the processing of the terminal exon take place, beginning with poly(A) site cleavage, continuing with polyadenylation of the 3' end, and then finishing with splicing of the last intron. ..
- Gong C, Maquat L. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature. 2011;470:284-8 pubmed publisher..We name these lncRNAs half-STAU1-binding site RNAs (1/2-sbsRNAs)...
- Karve R, Liu W, Willet S, Torii K, Shpak E. The presence of multiple introns is essential for ERECTA expression in Arabidopsis. RNA. 2011;17:1907-21 pubmed publisher..The ability of introns to promote ERECTA expression might be linked to the process of splicing and not to a particular intron sequence. ..
- Baranovskaya S, Martin Y, Alonso S, Pisarchuk K, Falchetti M, Dai Y, et al. Down-regulation of epidermal growth factor receptor by selective expansion of a 5'-end regulatory dinucleotide repeat in colon cancer with microsatellite instability. Clin Cancer Res. 2009;15:4531-7 pubmed publisher..These findings suggest that in microsatellite instability-positive tumors current therapies targeting EGFR overexpression may have either no effect or an opposite to the expected effect. ..
- Wang H, Morita M, Yang X, Suzuki T, Yang W, Wang J, et al. Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. EMBO J. 2010;29:2566-76 pubmed publisher..The resulting structures suggest a molecular deadenylase mechanism involving a pentacovalent phosphate transition. ..
- Millevoi S, Decorsière A, Loulergue C, Iacovoni J, Bernat S, Antoniou M, et al. A physical and functional link between splicing factors promotes pre-mRNA 3' end processing. Nucleic Acids Res. 2009;37:4672-83 pubmed publisher..Therefore, our results provide evidence of a concerted regulation of pA signal recognition by splicing factors bound to auxiliary polyadenylation sequence elements. ..
- Nagao A, Hino Shigi N, Suzuki T. Measuring mRNA decay in human mitochondria. Methods Enzymol. 2008;447:489-99 pubmed publisher..In this report, we describe a practical method for measuring the half-lives of human mitochondrial mRNAs using quantitative real-time reverse transcription PCR. ..
- Meijer H, de Moor C. Fractionation of mRNA based on the length of the poly(A) tail. Methods Mol Biol. 2011;703:123-35 pubmed publisher..The method is technically easy, fast, highly reproducible and can be performed on almost any sample containing RNA. ..
- Bonderoff J, Larey J, Lloyd R. Cleavage of poly(A)-binding protein by poliovirus 3C proteinase inhibits viral internal ribosome entry site-mediated translation. J Virol. 2008;82:9389-99 pubmed publisher..These results suggest that cleavage of PABP contributes to viral translation shutoff that is required for the switch from translation to RNA replication...
- Gilbert W, Zhou K, Butler T, Doudna J. Cap-independent translation is required for starvation-induced differentiation in yeast. Science. 2007;317:1224-7 pubmed..A 5'UTR mutation that impairs IRES activity compromises invasive growth, which indicates that cap-independent translation is required for physiological adaptation to stress. ..
- Cetinkol O, Hud N. Molecular recognition of poly(A) by small ligands: an alternative method of analysis reveals nanomolar, cooperative and shape-selective binding. Nucleic Acids Res. 2009;37:611-21 pubmed publisher..The ligands described here may also find biological or medicinal applications, owing to the 3'-polyadenylation of mRNA in living cells. ..
- Radford H, Meijer H, de Moor C. Translational control by cytoplasmic polyadenylation in Xenopus oocytes. Biochim Biophys Acta. 2008;1779:217-29 pubmed publisher..Finally we discuss some of the remaining questions regarding the mechanisms of translational regulation by cytoplasmic polyadenylation and give our view on where our knowledge is likely to be expanded in the near future. ..
- Regnier P, Hajnsdorf E. Poly(A)-assisted RNA decay and modulators of RNA stability. Prog Mol Biol Transl Sci. 2009;85:137-85 pubmed publisher..Destabilization is often consecutive to the translational inactivation of mRNA. However, there are examples where RNA degradation is the primary regulatory step. ..
- Weill L, Belloc E, Bava F, Mendez R. Translational control by changes in poly(A) tail length: recycling mRNAs. Nat Struct Mol Biol. 2012;19:577-85 pubmed publisher..However, in very few cases have all three levels--mechanisms, targets and functions--been studied together. ..
- Luz J, Ramos C, Santos M, Coltri P, Palhano F, Foguel D, et al. Identification of archaeal proteins that affect the exosome function in vitro. BMC Biochem. 2010;11:22 pubmed publisher..Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism. ..
- Ahmed F, Kumar M, Raghava G. Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies. In Silico Biol. 2009;9:135-48 pubmed..72. Moreover, for independent datasets this model achieved a precision ranging from 75.8-95.7% with a sensitivity of 57%, which is better than any other known methods. ..
- Zamorano A, López Camarillo C, Orozco E, Weber C, Guillen N, Marchat L. In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation. Comput Biol Chem. 2008;32:256-63 pubmed publisher..histolytica. To our knowledge, this paper is the first work about the identification of potential pre-mRNA 3'-UTR cis-regulatory sequences through in silico analysis of large sets of cDNA and genomic sequences in a protozoan parasite. ..
- Eckmann C, Rammelt C, Wahle E. Control of poly(A) tail length. Wiley Interdiscip Rev RNA. 2011;2:348-61 pubmed publisher..Finally, destabilizing oligoadenylation does not appear to have inherent length control. Rather, average tail length results from the balance between polyadenylation and deadenylation. ..
- Hillier L, Reinke V, Green P, Hirst M, Marra M, Waterston R. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009;19:657-66 pubmed publisher..Although most sequences align with protein-coding genes, a small fraction falls in introns and intergenic regions. One notable region on the X chromosome encodes a noncoding transcript of >10 kb localized to somatic nuclei. ..
- Wu Q, Kim Y, Lu J, Xuan Z, Chen J, Zheng Y, et al. Poly A- transcripts expressed in HeLa cells. PLoS ONE. 2008;3:e2803 pubmed publisherTranscripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail...
- Bazzini A, Lee M, Giraldez A. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science. 2012;336:233-7 pubmed publisher..These results show that miR-430 regulates translation initiation before inducing mRNA decay during zebrafish development. ..
- Giri P, Kumar G. Isoquinoline alkaloids and their binding with polyadenylic acid: potential basis of therapeutic action. Mini Rev Med Chem. 2010;10:568-77 pubmed
- Schwede A, Ellis L, Luther J, Carrington M, Stoecklin G, Clayton C. A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells. Nucleic Acids Res. 2008;36:3374-88 pubmed publisher..In both species, depletion of Caf1 homologues inhibited deadenylation of bulk RNA and resulted in an increase in average poly(A) tail length...
- Zheng D, Ezzeddine N, Chen C, Zhu W, He X, Shyu A. Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells. J Cell Biol. 2008;182:89-101 pubmed publisher..These results support a dynamic interplay among deadenylation, mRNP remodeling, and P-body formation in selective decay of mammalian mRNA...
- Murray E, Schoenberg D. Assays for determining poly(A) tail length and the polarity of mRNA decay in mammalian cells. Methods Enzymol. 2008;448:483-504 pubmed publisher..Finally, it requires only a short sequence for target recognition and quantitation. Therefore, it can be applied to determining the decay polarity of a mRNA by measuring the decay rates of different portions of that mRNA. ..
- Zimmer S, Schein A, Zipor G, Stern D, Schuster G. Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase. Plant J. 2009;59:88-99 pubmed publisher..Together, our results identify several Ntr-PAPs and PNPase in organelle polyadenylation, and reveal novel poly(U)-rich sequences in Chlamydomonas mitochondria. ..
- Guan F, Caratozzolo R, Goraczniak R, Ho E, Gunderson S. A bipartite U1 site represses U1A expression by synergizing with PIE to inhibit nuclear polyadenylation. RNA. 2007;13:2129-40 pubmed..Parallels with other examples where U1 snRNP inhibits expression are discussed. We expect that other cellular genes will harbor functional U1 sites. ..
- Beilharz T, Preiss T. Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA. 2007;13:982-97 pubmed..They further provide a molecular explanation for deadenylase function in the cell cycle and suggest additional cellular processes that depend on control of mRNA polyadenylation. ..
- Derti A, Garrett Engele P, Macisaac K, Stevens R, Sriram S, Chen R, et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 2012;22:1173-83 pubmed publisher..These quantitative maps of polyA usage in evolutionarily and functionally related samples constitute a resource for understanding the regulatory mechanisms underlying alternative polyadenylation. ..
- Kalkatawi M, Rangkuti F, Schramm M, Jankovic B, Kamau A, Chowdhary R, et al. Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. Bioinformatics. 2012;28:127-9 pubmed publisher..email@example.com Supplementary data are available at Bioinformatics online. ..
- Hu W, Sweet T, Chamnongpol S, Baker K, Coller J. Co-translational mRNA decay in Saccharomyces cerevisiae. Nature. 2009;461:225-9 pubmed publisher..The data indicate that dissociation of ribosomes from mRNA is not a prerequisite for decay and we suggest that the 5'-3' polarity of mRNA degradation has evolved to ensure that the last translocating ribosome can complete translation...
- Kuhn U, Gündel M, Knoth A, Kerwitz Y, Rüdel S, Wahle E. Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor. J Biol Chem. 2009;284:22803-14 pubmed publisher..PABPN1 measures the length of the tail and is responsible for disrupting the CPSF-poly(A) polymerase interaction. ..
- Chen C, Shyu A. Mechanisms of deadenylation-dependent decay. Wiley Interdiscip Rev RNA. 2011;2:167-83 pubmed publisher..Possible models for mechanisms of various deadenylation-dependent mRNA decay pathways are also discussed. ..
- Ji Z, Luo W, Li W, Hoque M, Pan Z, Zhao Y, et al. Transcriptional activity regulates alternative cleavage and polyadenylation. Mol Syst Biol. 2011;7:534 pubmed publisher..Taken together, our results indicate that polyA site usage is generally coupled to transcriptional activity, leading to regulation of alternative polyadenylation by transcription. ..
- Mohanty B, Giladi H, Maples V, Kushner S. Analysis of RNA decay, processing, and polyadenylation in Escherichia coli and other prokaryotes. Methods Enzymol. 2008;447:3-29 pubmed publisher..Methods useful for the analysis of post-transcriptionally modified transcripts and the processing of very large polycistronic transcripts are also presented. ..
- Byers R, Sakhinia E, Joseph P, Glennie C, Hoyland J, Menasce L, et al. Clinical quantitation of immune signature in follicular lymphoma by RT-PCR-based gene expression profiling. Blood. 2008;111:4764-70 pubmed publisher..They demonstrate the utility of polyA DNA and real-time PCR for measurement of gene signatures and the applicability of using this type of "molecular block" in clinical practice...
- Mangone M, Manoharan A, Thierry Mieg D, Thierry Mieg J, Han T, Mackowiak S, et al. The landscape of C. elegans 3'UTRs. Science. 2010;329:432-5 pubmed publisher..We identified conserved 3'UTR motifs, isoform-specific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3'UTRs, both genome-wide and throughout development. ..
- Lemieux C, Marguerat S, Lafontaine J, Barbezier N, Bahler J, Bachand F. A Pre-mRNA degradation pathway that selectively targets intron-containing genes requires the nuclear poly(A)-binding protein. Mol Cell. 2011;44:108-19 pubmed publisher..Our findings unveil a layer of regulation in the nucleus in which the turnover of specific pre-mRNAs, besides the turnover of mature mRNAs, is used to control gene expression. ..
- Henriksson N, Nilsson P, Wu M, Song H, Virtanen A. Recognition of adenosine residues by the active site of poly(A)-specific ribonuclease. J Biol Chem. 2010;285:163-70 pubmed publisher..The poly(U)-degrading property of PARN could be of biological significance as oligo(U) tails recently have been proposed to play a role in RNA stabilization and destabilization. ..
- Jan C, Friedman R, Ruby J, Bartel D. Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature. 2011;469:97-101 pubmed publisher..These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying post-transcriptional gene regulation. ..
- Avendaño Vázquez S, Dhir A, Bembich S, Buratti E, Proudfoot N, Baralle F. Autoregulation of TDP-43 mRNA levels involves interplay between transcription, splicing, and alternative polyA site selection. Genes Dev. 2012;26:1679-84 pubmed publisher..Overall, we uncover complex interplay between transcription, splicing, and 3' end processing to effect autoregulation of TDP-43. ..
- Wood A, Schulz R, Woodfine K, Koltowska K, Beechey C, Peters J, et al. Regulation of alternative polyadenylation by genomic imprinting. Genes Dev. 2008;22:1141-6 pubmed publisher..On methylated alleles, the internal promoter is inactive and elongation proceeds to downstream polyadenylation sites. This demonstrates that epigenetic modifications can influence utilization of alternative polyadenylation sites. ..
- Xie B, Jankovic B, Bajic V, Song L, Gao X. Poly(A) motif prediction using spectral latent features from human DNA sequences. Bioinformatics. 2013;29:i316-25 pubmed publisher..http://sfb.kaust.edu.sa/Pages/Software.aspx. Supplementary data are available at Bioinformatics online. ..