Tuning the engine: An introduction to resources on post-transcriptional regulation of gene expression

RNA Biology

Volumn 9, Issue 10, 2012, Pages 1224-1232

  Dassi, Erik ^a   Quattrone, Alessandro ^a  

^a UNIVERSITY OF TRENTO   (Italy)

Author keywords

Cis element; Database; MiRNA; NcRNA; Post transcriptional regulation; RBP; Tool; Trans factor; Translation; UTR

Indexed keywords

EID: 84868235742     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.22035     Document Type: Review

References (52)

1. Moore MJ. From birth to death: the complex lives of eukaryotic mRNAs. Science 2005; 309:1514-8; PMID:16141059; http://dx.doi.org/10.1126/sci-ence. 1111443.
2. Mignone F, Gissi C, Liuni S, Pesole G. Untranslated regions of mRNAs. Genome Biol 2002; 3: reviews0004.1; PMID:11897027; http://dx.doi.org/10.1186/gb- 2002-3-3-reviews0004.
3. Glisovic T, Bachorik JL, Yong J, Dreyfuss G. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 2008; 582:1977-86; PMID:18342629; http://dx.doi.org/10.1016/j.febslet.2008.03.004.
4. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012; 149:1393-406; PMID:22658674; http://dx.doi.org/10.1016/j.cell.2012. 04.031.
5. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell 2012; 46:674-90; PMID:22681889; http://dx.doi.org/10.1016/j.mol-cel.2012.05.021.
6. Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 2007; 8:479-90; PMID:17473849; http://dx.doi.org/10.1038/nrm2178.
7. Andreassi C, Riccio A. To localize or not to localize: mRNA fate is in 3'UTR ends. Trends Cell Biol 2009; 19:465-74; PMID:19716303; http://dx.doi.org/10.1016/j.tcb.2009.06.001.
8. Costa F F. Non-coding RNAs: Meet thy masters. Bioessays 2010; 32:599-608; PMID:20544733; http://dx.doi.org/10.1002/bies.200900112.
9. Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 2008; 9:102-14; PMID:18197166; http://dx.doi.org/10.1038/nrg2290.
10. Barreau C, Paillard L, Osborne HB. AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res 2005; 33:7138-50; PMID:16391004; http://dx.doi.org/10.1093/nar/gki1012.
11. Wang J, Pantopoulos K. Regulation of cellular iron metabolism. Biochem J 2011; 434:365-81; PMID:21348856; http://dx.doi.org/10.1042/BJ20101825.
12. Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, et al. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 2010; 38(Database issue):D75-80; PMID:19880380; http://dx.doi.org/10.1093/nar/gkp902.
13. Dassi E, Malossini A, Re A, Mazza T, Tebaldi T, Caputi L, et al. AURA: Atlas of UTR Regulatory Activity. Bioinformatics 2011; http://dx.doi.org/10. 1093/bioin-formatics/btr608
14. Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 2011; 39(suppl 1):D301-8; PMID:21036867; http://dx.doi.org/10.1093/nar/gkq1069.
15. Khorshid M, Rodak C, Zavolan M. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res 2011; 39(suppl 1):D245-52; PMID:21087992; http://dx.doi.org/10.1093/nar/gkq940.
16. Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 2011; 39(Database issue):D202-9; PMID:21037263; http://dx.doi.org/10.1093/nar/gkq1056.
17. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2011; 39(Database issue):D163-9; PMID:21071411; http://dx.doi.org/10. 1093/nar/gkq1107.
18. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRe-cords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009; 37(Database issue):D105-10; PMID:18996891; http://dx.doi.org/10.1093/nar/gkn851.
19. Hsu SD, Chu CH, Tsou A P, Chen SJ, Chen HC, Hsu PW, et al. miRNAMap 2.0: genomic maps of microR-NAs in metazoan genomes. Nucleic Acids Res 2008; 36(Database issue):D165-9; PMID:18029362; http://dx.doi.org/10.1093/nar/gkm1012.
20. Cho S, Jun Y, Lee S, Choi HS, Jung S, Jang Y, et al. miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res 2011; 39(Database issue):D158-62; PMID:21062822; http://dx.doi.org/10.1093/nar/ gkq1094.
21. Bu D, Yu K, Sun S, Xie C, Skogerbø G, Miao R, et al. NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 2012; 40(Database issue):D210-5; PMID:22135294; http://dx.doi.org/10.1093/nar/gkr1175.
22. Amaral P P, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011; 39(Database issue):D146-51; PMID:21112873; http://dx.doi.org/10.1093/nar/gkq1138.
23. Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. NRED: a database of long noncoding RNA expression. Nucleic Acids Res 2009; 37(Database issue):D122-6; PMID:18829717; http://dx.doi.org/10.1093/nar/gkn617.
24. Bisognin A, Sales G, Coppe A, Bortoluzzi S, Romualdi C. MAGIA²: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Res 2012; 40(Web Server issue):W13-21; PMID:22618880; http://dx.doi.org/ 10.1093/nar/gks460.
25. Bakheet T, Williams BR, Khabar KS. ARED 3.0: the large and diverse AU-rich transcriptome. Nucleic Acids Res 2006; 34(Database issue):D111-4; PMID:16381826; http://dx.doi.org/10.1093/nar/gkj052.
26. Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL. AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res 2011; 39(Database issue):D66-9; PMID:21071424; http://dx.doi.org/10.1093/ nar/gkq990.
27. Mokrejs M, Masek T, Vopálensky V, Hlubucek P, Delbos P, Pospísek M. IRESite - a tool for the examination of viral and cellular internal ribosome entry sites. Nucleic Acids Res 2010; 38(Database issue):D131-6; PMID:19917642; http://dx.doi.org/10.1093/nar/gkp981.
28. Castellano S, Gladyshev VN, Guigó R, Berry MJ. SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements. Nucleic Acids Res 2008; 36(Database issue):D332-8; PMID:18174224; http://dx.doi.org/10.1093/nar/ gkm731.
29. Andken BB, Lim I, Benson G, Vincent JJ, Ferenc M T, Heinrich B, et al. 3'-UTR SIRF: a database for identifying clusters of whort interspersed repeats in 3' untranslated regions. BMC Bioinformatics 2007; 8:274; PMID:17663765; http://dx.doi.org/10.1186/1471-2105-8-274.
30. Gardner P P, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, et al. Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 2011; 39(Database issue):D141-5; PMID:21062808; http://dx.doi.org/10.1093/ nar/gkq1129.
31. Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, et al. doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res 2012; 40(Database issue):D180-6; PMID:22086949; http://dx.doi.org/10.1093/nar/gkr1007.
32. Jacobs GH, Chen A, Stevens SG, Stockwell PA, Black MA, Tate W P, et al. Transterm: a database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Res 2009; 37(Database issue):D72-6; PMID:18984623; http://dx.doi.org/10.1093/nar/gkn763.
33. Campillos M, Cases I, Hentze MW, Sanchez M. SIREs: searching for iron-responsive elements. Nucleic Acids Res 2010; 38(Webserver issue):W360-7; PMID:20460462; http://dx.doi.org/10.1093/nar/gkq371.
34. Lewis B P, Burge CB, Bartel D P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120:15-20; PMID:15652477; http://dx.doi.org/10.1016/j.cell.2004.12.035.
35. Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, et al. Combinatorial microRNA target predictions. Nat Genet 2005; 37:495-500; PMID:15806104; http://dx.doi.org/10.1038/ng1536.
36. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004; 2:e363; PMID:15502875; http://dx.doi.org/10. 1371/journal.pbio.0020363.
37. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007; 39:1278-84; PMID:17893677; http://dx.doi.org/10.1038/ng2135.
38. Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, Maragkakis M, et al. DIANA miR-Path v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res 2012; 40(Webserver issue):W498-504; PMID:22649059; http://dx.doi.org/10.1093/nar/gks494.
39. Huang GT, Athanassiou C, Benos PV. mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res 2011; 39(Webserver issue):W416-23; PMID:21558324; http://dx.doi.org/10.1093/nar/gkr276.
40. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003; 302:1212-5; PMID:14615540; http://dx.doi.org/10.1126/science.1090095.
41. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, et al. Transcriptome-wide identification of RNA-binding protein and microR-NA target sites by PAR-CLIP. Cell 2010; 141:129-41; PMID:20371350; http://dx.doi.org/10.1016/j. cell.2010.03.009.
42. König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 2010; 17:909-15; PMID:20601959; http://dx.doi.org/10.1038/nsmb.1838.
43. German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, et al. Global identification of microR-NA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008; 26:941-6; PMID:18542052; http://dx.doi.org/10.1038/ nbt1417.
44. Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res 2012; 40(D1):D918-23; PMID:22086951; http://dx.doi.org/10.1093/nar/gkr1055.
45. Hoffmann PR, Berry MJ. Selenoprotein synthesis: a unique translational mechanism used by a diverse family of proteins. Thyroid 2005; 15:769-75; PMID:16131320; http://dx.doi.org/10.1089/thy.2005.15.769.
46. Gong C, Maquat LE. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature 2011; 470:284-8; PMID:21307942; http://dx.doi.org/10.1038/nature09701.
47. Yoon JH, Abdelmohsen K, Srikantan S, Yang X, Martindale JL, De S, et al. LincRNA-p21 Suppresses Target mRNA Translation. Mol Cell 2012; 47:648-55; PMID:22841487; http://dx.doi.org/10.1016/j.mol-cel.2012.06.027.
48. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011; 27:431-2; PMID:21149340; http://dx.doi.org/10.1093/bioinfor-matics/btq675.
49. Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4:44-57; PMID:19131956; http://dx.doi.org/10.1038/nprot.2008.211.
50. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, et al. Ensembl 2012. Nucleic Acids Res 2012; 40(D1):D84-90; PMID:22086963; http://dx.doi.org/10.1093/nar/gkr991.
51. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006; 38:1289-97; PMID:17013392; http://dx.doi.org/10.1038/ng1901.
52. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim I F, et al. NCBI GEO: archive for functional genomics data sets - 10 years on. Nucleic Acids Res 2011; 39(Database issue):D1005-10; PMID:21097893; http://dx.doi.org/ 10.1093/nar/gkq1184.