RNA–protein interactions: An overview

Methods in Molecular Biology

Volumn 1097, Issue , 2014, Pages 491-521

  Re, Angela ^a   Joshi, Tejal ^a   Kulberkyte, Eleonora ^a   Morris, Quaid ^a   Workman, Christopher T ^a  

^a NONE

Author keywords

Cross Linking and ImmunoPrecipitation; RNA binding proteins; RNA binding domains; RNA binding sites; RNA binding specificity; RNAcompete; RNA protein interactions

Indexed keywords

DOUBLE STRANDED RNA; MESSENGER RNA; PROTEIN; RNA; RNA BINDING PROTEIN; DEAD BOX PROTEIN; LSM PROTEIN; RNA RECOGNITION MOTIF PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; GENE LOCATION; GENETIC ALGORITHM; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN RNA BINDING; REGULATORY MECHANISM; RNA ANALYSIS; RNA DEGRADATION; RNA EDITING; RNA PROCESSING; RNA STABILITY; RNA TRANSLATION; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PROTEIN BINDING; REVIEW; BREAST CANCER; CONTROLLED STUDY; CROSS LINKING; DNA BINDING; FRAGILE X SYNDROME; HUMAN; IMMUNOPRECIPITATION; MOUSE; MYOTONIC DYSTROPHY; NONHUMAN; OCULOPHARYNGEAL MUSCULAR DYSTROPHY; PARANEOPLASTIC NEUROPATHY; PARKINSON DISEASE; PROSTATE CANCER; PROTEIN CROSS LINKING; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; RNA BINDING; RNA STRUCTURE; ZINC FINGER MOTIF;

BINDING SITES; GENE EXPRESSION REGULATION; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; RNA; RNA, MESSENGER; RNA-BINDING PROTEINS;

EID: 84908519178     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-709-9__23     Document Type: Article

References (134)

1. Dieci G, Ruotolo R, Braglia P, Carles C, Carpentieri A, Amoresano A, Ottonello S (2009) Positive modulation of RNA polymerase III transcription by ribosomal proteins. Biochem Biophys Res Commun 379 (2):489–493. doi:10.1016/j.bbrc.2008. 12.097
2. Wan F, Anderson DE, Barnitz RA, Snow A, Bidere N, Zheng L, Hegde V, Lam LT, Staudt LM, Levens D, Deutsch WA, Lenardo MJ (2007) Ribosomalprotein S3: a KH domain subunit inNF-kappaB complexes that mediates selectivegene regulation. Cell 131(5):927–939.doi:10.1016/j.cell.2007.10.009
3. Whitelaw E, Proudfoot N (1986) Alphathalassaemiacaused by a poly(a) site mutationreveals that transcriptional terminationis linked to 3’ end processing inthe human alpha 2 globin gene. EMBOJ 5(11):2915–2922. http://www.hubmed.org/fulltext.cgi?uids=3024968
4. Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE (2007) Unproductivesplicing of sr genes associatedwith highly conserved and ultraconserveddna elements. Nature 446(7138):926–929.doi:10.1038/nature05676
5. Holt CE, Bullock SL (2009) SubcellularmRNA localization in animal cells and whyit matters. Science 326(5957):1212–1216.doi:10.1126/science.1176488
6. Bertrand E, Chartrand P, Schaefer M, Shenoy SM, Singer RH, Long RM (1998) Localizationof ASH1 mRNA particles in livingyeast. Mol Cell 2(4):437–445. http://www.hubmed.org/fulltext.cgi?uids=9809065
7. Lécuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM (2007) Global analysis of mRNAlocalization reveals a prominent role inorganizing cellular architecture and function. Cell 131(1):174–187. doi:10.1016/j.cell.2007.08.003. http://www.hubmed.org/fulltext.cgi? uids=17923096
8. Grünwald D, Singer RH, Rout M (2011) Nuclear export dynamics of RNA-proteincomplexes. Nature 475(7356): 333–341doi:10.1038/nature10318
9. Wolke U, Weidinger G, Köprunner M, Raz E (2002) Multiple levels of posttranscriptionalcontrol lead to germ line-specificgene expression in the zebrafish. Curr Biol1 2 (4):289–294
10. Lipshitz HD, Smibert CA (2000) Mechanismsof RNA localization and translationalregulation. Curr Opin Genet Dev 10 (5):476–488. http://www.hubmed.org/fulltext.cgi?uids=10980424
11. Chartrand P, Meng XH, Huttelmaier S, Donato D, Singer RH (2002) Asymmetricsorting of ash1p in yeast results from inhibitionof translation by localization elements inthe mRNA. Mol Cell 10(6):1319–1330
12. Lewis RA, Kress TL, Cote CA, Gautreau D, Rokop ME, Mowry KL (2004) Conservedand clustered RNA recognition sequences area critical feature of signals directing RNAlocalization in xenopus oocytes. Mech Dev 121 (1):101–109
13. Macdonald PM, Struhl G (1988) cis-actingsequences responsible for anterior localizationof bicoid mRNA in drosophila embryos. Nature 336 (6199):595–598. doi:10.1038/336595a0
14. Cenik C, Chua HN, Zhang H, Tarnawsky SP, Akef A, Derti A, Tasan M, Moore MJ, Palazzo AF, Roth FP (2011) Genome analysisreveals interplay between 5’utr intronsand nuclear mRNA export for secretoryand mitochondrial genes. PLoS Genet 7 (4). doi:10.1371/journal.pgen.1001366. http://www.hubmed.org/fulltext.cgi?uids=21533221
15. Palazzo AF, Springer M, Shibata Y, Lee CS, Dias AP, Rapoport TA (2007) Thesignal sequence coding region promotesnuclear export of mRNA. PLoS Biol 5 (12). doi:10.1371/journal.pbio.0050322. http://www.hubmed.org/fulltext.cgi?uids=18052610
16. Arn EA, Cha BJ, Theurkauf WE, Macdonald PM (2003) Recognition of a bicoid mRNAlocalization signal by a protein complex containingswallow, nod, and RNA binding proteins. Dev Cell 4(1):41–51
17. Müller M, Heym RG, Mayer A, Kramer K, Schmid M, Cramer P, Urlaub H, Jansen RP, Niessing D (2011) A cytoplasmiccomplex mediates specific mRNA recognitionand localization in yeast. PLoS Biol 9 (4). doi:10.1371/journal.pbio.1000611. http://www.hubmed.org/fulltext.cgi?uids=21526221
18. Tadros W, Goldman AL, Babak T, Menzies F, Vardy L, Orr-Weaver T, Hughes TR, Westwood JT, Smibert CA, Lipshitz HD (2007) Smaug is a major regulatorof maternal mRNA destabilization indrosophila and its translation is activated bythe PAN GU kinase. Dev Cell 12(1):143–55.doi:10.1016/j.devcel.2006.10.005
19. Forrest KM, Gavis ER (2003) Live imagingof endogenous RNA reveals a diffusionand entrapment mechanism for nanosmRNA localization in drosophila. Curr Biol1 3 (14):1159–1168
20. Gebauer F, Hentze MW (2004) Molecularmechanisms of translational control. Nat Rev Mol Cell Biol 5(10):827–835.doi:10.1038/nrm1488
21. Jackson RJ, Hellen CUT, Pestova TV (2010) The mechanism of eukaryotic translationinitiation and principles of its regulation. Nat Rev Mol Cell Biol 11 (2):113–127.doi:10.1038/nrm2838
22. Loh PG, Song H (2010) Structural andmechanistic insights into translation termination. Curr Opin Struct Biol 20(1):98–103.doi:10.1016/j.sbi.2009.12.005
23. Gingold H, Pilpel Y (2011) Determinants oftranslation efficiency and accuracy. Mol SystBiol 7:481. doi:10.1038/msb.2011.14
24. Dever TE (2002) Gene-specific regulationby general translation factors. Cell1 08 (4):545–556
25. Muckenthaler M, Gray NK, Hentze MW (1998) Irp-1 binding to ferritin mRNA preventsthe recruitment of the small ribosomalsubunit by the cap-binding complex eif4f. Mol Cell 2 (3):383–388
26. Gebauer F, Grskovic M, Hentze MW (2003) Drosophila sex-lethal inhibits the stable associationof the 40S ribosomal subunit withmsl-2 mRNA. Mol Cell 11 (5):1397–1404
27. Grskovic M, Hentze MW, Gebauer F (2003) A co-repressor assembly nucleatedby sex-lethal in the 3’utr mediatestranslational control of drosophila msl-2 mRNA. EMBO J 22(20):5571–5581.doi:10.1093/emboj/cdg539
28. Beckmann K, Grskovic M, Gebauer F, Hentze MW (2005) A dual inhibitorymechanism restricts msl-2 mRNA translationfor dosage compensation in drosophila. Cell1 22 (4):529–540. doi:10.1016/j.cell.2005.06.011
29. Nelson MR, Leidal AM, Smibert CA (2004) Drosophila cup is an eif4e-binding proteinthat functions in smaug-mediated translationalrepression. EMBO J 23 (1):150–159.doi:10.1038/sj.emboj.7600026
30. Nakamura A, Sato K, Hanyu-Nakamura K (2004) Drosophila cup is an eif4e bindingprotein that associates with bruno and regulatesoskar mRNA translation in oogenesis. Dev Cell 6 (1):69–78
31. Stebbins-Boaz B, Cao Q, de Moor CH, Mendez R, Richter JD (1999) Maskin is acpeb-associated factor that transiently interactswith elf-4e. Mol Cell 4(6):1017–1027
32. Ostareck DH, Ostareck-Lederer A, Shatsky IN, Hentze MW (2001) LipoxygenasemRNA silencing in erythroid differentiation:The 3’utr regulatory complex controls60S ribosomal subunit joining. Cell1 04 (2):281–290
33. Chaudhury A, Hussey GS, Ray PS, Jin G, Fox PL, Howe PH (2010) TGF-betamediatedphosphorylation of hnRNP E1induces EMT via transcript-selective translationalinduction of Dab2 and ILEI. Nat CellBiol 12(3):286–293. doi:10.1038/ncb2029
34. Hussey GS, Chaudhury A, Dawson AE, Lindner DJ, Knudsen CR, Wilce MCJ, Merrick WC, Howe PH (2011) Identification ofan mRNP complex regulating tumorigenesisat the translational elongation step. MolCell 41(4): 419–431. doi:10.1016/j.molcel.2011.02.003
35. Doma MK, Parker R (2007) RNA qualitycontrol in eukaryotes. Cell 131(4):660–668.doi:10.1016/j.cell.2007.10.041
36. Villalba A, Coll O, Gebauer F (2011) Cytoplasmicpolyadenylation and translationalcontrol. Curr Opin Genet Dev 21(4):452–457. doi:10.1016/j.gde.2011. 04.006
37. Piqué M, López JM, Foissac S, Guigó R, Méndez R (2008) A combinatorialcode for cpe-mediated translational control. Cell 132(3):434–448. doi:10.1016/j.cell.2007.12.038
38. Kim KW, Nykamp K, Suh N, Bachorik JL, Wang L, Kimble J (2009) Antagonismbetween gld-2 binding partners controlsgamete sex. Dev Cell 16(5):723–733.doi:10.1016/j.devcel.2009.04.002
39. Reed R, Hurt E (2002) A conserved mRNAexport machinery coupled to pre-mRNAsplicing. Cell 108(4):523–531
40. Houseley J, LaCava J, Tollervey D (2006) RNA-quality control by the exosome. Nat Rev Mol Cell Biol 7 (7):529–539doi:10.1038/nrm1964
41. LaCava J, Houseley J, Saveanu C, Petfalski E, Thompson E, Jacquier A, Tollervey D (2005) RNA degradation bythe exosome is promoted by a nuclearpolyadenylation complex. Cell 121(5):713–724. doi:10.1016/j.cell.2005.04.029
42. Isken O, Maquat LE (2008) The multiplelives of nmd factors: balancing roles ingene and genome regulation. Nat Rev Genet 9 (9):699–712. doi:10.1038/nrg2402
43. Kong J, Liebhaber SA (2007) A cell typerestrictedmRNA surveillance pathway triggeredby ribosome extension into the 3’untranslated region. Nat Struct Mol Biol1 4 (7):670–676. doi:10.1038/nsmb1256
44. Hir HL, Gatfield D, Izaurralde E, Moore MJ (2001) The exon-exon junction complex providesa binding platform for factors involvedin mRNA export and nonsense-mediatedmRNA decay. EMBO J 20(17):4987–4997.doi:10.1093/emboj/20.17.4987
45. Behm-Ansmant I, Gatfield D, Rehwinkel J, Hilgers V, Izaurralde E (2007) A conservedrole for cytoplasmic poly(a)-bindingprotein 1 (pabpc1) in nonsense-mediatedmRNA decay. EMBO J 26(6):1591–601.doi:10.1038/sj.emboj.7601588
46. González CI, Ruiz-Echevarría MJ, Vasudevan S, Henry MF, Peltz SW (2000) Theyeast hnRNP-like protein Hrp1/Nab4 marksa transcript for nonsense-mediated mRNAdecay. Mol Cell 5(3):489–499
47. Hwang J, Sato H, Tang Y, Matsuda D, Maquat LE (2010) Upf1 association withthe cap-binding protein, cbp80, promotesnonsense-mediated mRNA decay at twodistinct steps. Mol Cell 39(3):396–409.doi:10.1016/j.molcel.2010.07.004
48. Ruiz-Echevarría MJ, Peltz SW (2000) TheRNA binding protein pub1 modulates thestability of transcripts containing upstreamopen reading frames. Cell 101(7):741–751
49. Chester A, Somasekaram A, Tzimina M, Jarmuz A, Gisbourne J, O’Keefe R, Scott J, Navaratnam N (2003) The apolipoproteinb mRNA editing complex performs a multifunctionalcycle and suppresses nonsensemediateddecay. EMBO J 22 (15) 3971–3982.doi:10.1093/emboj/cdg369
50. Stalder L, Mühlemann O (2008) The meaning of nonsense. Trends Cell Biol 18 (7):315–321.doi:10.1016/j.tcb.2008.04.005
51. Inada T, Aiba H (2005) Translation ofaberrant mRNAs lacking a terminationcodon or with a shortened 3’-UTR is repressed after initiation inyeast. EMBO J 24(8):1584–1595.doi:10.1038/sj.emboj.7600636
52. Kim YK, Furic L, Desgroseillers L, Maquat LE (2005) Mammalian Staufen1 recruitsUpf1 to specific mRNA 3’UTRs so as toelicit mRNA decay. Cell 120(2):195–208.doi:10.1016/j.cell.2004.11.050
53. Kaygun H, Marzluff WF (2005) Translationtermination is involved in histonemRNA degradation when DNA replication isinhibited. Mol Cell Biol 25(16):6879–6888.doi:10.1128/MCB.25.16.6879-6888.2005
54. Wulff BE, Sakurai M, Nishikura K (2011) Elucidating the inosinome: globalapproaches to adenosine-to-inosine RNAediting. Nat Rev Genet 12 (2):81–85. doi:10.1038/nrg2915. http://www.hubmed.org/fulltext.cgi?uids=21173775
55. Bass BL (2002) RNA editing byadenosine deaminases that act onRNA. Annu Rev Biochem 71:817–846.doi:10.1146/annurev.biochem.71.110601.135501. http://www.hubmed.org/fulltext.cgi?uids=12045112
56. Eggington JM, Greene T, Bass BL (2011) Predicting sites of adar editing in doublestrandedRNA. Nat Commun 2: 319–319.doi:10.1038/ncomms1324. http://www.hubmed.org/fulltext.cgi?uids=21587236
57. Hundley HA, Bass BL (2010) Adar editingin double-stranded utrs and other noncodingRNA sequences. Trends Biochem Sci 35 (7): 377–383. doi:10.1016/j.tibs.2010.02.008. http://www.hubmed.org/fulltext.cgi?uids=20382028
58. Jepson JE, Reenan RA (2008) RNA editingin regulating gene expression in thebrain. Biochim Biophys Acta 1779 (8):59–470. doi:10. 1016/j.bbagrm.2007.11.009. http:// www.hubmed.org/fulltext.cgi?uids=18086576
59. Hoopengardner B, Bhalla T, Staber C, Reenan R (2003) Nervous system targetsof RNA editing identified by comparativegenomics. Science 301 (5634): 832–836. doi:10.1126/science.1086763. http://www.hubmed.org/fulltext.cgi? uids=12907802
60. Paz-Yaacov N, Levanon EY, Nevo E, Kinar Y, Harmelin A, Jacob-Hirsch J, Amariglio N, Eisenberg E, Rechavi G(2010) Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates. Proc Natl Acad Sci USA 107(27):12174-12179. doi:10.1073/pnas.1006183107. http://www.hubmed.org/fulltext.cgi?uids= 20566853
61. Nishikura K (2010) Functions andregulation of RNA editing by adardeaminases. Annu Rev Biochem 79:321–349. doi:10.1146/annurev-biochem-060208-105251. http://www.hubmed.org/fulltext.cgi?uids=20192758
62. Chen SH, Habib G, Yang CY, Gu ZW, Lee BR, Weng SA, Silberman SR, Cai SJ, Deslypere JP, Rosseneu M (1987) Apolipoprotein b-48 is the productof a messenger RNA with an organspecificin-frame stop codon. Science 238 (4825): 363–366.http://www.hubmed.org/fulltext.cgi?uids=3659919
63. Powell LM, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J (1987) A novelform of tissue-specific RNA processing producesapolipoprotein-b48 in intestine. Cell 50 (6):831–840. http://www.hubmed.org/fulltext.cgi?uids=3621347
64. Rosenberg BR, Hamilton CE, Mwangi MM, Dewell S, Papavasiliou FN (2011) Transcriptome-wide sequencing revealsnumerous apobec1 mrna-editing targets intranscript 3’ UTRs. Nat Struct Mol Biol 18(2):230–236. doi:10.1038/nsmb.1975. http://www.hubmed.org/fulltext.cgi?uids=21258325
65. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG (2011) WidespreadRNA and DNA sequence differences inthe human transcriptome. Science 333 (6038):53–58. doi:10.1126/science.1207018. http://www.hubmed.org/fulltext.cgi?uids=21596952
66. Schrider DR, Gout JF, Hahn MW (2011) Very few RNA and DNA sequence differencesin the human transcriptome. PLoS One 6(10). doi:10.1371/journal.pone.0025842. http://www.hubmed.org/fulltext.cgi?uids=22022455
67. Barreau C, Paillard L, Osborne HB (2005) Au-rich elements and associatedfactors: are there unifying principles?. Nucleic Acids Res 33 (22):7138–7150.doi:10.1093/nar/gki1012
68. Lal A, Mazan-Mamczarz K, Kawai T, Yang X, Martindale JL, Gorospe M (2004) Concurrent versus individual binding ofHuR and AUF1 to common labile targetmRNAs. EMBO J 23 (15):3092–3102.doi:10.1038/sj.emboj.7600305
69. Sobue S, Murakami M, Banno Y, Ito H, Kimura A, Gao S, Furuhata A, Takagi A, Kojima T, Suzuki M, Nozawa Y, Murate T (2008) v-Src oncogene productincreases sphingosine kinase 1 expressionthrough mRNA stabilization: alterationof AU-rich element-binding proteins. Oncogene 27 (46):6023–6033. doi:10.1038/onc.2008.198
70. Kedde M, Strasser MJ, Boldajipour B, Oude Vrielink JA, Slanchev K, le Sage C, Nagel R, Voorhoeve PM, van Duijse J, Ørom UA, Lund AH, Perrakis A, Raz E, Agami R (2007) RNA-bindingprotein Dnd1 inhibits microRNA accessto target mRNA. Cell 131(7):1273–1286.doi:10.1016/j.cell.2007.11.034
71. Burns DM, D’Ambrogio A, Nottrott S, Richter JD (2011) Cpeb andtwo poly(a) polymerases controlmir-122 stability and p53 mRNAtranslation. Nature 473(7345):105–108.doi:10.1038/nature09908
72. Abdelmohsen K, Hutchison ER, Lee EK, Kuwano Y, Kim MM, Masuda K, Srikantan S, Subaran SS, Marasa BS, Mattson MP, Gorospe M (2010) miR-375 inhibits differentiationof neurites by lowering HuDlevels. Mol Cell Biol 30 (17):4197–4210.doi:10.1128/MCB.00316-10
73. Deschenes-Furry J, Perrone-Bizzozero N, Jasmin BJ (2006) The RNA-binding proteinHuD: a regulator of neuronal differentiation,maintenance and plasticity. Bioessays 28:822–833
74. Lukong K, Chang K, Khandjian E, Richard S (2008) RNA-binding proteins in humangenetic disease. Trends Genet 24 (8):416–425. ISSN 01689525. doi:10.1016/j.tig.2008.05.004. http://linkinghub.elsevier.com/retrieve/pii/S016895250800173X
75. Yang YY, Yin GL, Darnell RB (1998) Theneuronal RNA-binding protein Nova-2 isimplicated as the autoantigen targeted inPOMA patients with dementia. Proc NatlAcad Sci USA 95:13254–13259
76. Song L, Wang L, Li Y, Xiong H, Wu J, Li J, Li M (2010) Sam68 up-regulation correlateswith, and its down-regulation inhibits, proliferationand tumourigenicity of breast cancercells. J Pathol 222:227–237
77. Busa R, Paronetto MP, Farini D, Pierantozzi E, Botti F, Angelini DF, Attisani F, Vespasiani G, Sette C (2007) The RNAbindingprotein sam68 contributes to proliferationand survival of human prostate cancercells. Oncogene 26 (30):4372–4382. ISSN0950-9232. http://dx.doi.org/10.1038/sj.onc.1210224
78. Wang R, Geng J, Wang JH, Chu XY, Geng HC, Chen LB (2009) Overexpression ofeukaryotic initiation factor 4E (eIF4E) and itsclinical significance in lung adenocarcinoma. Lung Cancer 66:237–244
79. Keene JD (2007) RNA regulons: coordinationof post-transcriptional events. NatRev Genet 8 (7):533–543. ISSN 1471-0056.doi:10.1038/nrg2111. http://www.nature.com/doifinder/10.1038/nrg2111
80. Cléry A, Blatter M, Allain FH (2008) RNA recognition motifs: boring?. notquite. Curr Opin Struct Biol 18 (3):290–298. doi:10.1016/j.sbi.2008.04.002. http://www.hubmed.org/fulltext.cgi?uids=18515081
81. Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FH (2005) Structure of PTB bound to RNA:specific binding and implications for splicingregulation. Science 309 (5743): 2054–2057.doi:10.1126/science.1114066. http://www.hubmed.org/fulltext.cgi?uids=16179478
82. Lewis HA, Musunuru K, Jensen KB, Edo C, Chen H, Darnell RB, Burley SK (2000) Sequence-specific RNA binding by a NovaKH domain: implications for paraneoplasticdisease and the fragile X syndrome. Cell 100 (3): 323–332
83. Liu Z, Luyten I, Bottomley MJ, Messias AC, Houngninou-Molango S, Sprangers R, Zanier K, Krämer A, Sattler M (2001) Structural basis for recognition of theintron branch site RNA by splicingfactor 1. Science 294 (5544): 1098–1102. doi:10.1126/science.1064719
84. Beuth B, Pennell S, Arnvig KB, Martin SR, Taylor IA (2005) Structure of amycobacterium tuberculosis nusa-rnacomplex. EMBO J 24(20):3576–3587.doi:10.1038/sj.emboj.7600829
85. Diges CM, Uhlenbeck OC (2001) Escherichia coli DbpA is an RNAhelicase that requires hairpin 92 of 23SRNA. EMBO J 20 (19):5503–5512.doi:10.1093/emboj/20.19.5503
86. Wang S, Hu Y, Overgaard MT, Karginov FV, Uhlenbeck OC, McKay DB (2006) Thedomain of the Bacillus subtilis DEAD-boxhelicase YxiN that is responsible for specificbinding of 23S rRNA has an RNArecognition motif fold. RNA 12(6):959–967.doi:10.1261/rna.5906
87. Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) Nucleation, propagation andcleavage of target rnas in ago silencingcomplexes. Nature 461 (7265):754–761.doi:10.1038/nature08434
88. Siomi MC, Sato K, Pezic D, Aravin AA (2011) Piwi-interacting small RNAs: thevanguard of genome defence. Nat RevMol Cell Biol 12 (4):246–258. doi:10.1038/nrm3089
89. Wilusz CJ, Wilusz J (2005) EukaryoticLsm proteins: lessons from bacteria. NatStruct Mol Biol 12 (12):1031–1036. doi:10.1038/nsmb1037. http://www.hubmed.org/fulltext.cgi?uids=16327775
90. Qiao F, Bowie JU (2005) The many faces ofSAM. Sci STKE 2005(286). doi:10.1126/stke.2862005re7. http://www.hubmed.org/fulltext.cgi?uids=15928333
91. Aviv T, Lin Z, Ben-Ari G, Smibert CA, Sicheri F (2006) Sequence-specific recognition ofRNA hairpins by the SAM domain ofVts1p. Nat Struct Mol Biol 13 (2):168–176.doi:10.1038/nsmb1053. http://www.hubmed.org/fulltext.cgi?uids=16429151
92. Oberstrass FC, Lee A, Stefl R, Janis M, Chanfreau G, Allain FH (2006) Shapespecificrecognition in the structure ofthe Vts1p SAM domain with RNA. Nat Struct Mol Biol 13 (2):160–167.doi:10.1038/nsmb1038. http://www.hubmed.org/fulltext.cgi?uids=16429156
93. Stefl R, Skrisovska L, Allain FH-T (2005) RNA sequence- and shapedependentrecognition by proteins inthe ribonucleoprotein particle. EMBO Rep 6 (1):33–38. doi:10.1038/sj.embor.7400325
94. Lunde BM, Moore C, Varani G (2007) RNA-binding proteins: modular design forefficient function. Nat Rev Mol Cell Biol 8 (6):479–490. doi:10.1038/nrm2178
95. Mazza C, Segref A, Mattaj IW, Cusack S (2002) Large-scale induced fit recognitionof an m(7)GpppG cap analogue by thehuman nuclear cap-binding complex. EMBOJ 21 (20):5548–5557
96. Mackay JP, Font J, Segal DJ (2011) Theprospects for designer single-stranded rnabindingproteins. Nat Struct Mol Biol1 8 (3):256–261. doi:10.1038/nsmb.2005
97. Gagnon KT, Maxwell ES (2011) Electrophoretic mobility shift assay forcharacterizing rna-protein interaction.Method. Mol Biol 703: 275–291.doi:10.1007/978-1-59745-248-9-19
98. Tuerk C, Gold L (1990) Systematic evolutionof ligands by exponential enrichment: RNAligands to bacteriophage t4 DNA polymerase.Science 249(4968):505–510. http://www.hubmed.org/fulltext.cgi?uids=2200121
99. Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR (2009) Rapid and systematicanalysis of the rna recognition specificitiesof RNA-binding proteins. Nat Biotechnol 27 (7):667–670. doi:10.1038/nbt.1550
100. Keene JD, Komisarow JM, Friedersdorf MB (2006) Rip-chip: the isolation and identificationof mRNAs, microRNAs and proteincomponents of ribonucleoprotein complexesfrom cell extracts. Nat Protoc 1 (1): 302–307.doi:10.1038/nprot.2006.47
101. Mili S, Steitz JA (2004) Evidence forreassociation of rna-binding proteinsafter cell lysis: implications for theinterpretation of immunoprecipitationanalyses. RNA 10(11):1692–1694.doi:10.1261/rna.7151404
102. Zhang C, Darnell RB (2011) Mapping in vivoprotein-RNA interactions at single-nucleotideresolution from hits-clip data. Nat Biotechnol 29 (7): 607–614. doi:10.1038/nbt.1873. http://www.hubmed.org/fulltext.cgi?uids=21633356
103. Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M (2011) Aquantitative analysis of CLIP methods foridentifying binding sites of RNA–bindingproteins. Nat Method 8 (7):559–564.doi:10.1038/nmeth.1608. http://www.hubmed.org/fulltext.cgi?uids=21572407
104. Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U (2011) PARalyzer: definition of RNA bindingsites from PAR–CLIP short-read sequencedata. Genome Biol 12 (8). doi:10.1186/gb-2011-12-8-r79. http://www.hubmed.org/fulltext.cgi?uids=21851591
105. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T (2010) Transcriptome-wide identification of RNAbindingprotein and microRNA targetsites by par-clip. Cell 141 (1):129–141.doi:10.1016/j.cell.2010.03.009
106. Silness J, Berge M (1990) Changes over timein the clientele and restoration pattern in adental school prosthodontic department. IntDent J 40(2):109–116
107. Li X, Quon G, Lipshitz HD, Morris Q (2010) Predicting in vivo binding sitesof RNA-binding proteins using mRNAsecondary structure. RNA 16 (6):1096–1107. doi:10.1261/rna.2017210. http://www.hubmed.org/fulltext.cgi?uids=20418358
108. Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U (2010) Evidencerankedmotif identification. Genome Biol 11 (2):R19. doi:10.1186/gb-2010-11-2-r19
109. Siddharthan R, Siggia ED, vanNimwegen E (2005) Phylogibbs: a gibbssampling motif finder that incorporatesphylogeny. PLoS Comput Biol 1(7):e67.doi:10.1371/journal.pcbi.0010067
110. Zielinski J, Kilk K, Peritz T, Kannanayakal T, Miyashiro KY, Eiríksdóttir E, Jochems J, Langel U, Eberwine J (2006) In vivoidentification of ribonucleoprotein-RNAinteractions. Proc Natl Acad Sci USA 103 (5):1557–1562. doi:10.1073/pnas.0510611103. http://www.hubmed.org/fulltext.cgi?uids=16432185
111. Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognitionof DNA by strand displacement with athymine-substituted polyamide. Science 254 (5037):1497–1500. http://www.hubmed.org/fulltext.cgi?uids=1962210
112. Butter F, Scheibe M, Mörl M, Mann M (2009) Unbiased RNA-protein interactionscreen by quantitative proteomics. ProcNatl Acad Sci USA 106 (26): 10626–10631. doi:10.1073/pnas.0812099106. http://www.hubmed.org/fulltext.cgi?uids=19541640
113. Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR (2011) RBPDB: a databaseof RNA-binding specificities. NucleicAcids Res 39 (Database issue): 301–308. doi:10.1093/nar/gkq1069. http://www.hubmed.org/fulltext.cgi?uids=21036867
114. Khorshid M, Rodak C, Zavolan M (2011) Clipz: a database and analysis environmentfor experimentally determined bindingsites of RNA-binding proteins. NucleicAcids Res 39 (Database issue): 245–252. doi:10.1093/nar/gkq940. http://www.hubmed.org/fulltext.cgi?uids=21087992
115. Lewis BA, Walia RR, Terribilini M, Ferguson J, Zheng C, Honavar V, Dobbs D (2011) PRIDB: a protein-RNA interfacedatabase. Nucleic Acids Res 39 (Databaseissue): 277–282. doi:10.1093/nar/gkq1108. http://www.hubmed.org/fulltext.cgi?uids=21071426
116. Allers J, Shamoo Y (2001) Structurebasedanalysis of protein-RNAinteractions using the programentangle. J Mol Biol 311(1):75–86.doi:10.1006/jmbi.2001.4857
117. Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N (2010) Prosite, aprotein domain database for functionalcharacterization and annotation. NucleicAcids Res 38(Database issue):D161–D166.doi:10.1093/nar/gkp885
118. Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB (2008) Fr3d: finding localand composite recurrent structural motifsin RNA 3D structures. J Math Biol 56(1–2):215–252. doi:10.1007/s00285-007-0110-x
119. Paradis E, Claude J, Strimmer K (2004) Ape:analyses of phylogenetics and evolution inR language. Bioinformatics 20 (2):289–290. http://www.hubmed.org/fulltext.cgi?uids=14734327
120. Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM (2011) Computational methods for predictionof protein-RNA interactions. J Struct Biol.doi:10.1016/j.jsb.2011.10.001
121. Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ (2008) Prediction of interacting singlestrandedRNA bases by protein-bindingpatterns. J Mol Biol 379 (2): 299–316. doi:10.1016/j.jmb.2008.03.043
122. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (2005) Assessing computationaltools for the discovery of transcriptionfactor binding sites. Nat Biotechnol 23 (1): 137–144. doi:10.1038/nbt1053. http://www.hubmed.org/display.cgi?uids=15637633
123. Bailey TL, Elkan C (1994) Fitting a mixturemodel by expectation maximization to discovermotifs in biopolymers. Proc Int ConfIntell Syst Mol Biol 2:28–36. http://www.hubmed.org/display.cgi?uids=7584402
124. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematic discovery ofregulatory motifs in human promotersand 3’ UTRs by comparison of severalmammals. Nature 434(7031):338–345.doi:10.1038/nature03441
125. Hiller M, Pudimat R, Busch A, Backofen R (2006) Using RNA secondary structures toguide sequence motif finding towards singlestrandedregions. Nucleic Acids Res 34 (17).doi:10.1093/nar/gkl544. http://www.hubmed.org/fulltext.cgi?uids=16987907
126. Bompfünewerer AF, Backofen R, Bernhart SH, Hertel J, Hofacker IL, Stadler PF, Will S (2008) Variations on RNAfolding and alignment: lessons frombenasque. J Math Biol 56 (1–2):129–144. doi:10.1007/s00285-007-0107-5. http://www.hubmed.org/fulltext.cgi?uids=17611759
127. Pavesi G, Mauri G, Stefani M, Pesole G (2004) Rnaprofile: an algorithm forfinding conserved secondary structuremotifs in unaligned rna sequences. Nucleic Acids Res 32(10):3258–3269.doi:10.1093/nar/gkh650
128. Sankoff D (1985) Simultaneous solution ofthe RNA folding, alignment, and protosequenceproblems. SIAM J Appl Math 45:810–825
129. Eddy SR, Durbin R (1994) RNA sequenceanalysis using covariance models. NucleicAcids Res 22(11):2079–2088. http://www.hubmed.org/fulltext.cgi?uids=8029015
130. Yao Z, Weinberg Z, Ruzzo WL (2006) Cmfinder–a covariance modelbased RNA motif finding algorithm. Bioinformatics 22 (4): 445–452.doi:10.1093/bioinformatics/btk008
131. Michal Rabani, Michael Kertesz, Eran Segal (2008) Computational predictionof RNA structural motifs involved inposttranscriptional regulatory processes. ProcNatl Acad Sci USA 105(39):14885–14890.doi:10.1073/pnas.0803169105
132. Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ (2005) Profiling conditionspecific,genome-wide regulation of mRNAstability in yeast. Proc Natl Acad SciUSA 102 (49):17675–17680. doi:10.1073/pnas.0503803102. http://www.hubmed.org/fulltext.cgi?uids=16317069
133. Foat BC, Stormo GD (2009) Discoveringstructural cis-regulatory elements bymodeling the behaviors of mRNAs. Mol SystBiol 5: 268–268. doi:10.1038/msb.2009.24. http://www.hubmed.org/fulltext.cgi?uids=19401680
134. Kazan H, Ray D, Chan ET, Hughes TR, Morris Q (2010) Rnacontext: a newmethod for learning the sequence and structurebinding preferences of RNA-bindingproteins. PLoS Comput Biol 6:e1000832.doi:10.1371/journal.pcbi.1000832