Attar N: The RBPome: where the brains meet the brawn. Genome Biol. 2014, 15: 402-
Article
Google Scholar
Borsenberger V, Crowe MA, Lehbauer J, Raftery J, Helliwell M, Bhutia K, Cox T, Sutherland JD: Exploratory studies to investigate a linked prebiotic origin of RNA and coded peptides. Chem Biodivers. 2004, 1: 203-246. 10.1002/cbdv.200490020.
Article
CAS
Google Scholar
Bernhardt HS: The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biol Direct. 2012, 7: 23-10.1186/1745-6150-7-23.
Article
CAS
Google Scholar
Keren H, Lev-Maor G, Ast G: Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet. 2010, 11: 345-355. 10.1038/nrg2776.
Article
CAS
Google Scholar
Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J: Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell. 2013, 152: 453-466. 10.1016/j.cell.2012.12.023.
Article
CAS
Google Scholar
Gal-Mark N, Schwartz S, Ram O, Eyras E, Ast G: The pivotal roles of TIA proteins in 5′ splice-site selection of Alu exons and across evolution. PLOS Genet. 2009, 5: e1000717-10.1371/journal.pgen.1000717.
Article
Google Scholar
Kaneko S, Son J, Shen SS, Reinberg D, Bonasio R: PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells. Nat Struct Mol Biol. 2013, 20: 1258-1264. 10.1038/nsmb.2700.
Article
CAS
Google Scholar
Davidovich C, Zheng L, Goodrich KJ, Cech TR: Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol. 2013, 20: 1250-1257. 10.1038/nsmb.2679.
Article
CAS
Google Scholar
Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD: RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biol. 2014, 15: R3-10.1186/gb-2014-15-1-r3.
Article
Google Scholar
Schueler M, Munschauer M, Gregersen LH, Finzel A, Loewer A, Chen W, Landthaler M, Dieterich C: Differential protein occupancy profiling of the mRNA transcriptome. Genome Biol. 2014, 15: R15-10.1186/gb-2014-15-1-r15.
Article
Google Scholar
McHugh CA, Russell P, Guttman M: Methods for comprehensive experimental identification of RNA–protein interactions. Genome Biol. 2014, 15: 203-10.1186/gb4152.
Article
Google Scholar
Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB: CLIP identifies Nova-regulated RNA networks in the brain. Science. 2003, 302: 1212-1215. 10.1126/science.1090095.
Article
CAS
Google Scholar
Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J: Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol. 2012, 13: R67-10.1186/gb-2012-13-8-r67.
Article
Google Scholar
König J, Zarnack K, Luscombe NM, Ule J: Protein–RNA interactions: new genomic technologies and perspectives. Nat Rev Genet. 2011, 13: 77-83. 10.1038/ni.2154.
Article
Google Scholar
Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB: An RNA map predicting Nova-dependent splicing regulation. Nature. 2006, 444: 580-586. 10.1038/nature05304.
Article
CAS
Google Scholar
Zhang C, Lee KY, Swanson MS, Darnell RB: Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res. 2013, 41: 6793-6807. 10.1093/nar/gkt421.
Article
CAS
Google Scholar
Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB, Wang H, Licatalosi DD, Fak JJ, Darnell RB: Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science. 2010, 329: 439-443. 10.1126/science.1191150.
Article
CAS
Google Scholar
Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ: Deciphering the splicing code. Nature. 2010, 465: 53-59. 10.1038/nature09000.
Article
CAS
Google Scholar
Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ: AVISPA: a web tool for the prediction and analysis of alternative splicing. Genome Biol. 2013, 14: R114-10.1186/gb-2013-14-10-r114.
Article
Google Scholar
Fukunaka T, Ozaki H, Terai G, Asai K, Iwasaki W, Kiryu H: CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biol. 2014, 15: R16-10.1186/gb-2014-15-1-r16.
Article
Google Scholar
Chen B, Yun J, Kim MS, Mendell JT, Xie Y: PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. Genome Biol. 2014, 15: R18-10.1186/gb-2014-15-1-r18.
Article
Google Scholar
Wang T, Xie Y, Xiao G: dCLIP: a computational approach for comparative CLIP-seq analyses. Genome Biol. 2014, 15: R11-10.1186/gb-2014-15-1-r11.
Article
Google Scholar
Maticzka D, Lange SJ, Costa F, Backofen R: GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol. 2014, 15: R17-10.1186/gb-2014-15-1-r17.
Article
Google Scholar
Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, Ule J: RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol. 2014, 15: R20-
Article
Google Scholar
Mort M, Sterne-Weiler T, Li B, Ball EB, Cooper D, Radivojac P, Sanford J, Mooney SD: MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. Genome Biol. 2014, 15: R19-10.1186/gb-2014-15-1-r19.
Article
Google Scholar
Ulitsky I, Bartel DP: lincRNAs: genomics, evolution, and mechanisms. Cell. 2013, 154: 26-46. 10.1016/j.cell.2013.06.020.
Article
CAS
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. 2013, doi:10.1038/nature12756
Google Scholar
Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS: Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature. 2013, doi:10.1038/nature12894
Google Scholar
Jarvis K, Robertson M: The noncoding universe. BMC Biol. 2011, 9: 52-10.1186/1741-7007-9-52.
Article
Google Scholar
Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C: Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell. 2008, 32: 232-246. 10.1016/j.molcel.2008.08.022.
Article
CAS
Google Scholar
Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP: Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal. 2010, 3: ra8-
Google Scholar
Sun S, Del Rosario BC, Szanto A, Ogawa Y, Jeon Y, Lee JT: Jpx RNA activates Xist by evicting CTCF. Cell. 2013, 153: 1537-1551. 10.1016/j.cell.2013.05.028.
Article
CAS
Google Scholar
Marques AC, Tan J, Ponting CP: Wrangling for microRNAs provokes much crosstalk. Genome Biol. 2011, 12: 132-10.1186/gb-2011-12-11-132.
Article
CAS
Google Scholar
Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE: The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci U S A. 2011, 108: 20497-20502. 10.1073/pnas.1113536108.
Article
CAS
Google Scholar
Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M: The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013, 341: 1237973-10.1126/science.1237973.
Article
Google Scholar
Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA: Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell. 2008, 29: 499-509. 10.1016/j.molcel.2007.12.013.
Article
CAS
Google Scholar
Hussain S, Aleksic J, Blanco S, Dietmann S, Frye M: Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol. 2013, 14: 215-10.1186/gb4143.
Article
Google Scholar
Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE: The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol. 2012, 13: 175-10.1186/gb-2012-13-10-175.
Article
CAS
Google Scholar
Pinto Y, Cohen HY, Levanon EY: Mammalian conserved ADAR targets comprise only a small fragment of the human editosome. Genome Biol. 2014, 15: R5-10.1186/gb-2014-15-1-r5.
Article
Google Scholar
Lagier-Tourenne C, Cleveland DW: Rethinking ALS: the FUS about TDP-43. Cell. 2009, 136: 1001-1004. 10.1016/j.cell.2009.03.006.
Article
CAS
Google Scholar
Sterne-Weiler T, Sanford JR: Exon identity crisis: disease-causing mutations that disrupt the splicing code. Genome Biol. 2014, 15: 201-10.1186/gb4150.
Article
Google Scholar
Kechavarzi B, Janga SC: Dissecting the expression landscape of RNA-binding proteins in human cancers. Genome Biol. 2014, 15: R14-10.1186/gb-2014-15-1-r14.
Article
Google Scholar
Farazi TA, Hoeve JJ T, Brown M, Mihailovic A, Horlings HM, Vijver MJ Van D, Tuschl T, Wessels LF: Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets. Genome Biol. 2014, 15: R9-10.1186/gb-2014-15-1-r9.
Article
Google Scholar