mCarts: Genome-wide prediction of clustered sequence motifs as binding sites for RNA-binding proteins

Methods in Molecular Biology

Volumn 1421, Issue , 2016, Pages 215-226

  Weyn Vanhentenryck, Sebastien M ^a   Zhang, Chaolin ^a  

^a NONE

Author keywords

Binding site prediction; CLIP tag clusters; MCarts; Motif; RNA binding protein (RBP)

Indexed keywords

RNA; RNA BINDING PROTEIN;

ARTICLE; BINDING SITE; BIOINFORMATICS; EXON; GENE EXPRESSION REGULATION; IMMUNOPRECIPITATION; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN SECONDARY STRUCTURE; ANIMAL; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; CONFORMATION; GENOME; HUMAN; METABOLISM; PROBABILITY; PROCEDURES; SOFTWARE;

ANIMALS; BINDING SITES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; NUCLEIC ACID CONFORMATION; PROBABILITY; RNA; RNA-BINDING PROTEINS; SOFTWARE;

EID: 84961158630     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3591-8_17     Document Type: Article

References (20)

1. Licatalosi DD, Darnell RB (2010) RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 11:75–87
2. Ray D, Kazan H, Cook KB et al (2013) A compendium of RNA-binding motifs for decoding gene regulation. Nature 499:172–177
3. Cook KB, Kazan H, Zuberi K et al (2011) RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 39:D301–D308
4. Chasin LA (2007) Searching for splicing motifs. Adv Exp Med Biol 623:85–106
5. Galarneau A, Richard S (2005) Target RNA motif and target mRNAs of the Quaking STAR protein. Nat Struct Mol Biol 12:691–698
6. Licatalosi DD, Mele A, Fak JJ et al (2008) HITS- CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456:464–469
7. König J, Zarnack K, Rot G et al (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17:909–915
8. Moore MJ, Zhang C, Gantman EC et al (2014) Mapping Argonaute and conventional RNA- binding protein interactions with RNA at single- nucleotide resolution using HITSCLIP and CIMS analysis. Nat Protoc 9:263–293
9. Darnell RB (2010) HITS‐CLIP: panoramic views of protein–RNA regulation in living cells. Wiley Interdiscipl Rev RNA 1:266–286
10. Blencowe BJ, Ahmad S, Lee LJ (2009) Current- generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23:1379–1386
11. Maticzka D, Lange SJ, Costa F et al (2014) GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol 15:R17
12. Cereda M, Pozzoli U, Rot G et al (2014) RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol 15:R20
13. Han A, Stoilov P, Linares AJ et al (2014) De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PLoS Comput Biol 10:e1003442
14. Zhang C, Lee K-Y, Swanson MS et al (2013) Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res 41:6793–6807
15. Jelen N, Ule J, Živin M et al (2007) Evolution of nova-dependent splicing regulation in the brain. PLoS Genet 3:e173–e1847
16. Stein LD (2002) Unix survival guide. John Wiley, Hoboken, NJ
17. Buffalo V (2015) Bioinformatics data skills. O'Reilly Media, Sebastopol, CA
18. Zhang C, Frias MA, Mele A et al (2010) Integrative modeling defines the Nova splicing- regulatory network and its combinatorial controls. Science 329:439–443
19. Weyn-Vanhentenryck SM, Mele A, Yan Q et al (2014) HITS-CLIP and integrative modeling define the rbfox splicing-regulatory network linked to brain development and autism. Cell Rep 6:1139–1152
20. Hinrichs AS, Karolchik D, Baertsch R et al (2006) The UCSC genome browser database: update 2006. Nucleic Acids Res 34:D590–D598