Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

Nature Methods

Volumn 13, Issue 6, 2016, Pages 508-514

  Van Nostrand, Eric L ^a   Pratt, Gabriel A ^a   Shishkin, Alexander A ^b   Gelboin Burkhart, Chelsea ^a   Fang, Mark Y ^a   Sundararaman, Balaji ^a   Blue, Steven M ^a   Nguyen, Thai B ^a   Surka, Christine ^b   Elkins, Keri ^a   Stanton, Rebecca ^a   Rigo, Frank ^c   Guttman, Mitchell ^b   Yeo, Gene W ^a,d,e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b California Institute of Technology   (United States)

^c ISIS PHARMACEUTICALS   (United States)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^e AGENCY FOR SCIENCE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEOPROTEIN; RNA BINDING PROTEIN; TRANSCRIPTOME; UNTRANSLATED RNA; CROSS LINKING REAGENT;

ARTICLE; BINDING SITE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; PRIORITY JOURNAL; PROTEIN BINDING; SIGNAL NOISE RATIO; ULTRAVIOLET CROSSLINKING AND IMMUNOPRECIPITATION; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; HEP-G2 CELL LINE; K-562 CELL LINE; PHOTOCHEMISTRY; PROCEDURES; ULTRAVIOLET RADIATION;

BINDING SITES; CROSS-LINKING REAGENTS; GENE EXPRESSION PROFILING; HEP G2 CELLS; HUMANS; IMMUNOPRECIPITATION; K562 CELLS; PHOTOCHEMICAL PROCESSES; RNA-BINDING PROTEINS; TRANSCRIPTOME; ULTRAVIOLET RAYS;

EID: 84961683881     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3810     Document Type: Article

References (30)

1. Gerstberger, S., Hafner, M., Tuschl, T. A census of human RNA-binding proteins. Nat. Rev. Genet. 15, 829-845 (2014).
2. Castello, A., Fischer, B., Hentze, M.W., Preiss, T. RNA-binding proteins in Mendelian disease. Trends. Genet. 29, 318-327 (2013).
3. Nussbacher, J.K., Batra, R., Lagier-Tourenne, C., Yeo, G.W. RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci. 38, 226-236 (2015).
4. Ule, J. et al. CLIP identifies Nova-regulated RNA networks in the brain. Science 302, 1212-1215 (2003).
5. Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141 (2010).
6. König, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909-915 (2010).
7. Shishkin, A.A. et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat. Methods 12, 323-325 (2015).
8. Huppertz, I. et al. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274-287 (2014).
9. Yeo, G.W. et al. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat. Struct. Mol. Biol. 16, 130-137 (2009).
10. Darnell, J.C. et al. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 146, 247-261 (2011).
11. Lovci, M.T. et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat. Struct. Mol. Biol. 20, 1434-1442 (2013).
12. Weyn-Vanhentenryck, S.M. et al. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. http://dx.doi.org/10.1016/j.celrep.2014.02.005 (2014).
13. Brooks, L. III et al. A multiprotein occupancy map of the mRNP on the 3 end of histone mRNAs. RNA 21, 1943-1965 (2015).
14. Reyes-Herrera, P.H., Speck-Hernandez, C.A., Sierra, C.A., Herrera, S. BackCLIP: a tool to identify common background presence in PAR-CLIP datasets. Bioinformatics (2015).
15. Friedersdorf, M.B., Keene, J.D. Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. Genome Biol. 15, R2 (2014).
16. Tenenbaum, S.A., Carson, C.C., Lager, P.J., Keene, J.D. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc. Natl. Acad. Sci. USA 97, 14085-14090 (2000).
17. Rozowsky, J. et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27, 66-75 (2009).
18. Li, Q., Brown, J.B., Huang, H., Bickel, P.J. Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 5, 1752-1779 (2011).
19. Sundararaman, B. et al. Resources for the comprehensive discovery of functional RNA elements. Mol. Cell http://dx.doi.org/10.1016/j.molcel.2016.02.012 (2016).
20. Richman, T.R. et al. A bifunctional protein regulates mitochondrial protein synthesis. Nucleic Acids Res. 42, 5483-5494 (2014).
21. Grainger, R.J., Beggs, J.D. Prp8 protein: at the heart of the spliceosome. RNA 11, 533-557 (2005).
22. Rappsilber, J., Ajuh, P., Lamond, A.I., Mann, M. SPF30 is an essential human splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. J. Biol. Chem. 276, 31142-31150 (2001).
23. Rackham, O., Mercer, T.R., Filipovska, A. The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. Wiley Interdiscip. Rev. RNA. 3, 675-695 (2012).
24. Matera, A.G., Wang, Z. A day in the life of the spliceosome. Nat. Rev. Mol. Cell Biol. 15, 108-121 (2014).
25. Krueger, B.J. et al. LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res. 36, 2219-2229 (2008).
26. McHugh, C.A. et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521, 232-236 (2015).
27. Chu, C. et al. Systematic discovery of Xist RNA binding proteins. Cell 161, 404-416 (2015).
28. Royce-Tolland, M.E. et al. The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation. Nat. Struct. Mol. Biol. 17, 948-954 (2010).
29. Guo, F. et al. Regulation of MALAT1 expression by TDP43 controls the migration and invasion of non-small cell lung cancer cells in vitro. Biochem. Biophys. Res. Commun. 465, 293-298 (2015).
30. Tripathi, V. et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 39, 925-938 (2010).