@article{995e58cc89ec41e7a137c1d691f46a52,
title = "A compendium of RNA-binding motifs for decoding gene regulation",
abstract = "RNA-binding proteins are key regulators of gene expression, yet only a small fraction have been functionally characterized. Here we report a systematic analysis of the RNA motifs recognized by RNA-binding proteins, encompassing 205 distinct genes from 24 diverse eukaryotes. The sequence specificities of RNA-binding proteins display deep evolutionary conservation, and the recognition preferences for a large fraction of metazoan RNA-binding proteins can thus be inferred from their RNA-binding domain sequence. The motifs that we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA-binding proteins both in normal physiology and in human disease. These data provide an unprecedented overview of RNA-binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukaryotes.",
author = "Debashish Ray and Hilal Kazan and Cook, {Kate B.} and Weirauch, {Matthew T.} and Najafabadi, {Hamed S.} and Xiao Li and Serge Gueroussov and Mihai Albu and Hong Zheng and Ally Yang and Hong Na and Manuel Irimia and Matzat, {Leah H.} and Dale, {Ryan K.} and Smith, {Sarah A.} and Yarosh, {Christopher A.} and Kelly, {Seth M.} and Behnam Nabet and Desirea Mecenas and Weimin Li and Laishram, {Rakesh S.} and Mei Qiao and Lipshitz, {Howard D.} and Fabio Piano and Corbett, {Anita H.} and Carstens, {Russ P.} and Frey, {Brendan J.} and Anderson, {Richard A.} and Lynch, {Kristen W.} and Penalva, {Luiz O.F.} and Lei, {Elissa P.} and Fraser, {Andrew G.} and Blencowe, {Benjamin J.} and Morris, {Quaid D.} and Hughes, {Timothy R.}",
note = "Funding Information: Acknowledgements We thank H. van Bakel for computational support, A. Ramani and J. Calarco for discussions, Y. Wu, G. Rasanathan, M. Krishnamoorthy, O. Boright, A.Janska,J.Li, S. Talukder, A.CoteandS.Votruba for technicalassistance,L.Sutherland for purchasing RBM5 protein and for feedback on the manuscript, S. Jain for software modified to create Fig. 2, and N. Barbosa-Morais for generating cRPKM values from autism RNA-seq data. We thank M. Kiledjian (PCBP1 and PCBP2), J. Stevenin (SRSF2 and SFRS7), S. Richard (QKI), M. Gorospe (TIA1), B. Chabot (SRSF9), A. Berglund (MBNL1), F. Pagani (DAZAP1), A. Bindereif (HNRNPL), M. Freeman (HNRNPK), E. Miska (LIN28A), K. Kohno (YBX1), M. Garcia-Blanco (PTBP1), R. Wharton (PUM-HD), C. Smibert (Vts1p) and M. Blanchette (Hrb27C, Hrb87F and Hrb98DE) for sending published constructs. This work was supported by funding from NIH (1R01HG00570 to T.R.H. and Q.D.M., R01GM084034 to K.W.L.), CIHR (MOP-49451 to T.R.H., MOP-93671 to Q.D.M., MOP-125894 to Q.D.M. and T.R.H., MOP-67011 to B.J.B., and MOP-14409 to H.D.L.), and the Intramural Program of the NIDDK (DK015602-05 to E.P.L.). K.B.C. and S.G. hold NSERC Alexander Graham Bell Canada Graduate Scholarships. M.T.W. was funded by fellowships from CIHR and CIFAR. H.S.N. holds a Charles H.BestFellowship andwasfundedpartiallybyawardsfromCIFAR toT.R.H.and B.J.F. M.I. is the recipient of an HFSP LT Fellowship.",
year = "2013",
doi = "10.1038/nature12311",
language = "English (US)",
volume = "499",
pages = "172--177",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Research",
number = "7457",
}