A compendium of RNA-binding motifs for decoding gene regulation (original) (raw)

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Accessions

Gene Expression Omnibus

Data deposits

Raw and processed microarray data are available at GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE41235. The derived motifs and results of analyses are available at http://hugheslab.ccbr.utoronto.ca/supplementary-data/RNAcompete_eukarya/.

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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. Cote and S. Votruba for technical assistance, 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. Best Fellowship and was funded partially by awards from CIFAR to T.R.H. and B.J.F. M.I. is the recipient of an HFSP LT Fellowship.

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Author notes

1. Matthew T. Weirauch
   Present address: Present address: Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Rheumatology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA.,
2. Debashish Ray, Hilal Kazan, Kate B. Cook, Matthew T. Weirauch and Hamed S. Najafabadi: These authors contributed equally to this work.

Authors and Affiliations

1. Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada ,
   Debashish Ray, Matthew T. Weirauch, Hamed S. Najafabadi, Mihai Albu, Hong Zheng, Ally Yang, Hong Na, Manuel Irimia, Andrew G. Fraser, Benjamin J. Blencowe, Quaid D. Morris & Timothy R. Hughes
2. Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada,
   Hilal Kazan & Quaid D. Morris
3. Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada,
   Kate B. Cook, Xiao Li, Serge Gueroussov, Howard D. Lipshitz, Andrew G. Fraser, Benjamin J. Blencowe, Quaid D. Morris & Timothy R. Hughes
4. Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada,
   Hamed S. Najafabadi, Brendan J. Frey & Quaid D. Morris
5. Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892, Maryland, USA
   Leah H. Matzat, Ryan K. Dale & Elissa P. Lei
6. Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA
   Sarah A. Smith, Christopher A. Yarosh, Behnam Nabet, Russ P. Carstens & Kristen W. Lynch
7. Department of Biochemistry, Emory University School of Medicine, Atlanta, 30322, Georgia, USA
   Seth M. Kelly & Anita H. Corbett
8. Department of Biology and Center for Genomics and Systems Biology, New York University, New York, 10003, New York, USA
   Desirea Mecenas & Fabio Piano
9. Molecular and Cellular Pharmacology Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, 53706, Wisconsin, USA
   Weimin Li, Rakesh S. Laishram & Richard A. Anderson
10. Children’s Cancer Research Institute, UTHSCSA, San Antonio, 78229, Texas, USA
    Mei Qiao & Luiz O. F. Penalva

Authors

1. Debashish Ray
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2. Hilal Kazan
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3. Kate B. Cook
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4. Matthew T. Weirauch
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5. Hamed S. Najafabadi
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6. Xiao Li
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7. Serge Gueroussov
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8. Mihai Albu
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9. Hong Zheng
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10. Ally Yang
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11. Hong Na
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12. Manuel Irimia
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13. Leah H. Matzat
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14. Ryan K. Dale
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15. Sarah A. Smith
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16. Christopher A. Yarosh
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17. Seth M. Kelly
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18. Behnam Nabet
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19. Desirea Mecenas
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20. Weimin Li
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21. Rakesh S. Laishram
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22. Mei Qiao
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23. Howard D. Lipshitz
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24. Fabio Piano
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25. Anita H. Corbett
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26. Russ P. Carstens
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27. Brendan J. Frey
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28. Richard A. Anderson
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29. Kristen W. Lynch
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30. Luiz O. F. Penalva
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31. Elissa P. Lei
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32. Andrew G. Fraser
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33. Benjamin J. Blencowe
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34. Quaid D. Morris
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35. Timothy R. Hughes
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Contributions

D.R., H.K., K.B.C., M.T.W. and H.S.N. made unique, essential and extensive contributions to the manuscript, and are ordered by amount of time and effort contributed. D.R. and H.K. developed most of the laboratory and computational components of RNAcompete, respectively. D.R., H.Z., A.Y., H.N., L.H.M., S.A.S., C.A.Y., S.M.K., B.N., D.M., W.L., R.S.L. and M.Q. cloned, expressed and purified the proteins. D.R. ran the RNAcompete assays, including data extraction. H.K. and K.B.C. processed the data, H.K. and K.B.C. generated motifs, and H.K., K.B.C., M.T.W. and H.S.N. performed the motif analyses. H.K. assembled the in vivo protein-RNA data sets. L.H.M. and R.K.D. performed and analysed RIP-seq data. K.B.C. developed the supplementary website and Figs 1 and 2 with assistance from H.K. and M.T.W. M.T.W. and M.A. created the cisBP-RNA database. M.T.W., H.S.N. and T.R.H. created Fig. 3. H.S.N. performed the analyses of human splicing, RNA stability data and human sequence conservation, and created Figs 4 and 5. M.I. and S.G. generated and analysed RNA-seq data and S.G. performed reporter-based RNA stability assays. X.L. performed Drosophila data analysis. H.D.L., F.P., A.H.C., R.P.C., B.J.F., R.A.A., K.W.L., L.O.F.P., E.P.L., B.J.B. and A.G.F. helped organize and support the project, and provided feedback on the manuscript. B.J.F., B.J.B. and A.G.F. provided critical advice and commentary on data analysis. Q.D.M. and T.R.H. conceived of the study, supervised the project and wrote the manuscript with contributions from D.R., H.K., K.B.C., B.J.B., A.F. and H.S.N.

Corresponding authors

Correspondence toQuaid D. Morris or Timothy R. Hughes.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary Figures 1-6, Supplementary Tables 1-4 and additional references. (PDF 2569 kb)

Supplementary Data 1

This file shows RNA-binding proteins with known consensus motifs. It contains panels for human and Drosophila listing RBPs with known consensus motifs as well as the Pubmed ID of the publication that defined the motif. (XLSX 27 kb)

Supplementary Data 2

The RNAcompete master file. This file contains data on all RNAcompete experiments indexed by motif ID including: name, systematic ID and species of protein queried, the resulting motif, amino acid sequence of plasmid insert, and information on binding conditions used. (XLSX 2614 kb)

Supplementary Data 3

Secondary structure analysis. This file contains data panels in which each row corresponds to a significantly enriched secondary structure context for a given RNAcompete experiment along with P-values and effect sizes. Classification panel summarizes analysis results by motif. (XLSX 30 kb)

Supplementary Data 4

Clustered E-scores. This file contains the data matrix used in Figures 1b and S7. (TXT 16827 kb)

Supplementary Data 5

Comparison of RNAcompete and literature motifs. This file shows the results of comparison with previously defined motifs for RNAcompete RBPs. (XLSX 515 kb)

Supplementary Data 6

AUROC scores for in vivo and in vitro defined motifs on in vivo binding data. This file contains AUROCs for RNAcompete motifs on in vivo binding data described in Table S2, along with motifs learned by Malarkey on these data and AUROC scores for previously defined motifs for these RBPs. (XLSX 19 kb)

Supplementary Data 7

Post-transcriptional regulation (PTR) analysis in human. This file contains additional details and results of PTR analysis in human including predicted RBP-transcript regulatory networks for splicing and stability analysis. (XLSX 1445 kb)

Supplementary Data 8

Post-transcriptional regulation (PTR) analysis in Drosophila. This file contains details and results of PTR analysis for Drosophila including lists of PTR categories enriched for RNAcompete-derived IUPAC motifs, weights of trained logistic regression classifiers, Drosophila RBP(s) associated with each IUPAC motif, and IUPAC motifs queried. (XLSX 44 kb)

Supplementary Data 9

Sources of gene and Pfam models. This file details sources for gene and protein models for all organisms used in cisBP-RNA and in this paper. Also indicates Pfam models used to scan for RBDs.Sources of gene and Pfam models. This file details sources for gene and protein models for all organisms used in cisBP-RNA and in this paper. Also indicates Pfam models used to scan for RBDs. (XLSX 34 kb)

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Ray, D., Kazan, H., Cook, K. et al. A compendium of RNA-binding motifs for decoding gene regulation.Nature 499, 172–177 (2013). https://doi.org/10.1038/nature12311

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• Received: 08 January 2013
• Accepted: 17 May 2013
• Published: 10 July 2013
• Issue Date: 11 July 2013
• DOI: https://doi.org/10.1038/nature12311