1. A compendium of RNA-binding motifs for decoding gene regulation
- Author
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Ray, Debashish, Kazan, Hilal, Cook, Kate B., Weirauch, Matthew T., Najafabadi, Hamed S., Li, Xiao, Gueroussov, Serge, Albu, Mihai, Zheng, Hong, Yang, Ally, Na, Hong, Irimia, Manuel, Matzat, Leah H., Dale, Ryan K., Smith, Sarah A., Yarosh, Christopher A., Kelly, Seth M., Nabet, Behnam, Mecenas, Desirea, Li, Weimin, Laishram, Rakesh S., Qiao, Mei, Lipshitz, Howard D., Piano, Fabio, Corbett, Anita H., Carstens, Russ P., Frey, Brendan J., Anderson, Richard A., Lynch, Kristen W., Penalva, Luiz O.F., Lei, Elissa P., Fraser, Andrew G., Blencowe, Benjamin J., Morris, Quaid D., and Hughes, Timothy R.
- Subjects
Binding sites (Biochemistry) -- Identification and classification -- Genetic aspects ,Binding proteins -- Genetic aspects ,RNA -- Research ,Genetic regulation -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - 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., RNA-binding proteins (RBPs) regulate numerous aspects of co- and post-transcriptional gene expression, including RNA splicing, polyadenylation, capping, modification, export, localization, translation and turnover (1,2). Sequence-specific associations between RBPs and their [...]
- Published
- 2013