Ray, D., Kazan, H., Cook, K.B., Weirauch, M.T., Najafabadi, H.S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., Na, H., Irimia, M., Matzat, L.H., Dale, R.K., Smith, S.A., Yarosh, C.A., Kelly, S.M., Nabet, B., Mecenas, D., Li, W., Laishram, R.S., Qiao, M., Lipshitz, H.D., Piano, F., Corbett, A.H., Carstens, R.P., Frey, B.J., Anderson, R.A., Lynch, K.W., Penalva, L.O.F., Lei, E.P., Fraser, A.G., Blencowe, B.J., Morris, Q.D., Hughes, T.R. (2013). A compendium of RNA-binding motifs for decoding gene regulation.  Nature 499(7457): 172--177.

FBrf0242551

Research paper

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.

PMC3929597 (PMC) (EuropePMC)