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Deciphering human ribonucleoprotein regulatory networks

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Item Type:Article
Title:Deciphering human ribonucleoprotein regulatory networks
Creators Name:Mukherjee, N., Wessels, H.H., Lebedeva, S., Sajek, M., Ghanbari, M., Garzia, A., Munteanu, A., Yusuf, D., Farazi, T., Hoell, J.I., Akat, K.M., Akalin, A., Tuschl, T. and Ohler, U.
Abstract:RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i.e. specific combinations of RBPs that bind to specific sets of RNAs and targeted regions. These regulatory modules represented functionally related proteins and exhibited distinct differences in RNA metabolism, expression variance, as well as subcellular localization. This integrative investigation of experimental RBP-RNA interaction evidence and RBP regulatory function in a human cell line will be a valuable resource for understanding the complexity of post-transcriptional regulation.
Keywords:Base Sequence, Binding Sites, Gene Expression Regulation, HEK293 Cells, RNA, Ribonucleoproteins
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:570-581
Date:25 January 2019
Official Publication:https://doi.org/10.1093/nar/gky1185
PubMed:View item in PubMed

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