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  Identification of new high affinity targets for Roquin based on structural conservation.

Braun, J., Fischer, S., Xu, Z. Z., Dalia, S., Ghoneim, D. H., Gimbel, A. T., et al. (2018). Identification of new high affinity targets for Roquin based on structural conservation. Nucleic Acids Research, 46(22), 12109-12125. doi:10.1093/nar/gky908.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0002-5562-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-38B6-1
Genre: Journal Article

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Braun, J., Author
Fischer, S., Author
Xu, Z. Z., Author
Dalia, S., Author
Ghoneim, D. H., Author
Gimbel, A. T., Author
Plessmann, U.1, Author              
Urlaub, H.1, Author              
Mathews, D. H., Author
Weigand, J. E., Author
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1Research Group of Bioanalytical Mass Spectrometry, MPI for biophysical chemistry, Max Planck Society, ou_578613              

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 Abstract: Post-transcriptional gene regulation controls the amount of protein produced from a specific mRNA by altering both its decay and translation rates. Such regulation is primarily achieved by the interaction of trans-acting factors with cis-regulatory elements in the untranslated regions (UTRs) of mRNAs. These interactions are guided either by sequence- or structure-based recognition. Similar to sequence conservation, the evolutionary conservation of a UTR’s structure thus reflects its functional importance. We used such structural conservation to identify previously unknown cis-regulatory elements. Using the RNA folding program Dynalign, we scanned all UTRs of humans and mice for conserved structures. Characterizing a subset of putative conserved structures revealed a binding site of the RNA-binding protein Roquin. Detailed functional characterization in vivo enabled us to redefine the binding preferences of Roquin and identify new target genes. Many of these new targets are unrelated to the established role of Roquin in inflammation and immune responses and thus highlight additional, unstudied cellular functions of this important repressor. Moreover, the expression of several Roquin targets is highly cell-type-specific. In consequence, these targets are difficult to detect using methods dependent on mRNA abundance, yet easily detectable with our unbiased strategy.

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Language(s): eng - English
 Dates: 2018-10-082018-12-14
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1093/nar/gky908
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 46 (22) Sequence Number: - Start / End Page: 12109 - 12125 Identifier: -