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  Transcriptome maps of general eukaryotic RNA degradation factors.

Sohrabi-Jahromi, S., Hofmann, K. B., Boltendahl, A., Roth, C., Gressel, S., Baejen, C., et al. (2019). Transcriptome maps of general eukaryotic RNA degradation factors. eLife, 8: e47040. doi:10.7554/eLife.47040.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0003-B085-F Version Permalink: http://hdl.handle.net/21.11116/0000-0003-CAEA-2
Genre: Journal Article

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 Creators:
Sohrabi-Jahromi, S.1, Author              
Hofmann, K. B.2, Author              
Boltendahl, A.2, Author              
Roth, C.1, Author              
Gressel, S.2, Author              
Baejen, C.2, Author              
Söding, J.1, Author              
Cramer, P.2, Author              
Affiliations:
1Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1933286              
2Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1863498              

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Free keywords: S. cerevisiae; chromosomes; computational biology; gene expression; systems biology
 Abstract: RNA degradation pathways enable RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. The profiles reveal the distribution of degradation factors between different RNA classes. They are consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Decapping factors preferentially bind mRNAs with non-optimal codons, consistent with rapid degradation of inefficiently translated mRNAs. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3 and TRAMP4, targets aberrant nuclear RNAs and processes snoRNAs.

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Language(s): eng - English
 Dates: 2019-05-28
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.7554/eLife.47040
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Title: eLife
Source Genre: Journal
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Pages: 29 Volume / Issue: 8 Sequence Number: e47040 Start / End Page: - Identifier: -