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Transcriptome maps of general eukaryotic RNA degradation factors.

MPS-Authors
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Sohrabi-Jahromi,  S.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Hofmann,  K. B.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Boltendahl,  A.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Roth,  C.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Gressel,  S.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Baejen,  C.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Söding,  J.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Cramer,  P.
Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Citation

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.


Cite as: https://hdl.handle.net/21.11116/0000-0003-B085-F
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.