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  Determinants of RNA metabolism in the Schizosaccharomyces pombe genome.

Eser, P., Wachutka, L., Maier, K. C., Demel, C., Boroni, M., Iyer, S., et al. (2016). Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Molecular Systems Biology, 12(2): 857. doi:10.15252/msb.20156526.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0029-B90D-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-A4E4-C
Genre: Journal Article

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 Creators:
Eser, P., Author
Wachutka, L., Author
Maier, K. C., Author
Demel, C.1, Author              
Boroni, M., Author
Iyer, S., Author
Cramer, P.1, Author              
Gagneur, J., Author
Affiliations:
1Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1863498              

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Free keywords: Cis‐regulatory element; gene regulation; RNA degradation; RNA synthesis; splicing
 Abstract: To decrypt the regulatory code of the genome, sequence elements must be defined that determine the kinetics of RNA metabolism and thus gene expression. Here, we attempt such decryption in an eukaryotic model organism, the fission yeast S. pombe. We first derive an improved genome annotation that redefines borders of 36% of expressed mRNAs and adds 487 non-coding RNAs (ncRNAs). We then combine RNA labeling in vivo with mathematical modeling to obtain rates of RNA synthesis and degradation for 5,484 expressed RNAs and splicing rates for 4,958 introns. We identify functional sequence elements in DNA and RNA that control RNA metabolic rates and quantify the contributions of individual nucleotides to RNA synthesis, splicing, and degradation. Our approach reveals distinct kinetics of mRNA and ncRNA metabolism, separates antisense regulation by transcription interference from RNA interference, and provides a general tool for studying the regulatory code of genomes.

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Language(s): eng - English
 Dates: 2016-02-16
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.15252/msb.20156526
 Degree: -

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Title: Molecular Systems Biology
Source Genre: Journal
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Pages: 15 Volume / Issue: 12 (2) Sequence Number: 857 Start / End Page: - Identifier: -