Determinants of RNA metabolism in the Schizosaccharomyces pombe genome
Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J (2016)
Publication Type: Journal article
Publication year: 2016
Journal
Book Volume: 12
Article Number: 857
Journal Issue: 2
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.
Involved external institutions
Max-Planck-Institut für biophysikalische Chemie (Karl-Friedrich-Bonhoeffer-Institut) / Max Planck Institute for Biophysical Chemistry
Germany (DE)
Ludwig-Maximilians-Universität (LMU)
Germany (DE)
Germany (DE)
Ludwig-Maximilians-Universität (LMU)
Germany (DE)
How to cite
APA:
Eser, P., Wachutka, L., Maier, K.C., Demel, C., Boroni, M., Iyer, S.,... Gagneur, J. (2016). Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Molecular Systems Biology, 12(2). https://doi.org/10.15252/msb.20156526
MLA:
Eser, Philipp, et al. "Determinants of RNA metabolism in the Schizosaccharomyces pombe genome." Molecular Systems Biology 12.2 (2016).
BibTeX: Download