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Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

Philipp Eser, Leonhard Wachutka, Kerstin C. Maier, Carina Demel, Mariana Boroni, Srignanakshi Iyer, Patrick Cramer, Julien Gagneur
doi: https://doi.org/10.1101/025585
Philipp Eser
Max-Planck-Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faβberg 11, 37077 Göttingen, GermanyGene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straβe 25, 81377 Munich, Germany
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Leonhard Wachutka
Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straβe 25, 81377 Munich, Germany
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Kerstin C. Maier
Max-Planck-Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faβberg 11, 37077 Göttingen, Germany
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Carina Demel
Max-Planck-Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faβberg 11, 37077 Göttingen, Germany
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Mariana Boroni
Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straβe 25, 81377 Munich, Germany
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Srignanakshi Iyer
Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straβe 25, 81377 Munich, Germany
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Patrick Cramer
Max-Planck-Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faβberg 11, 37077 Göttingen, Germany
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Julien Gagneur
Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straβe 25, 81377 Munich, Germany
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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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 26, 2015.
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Determinants of RNA metabolism in the Schizosaccharomyces pombe genome
Philipp Eser, Leonhard Wachutka, Kerstin C. Maier, Carina Demel, Mariana Boroni, Srignanakshi Iyer, Patrick Cramer, Julien Gagneur
bioRxiv 025585; doi: https://doi.org/10.1101/025585
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Determinants of RNA metabolism in the Schizosaccharomyces pombe genome
Philipp Eser, Leonhard Wachutka, Kerstin C. Maier, Carina Demel, Mariana Boroni, Srignanakshi Iyer, Patrick Cramer, Julien Gagneur
bioRxiv 025585; doi: https://doi.org/10.1101/025585

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