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CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses

View ORCID ProfileChuanyi Zhang, View ORCID ProfilePalash Sashittal, View ORCID ProfileMohammed El-Kebir
doi: https://doi.org/10.1101/2021.11.10.468129
Chuanyi Zhang
1Department of Electrical & Computer Engineering, University of Illinois at Urbana-Champaign, IL 61801
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Palash Sashittal
2Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801
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Mohammed El-Kebir
2Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801
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  • For correspondence: melkebir@illinois.edu
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Abstract

Genes in coronaviruses are preceded by transcription regulatory sequences (TRSs), which play a critical role in gene expression mediated by the viral RNA-dependent RNA-polymerase via the process of discontinuous transcription. In addition to being crucial for our understanding of the regulation and expression of coronavirus genes, we demonstrate for the first time how TRSs can be leveraged to identify gene locations in the coronavirus genome. To that end, we formulate the TRS AND Gene Identification (TRS-Gene-ID) problem of simultaneously identifying TRS sites and gene locations in unannotated coronavirus genomes. We introduce CORSID (CORe Sequence IDentifier), a computational tool to solve this problem. We also present CORSID-A, which solves a constrained version of the TRS-Gene-ID problem, the TRS Identification (TRS-ID) problem, identifying TRS sites in a coronavirus genome with specified gene annotations. We show that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses and that CORSID outperforms state-of-the-art gene finding methods in finding genes in coronavirus genomes. We demonstrate that CORSID enables de novo identification of TRS sites and genes in previously unannotated coronaviruses. CORSID is the first method to perform accurate and simultaneous identification of TRS sites and genes in coronavirus genomes without the use of any prior information.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* Joint first authorship

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 12, 2021.
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CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses
Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir
bioRxiv 2021.11.10.468129; doi: https://doi.org/10.1101/2021.11.10.468129
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CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses
Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir
bioRxiv 2021.11.10.468129; doi: https://doi.org/10.1101/2021.11.10.468129

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