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QPromoters: Sequence based prediction of promoter strength in Saccharomyces cerevisiae

Devang Haresh Liya, Mirudula Elanchezhian, Mukulika Pahari, Nithishwer Mouroug Anand, Shivani Suresh, Nivedha Balaji, View ORCID ProfileAshwin Kumar Jainarayanan
doi: https://doi.org/10.1101/2021.04.27.441621
Devang Haresh Liya
1Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
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Mirudula Elanchezhian
2Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
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Mukulika Pahari
3Department of Computer Engineering, Ramrao Adik Institute of Technology, DY Patil Deemed to be University, Navi Mumbai, India
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Nithishwer Mouroug Anand
1Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
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Shivani Suresh
4Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
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Nivedha Balaji
2Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
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Ashwin Kumar Jainarayanan
5Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
6Interdisciplinary Bioscience Doctoral Training Program and Exeter College, University of Oxford, Oxford OX3 7DQ, UK
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  • ORCID record for Ashwin Kumar Jainarayanan
  • For correspondence: ashwin.jainarayanan@dtc.ox.ac.uk
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Abstract

Promoters play a key role in influencing transcriptional regulation for fine-tuning expression of genes. Heterologous promoter engineering has been a widely used concept to control the level of transcription in all model organisms. The strength of a promoter is mainly determined by its nucleotide composition. Many promoter libraries have been curated but few have attempted to develop theoretical methods to predict the strength of promoters from its nucleotide sequence.

Such theoretical methods are not only valuable in the design of promoters with specified strength, but are also meaningful to understand the mechanism of promoters in gene transcription. In this study, we present a theoretical model to describe the relationship between promoter strength and nucleotide sequence in Saccharomyces cerevisiae. We infer from our analysis that the −49 to 10 sequence with respect to the Transcription Start Site represents the minimal region that can be used to predict the promoter strength. We present an online tool https://qpromoters.com/ that takes advantage of this fact to quickly quantify the strength of the promoters.

Competing Interest Statement

The authors have declared no competing interest.

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-ND 4.0 International license.
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Posted April 28, 2021.
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QPromoters: Sequence based prediction of promoter strength in Saccharomyces cerevisiae
Devang Haresh Liya, Mirudula Elanchezhian, Mukulika Pahari, Nithishwer Mouroug Anand, Shivani Suresh, Nivedha Balaji, Ashwin Kumar Jainarayanan
bioRxiv 2021.04.27.441621; doi: https://doi.org/10.1101/2021.04.27.441621
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QPromoters: Sequence based prediction of promoter strength in Saccharomyces cerevisiae
Devang Haresh Liya, Mirudula Elanchezhian, Mukulika Pahari, Nithishwer Mouroug Anand, Shivani Suresh, Nivedha Balaji, Ashwin Kumar Jainarayanan
bioRxiv 2021.04.27.441621; doi: https://doi.org/10.1101/2021.04.27.441621

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