Open Access
Molecular Biology and Evolution, pages msv203
High-Throughput Identification ofCis-Regulatory Rewiring Events in Yeast
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Center for Bioinformatics and Computational Biology, University of Maryland, College Park.
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Publication type: Journal Article
Publication date: 2015-09-23
Journal:
Molecular Biology and Evolution
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 10.7
ISSN: 07374038, 15371719
PubMed ID:
26399482
Molecular Biology
Genetics
Ecology, Evolution, Behavior and Systematics
Abstract
A coregulated module of genes ("regulon") can have evolutionarily conserved expression patterns and yet have diverged upstream regulators across species. For instance, the ribosomal genes regulon is regulated by the transcription factor (TF) TBF1 in Candida albicans, while in Saccharomyces cerevisiae it is regulated by RAP1. Only a handful of such rewiring events have been established, and the prevalence or conditions conducive to such events are not well known. Here, we develop a novel probabilistic scoring method to comprehensively screen for regulatory rewiring within regulons across 23 yeast species. Investigation of 1,713 regulons and 176 TFs yielded 5,353 significant rewiring events at 5% false discovery rate (FDR). Besides successfully recapitulating known rewiring events, our analyses also suggest TF candidates for certain processes reported to be under distinct regulatory controls in S. cerevisiae and C. albicans, for which the implied regulators are not known: 1) Oxidative stress response (Sc-MSN2 to Ca-FKH2) and 2) nutrient modulation (Sc-RTG1 to Ca-GCN4/Ca-UME6). Furthermore, a stringent screen to detect TF rewiring at individual genes identified 1,446 events at 10% FDR. Overall, these events are supported by strong coexpression between the predicted regulator and its target gene(s) in a species-specific fashion (>50-fold). Independent functional analyses of rewiring TF pairs revealed greater functional interactions and shared biological processes between them (P = 1 × 10(-3)).Our study represents the first comprehensive assessment of regulatory rewiring; with a novel approach that has generated a unique high-confidence resource of several specific events, suggesting that evolutionary rewiring is relatively frequent and may be a significant mechanism of regulatory innovation.
Citations by journals
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1
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Scientific Reports
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Scientific Reports
1 publication, 20%
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Current Genetics
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Current Genetics
1 publication, 20%
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Genes and Development
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Genes and Development
1 publication, 20%
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1
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Citations by publishers
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1
2
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Springer Nature
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Springer Nature
2 publications, 40%
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Cold Spring Harbor Laboratory
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Cold Spring Harbor Laboratory
1 publication, 20%
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1
2
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Sarda S., Hannenhalli S. High-Throughput Identification ofCis-Regulatory Rewiring Events in Yeast // Molecular Biology and Evolution. 2015. p. msv203.
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Sarda S., Hannenhalli S. High-Throughput Identification ofCis-Regulatory Rewiring Events in Yeast // Molecular Biology and Evolution. 2015. p. msv203.
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TY - JOUR
DO - 10.1093/molbev/msv203
UR - https://doi.org/10.1093%2Fmolbev%2Fmsv203
TI - High-Throughput Identification ofCis-Regulatory Rewiring Events in Yeast
T2 - Molecular Biology and Evolution
AU - Sarda, Shrutii
AU - Hannenhalli, Sridhar
PY - 2015
DA - 2015/09/23 00:00:00
PB - Oxford University Press
SP - msv203
PMID - 26399482
SN - 0737-4038
SN - 1537-1719
ER -
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@article{2015_Sarda,
author = {Shrutii Sarda and Sridhar Hannenhalli},
title = {High-Throughput Identification ofCis-Regulatory Rewiring Events in Yeast},
journal = {Molecular Biology and Evolution},
year = {2015},
publisher = {Oxford University Press},
month = {sep},
url = {https://doi.org/10.1093%2Fmolbev%2Fmsv203},
pages = {msv203},
doi = {10.1093/molbev/msv203}
}