Document Type
Article
Abstract
The steady-state abundance of an mRNA is determined by the balance between transcription and decay. Although regulation of transcription has been well studied both experimentally and computationally, regulation of transcript stability has received little attention. We developed an algorithm, MatrixREDUCE, that discovers the position-specific affinity matrices for unknown RNA-binding factors and infers their condition-specific activities, using only genomic sequence data and steady-state mRNA expression data as input. We identified and computationally characterized the binding sites for six mRNA stability regulators in Saccharomyces cerevisiae, which include two members of the Pumilio-homology domain (Puf) family of RNA-binding proteins, Puf3p and Puf4p. We provide computational and experimental evidence that regulation of mRNA stability by these factors is modulated in response to a variety of environmental stimuli.
Publication Date
January 2005
Publication Title
Proceedings of the National Academy of Science of the United States of America
Volume
102
Issue
49
First Page
17675
Last Page
17680
DOI
10.1073/pnas.0503803102
Recommended Citation
Olivas, Wendy; Foat, B.; Houshmandi, S.; and Bussemaker, H., "Profiling Condition-specific, Genome-wide Regulation of mRNA Stability in Yeast" (2005). Biology Department Faculty Works. 15.
DOI: https://doi.org/10.1073/pnas.0503803102
Available at:
https://irl.umsl.edu/biology-faculty/15