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Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.

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.

SUBMITTER: Foat BC

PROVIDER: S-EPMC1295595 | biostudies-literature | 2005 Dec

REPOSITORIES: biostudies-literature

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Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.

Foat Barrett C BC Houshmandi S Sean SS Olivas Wendy M WM Bussemaker Harmen J HJ

Proceedings of the National Academy of Sciences of the United States of America 20051129 49

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 exp ...[more]

PMID: 16317069

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