Genome wide expression analysis of the CCR4-NOT complex indicates that it consists of three modules with the NOT module controlling SAGA-responsive genes

Yajun Cui, Deepti B. Ramnarain, Yueh Chin Chiang, Liang Hao Ding, Jeffrey S. McMahon, Clyde L. Denis

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

Of the nine known members of the CCR4-NOT complex, CCR4/CAF1 are most important in mRNA deadenylation whereas the NOT1-5 proteins are most critical for transcriptional repression. Whole genome microarray analysis using deletions in seven of the CCR4-NOT genes was used to determine the overall mRNA expression patterns that are affected by members of the yeast CCR4-NOT complex. Under glucose conditions, ccr4 and caf1 displayed a high degree of similarity in the manner that they affected gene expression. In contrast, the not deletions were similar in the way they affected genes, but showed no correlation with that of ccr4/caf1. A number of groups of functionally related proteins were specifically controlled by the CCR4/CAF1 or NOT modules. Importantly, the NOT proteins preferentially affected SAGA-controlled gene expression. Also, both the CCR4/CAF1 and NOT group of proteins shared much greater similarities in their effects on gene expression during the stress of glucose deprivation. BTT1, a member of the nascent polypeptide association complex that binds the ribosome, was shown to be a tenth member of the CCR4-NOT complex, interacting through CAF130. Microarray analysis indicated that BTT1 and CAF130 correlate very highly in their control of gene expression and preferentially repress genes involved in ribosome biogenesis. These results indicate that distinct portions of the CCR4-NOT complex control a number of different cellular processes.

Original languageEnglish (US)
Pages (from-to)323-337
Number of pages15
JournalMolecular Genetics and Genomics
Volume279
Issue number4
DOIs
StatePublished - Apr 1 2008

Keywords

  • BTT1
  • CCR4-NOT
  • Microarray
  • SAGA

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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