Molecular Genetics and Genomics

, Volume 279, Issue 4, pp 323–337 | Cite as

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. DenisEmail author
Original Paper


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.


CCR4-NOT SAGA BTT1 Microarray 



We would like to thank J. Franke for sending strains and antibodies. This research was supported by an NIH grant, GM41215 and Hatch Project H291. This is Scientific Contribution 2307 from the New Hampshire Agriculture Experiment Station.

Supplementary material (3.1 mb)
Supplementary data (ZIP 3189 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Yajun Cui
    • 1
  • Deepti B. Ramnarain
    • 1
  • Yueh-Chin Chiang
    • 1
  • Liang-Hao Ding
    • 2
    • 3
  • Jeffrey S. McMahon
    • 1
  • Clyde L. Denis
    • 1
    Email author
  1. 1.Department of Biochemistry and Molecular BiologyRudman Hall, University of New HampshireDurhamUSA
  2. 2.Simmons Comprehensive Cancer Center Genomics Core FacilityUniversity of Texas Southwestern Medical CenterDallasUSA
  3. 3.Division of Molecular Radiation Biology, Department of Radiation OncologyUniversity of Texas Southwestern Medical CenterDallasUSA

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