Global effects on gene expression in fission yeast by silencing and RNA interference machineries

Hansen, K. R., Burns, G., Mata, J., Volpe, T. A., Martienssen, R. A., Bahler, J., Thon, G. (2005) Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Molecular and Cellular Biology, 25 (2). pp. 590-601. ISSN 0270-7306

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URL: http://www.ncbi.nlm.nih.gov/pubmed/15632061
DOI: 10.1128/MCB.25.2.590-601.2005

Abstract

Histone modifications influence gene expression in complex ways. The RNA interference (RNAi) machinery can repress transcription by recruiting histone-modifying enzymes to chromatin, although it is not clear whether this is a general mechanism for gene silencing or whether it requires repeated sequences such as long terminal repeats (LTRs). We analyzed the global effects of the Clr3 and Clr6 histone deacetylases, the Clr4 methyltransferase, the zinc finger protein Clr1, and the RNA, proteins Dicer, RdRP, and Argonaute on the transcriptome of Schizosaccharomyces pombe (fission yeast). The clr mutants derepressed similar subsets of genes, many of which also became transcriptionally activated in cells that were exposed to environmental stresses such as nitrogen starvation. Many genes that were repressed by the Clr proteins clustered in extended regions close to the telomeres. Surprisingly few genes were repressed by both the silencing and RNAi machineries, with transcripts from centromeric repeats and Tf2 retrotransposons being notable exceptions. We found no correlation between repression by RNAi and proximity to LTRs, and the wtf family of repeated sequences seems to be repressed by histone deacetylation independent of RNAi. Our data indicate that the RNAi and Clr proteins show only a limited functional overlap and that the Clr proteins play more global roles in gene silencing.

Item Type: Paper
Uncontrolled Keywords: disrupt chromosome regulation open reading frames mating type loci schizosaccaromyces pombe repress transcription transposable elements ELEMENTS lysine-9 methylation histone decatylases DNA methylation c-elegans
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > histone
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > histone deacetylase
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > zinc finger proteins
CSHL Authors:
Communities: CSHL labs > Martienssen lab
Depositing User: CSHL Librarian
Date Deposited: 13 Jan 2012 15:22
Last Modified: 10 Apr 2014 14:11
PMCID: PMC543407
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22586

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