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A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
Author(s) -
Venters Bryan J,
Pugh B. Franklin
Publication year - 2009
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.23.1_supplement.493.2
Subject(s) - nucleosome , promoter , genetics , chromatin , biology , saccharomyces cerevisiae , transcription (linguistics) , chromatin remodeling , gene , rna polymerase ii , genome , transcription factor , microbiology and biotechnology , gene expression , linguistics , philosophy
The Pol II transcription machinery assembles and operates in the context of nucleosomes, which have well‐defined canonical positions at the beginning and end of protein‐coding genes. However, the predominant organizational theme by which the transcription machinery and chromatin regulators are positioned within promoter regions or throughout genes in a genome is largely unknown. We have mapped the genomic location of diverse representative components of the gene regulatory machinery in Saccharomyces cerevisiae to an experimental resolution of <40 bp using ChIP‐chip. Defining how these factors are arranged with respect to each other and to promoter nucleosome positions should provide insight into how the organization of the transcription machinery at promoters regulates gene expression. We find that the ‐1 nucleosome, which establishes the upstream border of the promoter region, is a likely target of substantial regulation (assuming that occupancy is linked to function) since nearly all tested chromatin remodeling complexes selectively occupy the ‐1 nucleosomal region compared to the +1 region. Furthermore, we find that the ‐1 nucleosome is depleted rather than laterally displaced when Pol II is present, but not when only TBP and TFIIB are recruited. This suggests that the ‐1 nucleosome is removed during PIC assembly, after TBP and TFIIB have been recruited, but before or concurrent with Pol II recruitment, which might explain the prevalence of remodeling complexes in the vicinity of the ‐1 nucleosome. This work was supported by NIH grant ES013768.