Title: Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast
Authors: Chiang, Sufeng
Swamy, Krishna B. S.
Hsu, Ting-Wei
Tsai, Zing Tsung-Yeh
Lu, Henry Horng-Shing
Wang, Daryi
Tsai, Huai-Kuang
統計學研究所
Institute of Statistics
Keywords: Transcription factor binding site;Variable position;Co-occurring TFs;Gene expression
Issue Date: 10-Jan-2012
Abstract: It is generally accepted that genes are regulated by the interactions between transcription factors (TFs) and their binding sites (TFBSs). Some studies have demonstrated that nucleotide variants at variable positions in TFBSs affect yeast gene regulation. Furthermore, variable positions in TFBSs in association with distinct accompanying regulatory motifs of other TFs (i.e., co-TFs) can also impact gene regulation in eukaryotes. Given that, even low-affinity IF-DNA interactions are abundant in vivo; we used both low- and high-affinity TFBSs and performed a genome-wide analysis of associations between variable positions and co-TFs. We found that in Saccharomyces cerevisiae, approximately 14% of the variable positions in TFBSs demonstrate such associations. These associations occurred in close proximity on the same promoters (i.e., highly co-localized). Moreover, such associations were highly conserved between sensu stricto yeasts and also influenced gene expression, which were consistent with enriched functional categories. (C) 2011 Elsevier B.V. All rights reserved.
URI: http://dx.doi.org/10.1016/j.gene.2011.08.028
http://hdl.handle.net/11536/15011
ISSN: 0378-1119
DOI: 10.1016/j.gene.2011.08.028
Journal: GENE
Volume: 491
Issue: 2
Begin Page: 237
End Page: 245
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