Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast

Sufeng Chiang*, Krishna B.S. Swamy, Ting Wei Hsu, Zing Tsung Yeh Tsai, Henry Horng Shing Lu, Daryi Wang, Huai Kuang Tsai

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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 TF-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.

Original languageEnglish
Pages (from-to)237-245
Number of pages9
JournalGene
Volume491
Issue number2
DOIs
StatePublished - 10 Jan 2012

Keywords

  • Co-occurring TFs
  • Gene expression
  • Transcription factor binding site
  • Variable position

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