title: Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast.
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.
authors.affiliation: Institute of Information Science, Academia Sinica, Taiwan. schiang@iis.sinica.edu.tw
authors.forename: Sufeng
authors.initials: S
authors.lastname: Chiang
authors.forename: Krishna B S
authors.initials: KB
authors.lastname: Swamy
authors.forename: Ting-Wei
authors.initials: TW
authors.lastname: Hsu
authors.forename: Zing Tsung-Yeh
authors.initials: ZT
authors.lastname: Tsai
authors.forename: Henry Horng-Shing
authors.initials: HH
authors.lastname: Lu
authors.forename: Daryi
authors.initials: D
authors.lastname: Wang
authors.forename: Huai-Kuang
authors.initials: HK
authors.lastname: Tsai
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors