| Title: | Genetic analysis of variation in transcription factor binding in yeast |
| Author(s): | Zheng W; Zhao H; Mancera E; Steinmetz LM; Snyder M; |
| Address: | "Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA" |
| ISSN/ISBN: | 1476-4687 (Electronic) 0028-0836 (Print) 0028-0836 (Linking) |
| Abstract: | "Variation in transcriptional regulation is thought to be a major cause of phenotypic diversity. Although widespread differences in gene expression among individuals of a species have been observed, studies to examine the variability of transcription factor binding on a global scale have not been performed, and thus the extent and underlying genetic basis of transcription factor binding diversity is unknown. By mapping differences in transcription factor binding among individuals, here we present the genetic basis of such variation on a genome-wide scale. Whole-genome Ste12-binding profiles were determined using chromatin immunoprecipitation coupled with DNA sequencing in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains and their parental lines. We identified extensive Ste12-binding variation among individuals, and mapped underlying cis- and trans-acting loci responsible for such variation. We showed that most transcription factor binding variation is cis-linked, and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several proposed Ste12 cofactors. We also identified two trans-factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than ten genes under alpha-factor treatment. Neither of these two genes was previously known to regulate Ste12, and we suggest that they may be mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes, indicating that binding variation is functional. Many of the variable-bound genes are involved in cell wall organization and biogenesis. Overall, these studies identified genetic regulators of molecular diversity among individuals and provide new insights into mechanisms of gene regulation" |
| Keywords: | "Amino Acid Motifs/genetics Binding Sites/genetics Cell Cycle Proteins/genetics/metabolism Cell Wall/genetics/metabolism Gene Expression Regulation, Fungal Genes, Fungal/genetics Genetic Variation/*genetics Genome, Fungal/genetics Mating Factor Nuclear Pro;" |
| Notes: | "MedlineZheng, Wei Zhao, Hongyu Mancera, Eugenio Steinmetz, Lars M Snyder, Michael eng R01 CA077808-09/CA/NCI NIH HHS/ R01 CA077808/CA/NCI NIH HHS/ R01 GM068717-08/GM/NIGMS NIH HHS/ P01 HG000205/HG/NHGRI NIH HHS/ RR19895/RR/NCRR NIH HHS/ P01 HG000205-10/HG/NHGRI NIH HHS/ R01 GM068717/GM/NIGMS NIH HHS/ R01 GM059507-09/GM/NIGMS NIH HHS/ R01 GM059507/GM/NIGMS NIH HHS/ Research Support, N.I.H., Extramural England 2010/03/20 Nature. 2010 Apr 22; 464(7292):1187-91. doi: 10.1038/nature08934. Epub 2010 Mar 17" |
