title: Systems-level evidence of transcriptional co-regulation of yeast protein complexes.
abstract: Protein complexes are functional units in the cell whose formation is regulated by a number of mechanisms. Previous studies have suggested that transcriptional co-regulation of protein components play a minor role in assembly of individual complexes. Recent developments in experimental approaches and bioinformatic analyses offer an opportunity to investigate the cell at a global or systems level with better quality. Here we show that, using genome/proteome-wide yeast data of protein complexes and protein-DNA interactions in normal growth conditions, a contribution of transcriptional co-regulation to global formation of protein complexes is statistically significant at a systems level. A significant fraction of proteins that form complexes shares common transcription factors on a global scale. We provide evidence for the significant contribution by quantifying transcriptional co-regulation of complexes as a global topological pattern of an integrated network. Biological relevance is examined by functional analysis of highly co-regulated complexes such as transport complexes. Our finding indicates that there exists linear causality at a systems level between transcriptional co-regulation of genes and formation of multi-protein complexes in the unicellular organism.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. lee55@fas.harvard.edu
authors.forename: J William
authors.initials: JW
authors.lastname: Lee
authors.forename: Tomasz
authors.initials: T
authors.lastname: Zemojtel
authors.forename: Eugene
authors.initials: E
authors.lastname: Shakhnovich
mesh_terms: D047369:Chromatin Immunoprecipitation; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D046912:Multiprotein Complexes / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D005656:Fungal Proteins; D046912:Multiprotein Complexes