Transcriptional regulation of protein complexes in yeast.

TitleTranscriptional regulation of protein complexes in yeast.
Publication TypeJournal Article
Year of Publication2004
AuthorsSimonis, N., van Helden J., Cohen G. N., and Wodak S. J.
JournalGenome Biol
Date Published2004
KeywordsComputational Biology, Gene Expression Regulation, Fungal, Genes, Fungal, Genes, Regulator, Macromolecular Substances, Nucleosomes, Predictive Value of Tests, Regulon, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic

BACKGROUND: Multiprotein complexes play an essential role in many cellular processes. But our knowledge of the mechanism of their formation, regulation and lifetimes is very limited. We investigated transcriptional regulation of protein complexes in yeast using two approaches. First, known regulons, manually curated or identified by genome-wide screens, were mapped onto the components of multiprotein complexes. The complexes comprised manually curated ones and those characterized by high-throughput analyses. Second, putative regulatory sequence motifs were identified in the upstream regions of the genes involved in individual complexes and regulons were predicted on the basis of these motifs.RESULTS: Only a very small fraction of the analyzed complexes (5-6%) have subsets of their components mapping onto known regulons. Likewise, regulatory motifs are detected in only about 8-15% of the complexes, and in those, about half of the components are on average part of predicted regulons. In the manually curated complexes, the so-called 'permanent' assemblies have a larger fraction of their components belonging to putative regulons than 'transient' complexes. For the noisier set of complexes identified by high-throughput screens, valuable insights are obtained into the function and regulation of individual genes.CONCLUSIONS: A small fraction of the known multiprotein complexes in yeast seems to have at least a subset of their components co-regulated on the transcriptional level. Preliminary analysis of the regulatory motifs for these components suggests that the corresponding genes are likely to be co-regulated either together or in smaller subgroups, indicating that transcriptionally regulated modules might exist within complexes.

Alternate JournalGenome Biol.
PubMed ID15128447
PubMed Central IDPMC416469