Genome-wide analysis of transcription factors and chromatin in Saccharomyces cerevisiae

Abstract

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2002.Includes bibliographical references.The regulation of transcription initiation is a complex phenomenon, involving DNA-binding activator and repressor proteins, histones and chromatin factors, histone-modifying enzymes, and the general transcription apparatus. Though many of the genes encoding these factors have been identified in yeast, the role they play in regulating the expression of the yeast genome was not known. Genome-wide expression analysis of mutations in the Rpbl subunit of RNA polymerase II, the Srb4 subunit of Srb/Mediator complex, and the Kin28 subunit of TFIIH demonstrated that these factors are required for the transcription of essentially all protein-coding genes in yeast. However, other components of the Srb/Mediator complex (Srb5, Med6, SrblO, Swi2), the general transcription factor TFIID (Taf145, Taf17), and the SAGA histone-modifying complex (Gcn5, Taf17) were found not to be required for the transcription of all yeast genes but for distinct subsets of genes, revealing a surprising level of gene-specific regulation by the general transcription apparatus. The packaging of histones and DNA into nucleosomes was thought to generally repress gene expression, particularly at yeast telomeres, where the Sir protein complex silences genes located in the telomeric heterochromatin. To test this model, DNA microarrays were used to monitor the effects of depleting nucleosomal histones and silencing factors in yeast. Reducing nucleosome content caused increased expression of 15% of genes, reduced expression of 10% of genes, but had surprisingly little effect on expression of the majority (75%) of yeast genes.(cont.) Telomere-proximal genes were derepressed over regions extending 20 kb from telomere ends, well beyond the extent of Sir protein binding and the effects resulting from loss of Sir function. These results indicate that histones make Sir-independent contributions to telomeric silencing, and that the role of histones located elsewhere in chromosomes is gene specific To map the in vivo binding sites of transcription factors, a new technique-genome-wide location analysis-was developed. Genome-wide location and expression analysis was used to identify the target genes of the yeast activator proteins Gal4 and Ste 12. All of the known targets for these two activators were confirmed, and new target genes in multiple functional pathways were identified.by John J. Wyrick.Ph.D