Genome-wide analysis of transcription factors and chromatin in S. cerevisiae

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Biology.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2002

Author dc:creator

• Wyrick, John J. (John Jason), 1974-

Advisor dc:contributor.advisor

• Richard A. Young.

• Biology.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/8308

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/8308