DOI: 1010.0713Jun 2, 2011Paper

Classification of Saccharomyces cerevisiae promoter regions into distinct chromatin classes reveals the existence of nucleosome-depleted hotspots of transcription factor occupancy

ArXiv
Junbai WangHarmen J. Bussemaker

Abstract

Transcription factors (TF) play an essential role in the cell as locus- and condition-specific recruiters of transcriptional machinery or chromatin-modifying complexes. However, predicting the in vivo profile of TF occupancy along the genome, which depends on complex interactions with other chromatin-associated proteins, from the DNA sequence remains a major challenge. Through careful reanalysis of ChIP-chip data for 138 TFs obtained in rich media, we were able to classify the upstream promoter regions of S. cerevisiae into 15 distinct chromatin types. One of these encompasses 5% of all promoters and is unique in that it is highly occupied by (essentially) all TFs expressed in rich media. These "hotspots" of TF occupancy are strongly nucleosome-depleted and preferentially targeted by chromatin-remodeling complexes and the origin-of-replication complex (ORC). They are also the only chromatin type enriched for predicted Rap1p and Pdr1p binding sites, which we found to work cooperatively with AAA/TTT motifs, known to affect local DNA structure, to reduce nucleosome occupancy. Taken together, our results reveal and characterize a new type of local chromatin structure in yeast.

Related Concepts

Related Feeds

Aneurysm

Aneurysms are outward distensions or bulges that occurs in a weakened wall of blood vessels. Discover the latest research on aneurysms here.

Aortic Aneurysm

An aortic aneurysm is the weakening and bulging of the blood vessel wall in the aorta. This causes dilatation of the aorta, which is usually asymptomatic but carries the risk of rupture and hemorrhage. Find the latest research on aortic aneurysms here.