The Specificity and Topology of Chromatin Interaction Pathways in Yeast

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2011 May 21

PMID 21596317

Citations 148

Authors

Tineke L Lenstra

Joris J Benschop

Taesoo Kim

Julia M Schulze

Nathalie A C H Brabers

Thanasis Margaritis

Loes A L van de Pasch

Sebastiaan A A C van Heesch

Mariel O Brok

Marian J A Groot Koerkamp

Cheuk W Ko

Dik van Leenen

Katrin Sameith

Sander R van Hooff

Philip Lijnzaad

Patrick Kemmeren

Thomas Hentrich

Michael S Kobor

Stephen Buratowski

Frank C P Holstege

Affiliations

Soon will be listed here.

Abstract

Packaging of DNA into chromatin has a profound impact on gene expression. To understand how changes in chromatin influence transcription, we analyzed 165 mutants of chromatin machinery components in Saccharomyces cerevisiae. mRNA expression patterns change in 80% of mutants, always with specific effects, even for loss of widespread histone marks. The data are assembled into a network of chromatin interaction pathways. The network is function based, has a branched, interconnected topology, and lacks strict one-to-one relationships between complexes. Chromatin pathways are not separate entities for different gene sets, but share many components. The study evaluates which interactions are important for which genes and predicts additional interactions, for example between Paf1C and Set3C, as well as a role for Mediator in subtelomeric silencing. The results indicate the presence of gene-dependent effects that go beyond context-dependent binding of chromatin factors and provide a framework for understanding how specificity is achieved through regulating chromatin.

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