title: The specificity and topology of chromatin interaction pathways in yeast.
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.
authors: Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
authors: Tineke L
authors: TL
authors: Lenstra
authors: Joris J
authors: JJ
authors: Benschop
authors: Taesoo
authors: T
authors: Kim
authors: Julia M
authors: JM
authors: Schulze
authors: Nathalie A C H
authors: NA
authors: Brabers
authors: Thanasis
authors: T
authors: Margaritis
authors: Loes A L
authors: LA
authors: van de Pasch
authors: Sebastiaan A A C
authors: SA
authors: van Heesch
authors: Mariel O
authors: MO
authors: Brok
authors: Marian J A
authors: MJ
authors: Groot Koerkamp
authors: Cheuk W
authors: CW
authors: Ko
authors: Dik
authors: D
authors: van Leenen
authors: Katrin
authors: K
authors: Sameith
authors: Sander R
authors: SR
authors: van Hooff
authors: Philip
authors: P
authors: Lijnzaad
authors: Patrick
authors: P
authors: Kemmeren
authors: Thomas
authors: T
authors: Hentrich
authors: Michael S
authors: MS
authors: Kobor
authors: Stephen
authors: S
authors: Buratowski
authors: Frank C P
authors: FC
authors: Holstege
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