TY - JOUR
T1 - The Specificity and Topology of Chromatin Interaction Pathways in Yeast
AU - Lenstra, Tineke L.
AU - Benschop, Joris J.
AU - Kim, Tae Soo
AU - Schulze, Julia M.
AU - Brabers, Nathalie A.C.H.
AU - Margaritis, Thanasis
AU - van de Pasch, Loes A.L.
AU - van Heesch, Sebastiaan A.A.C.
AU - Brok, Mariel O.
AU - Groot Koerkamp, Marian J.A.
AU - Ko, Cheuk W.
AU - van Leenen, Dik
AU - Sameith, Katrin
AU - van Hooff, Sander R.
AU - Lijnzaad, Philip
AU - Kemmeren, Patrick
AU - Hentrich, Thomas
AU - Kobor, Michael S.
AU - Buratowski, Stephen
AU - Holstege, Frank C.P.
N1 - Funding Information:
We thank V. Geli and T. van Welsem for strains; and H.Th.M. Timmers, M. Vermeulen, F. van Leeuwen, and J.A. Lenstra for critical reading. Supported by the Netherlands Bioinformatics Centre (NBIC) and the Netherlands Organization of Scientific Research (NWO), grants 016108607, 81702015, 05071057, 91106009, 021002035 (T.L.L.), 86307007 (P.K.), and 70057407 (J.J.B.).
PY - 2011/5/20
Y1 - 2011/5/20
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=79955949044&partnerID=8YFLogxK
U2 - 10.1016/j.molcel.2011.03.026
DO - 10.1016/j.molcel.2011.03.026
M3 - Article
C2 - 21596317
AN - SCOPUS:79955949044
SN - 1097-2765
VL - 42
SP - 536
EP - 549
JO - Molecular Cell
JF - Molecular Cell
IS - 4
ER -