RT Journal
A1 van Steensel, Bas
A1 Braunschweig, Ulrich
A1 Filion, Guillaume J.
A1 Chen, Menzies
A1 van Bemmel, Joke G.
A1 Ideker, Trey
T1 Bayesian network analysis of targeting interactions in chromatin
JF Genome Research 
JO Genome Research 
YR 2010 
FD February 01 
VO 20 
IS 2 
SP 190 
OP 200 
DO 10.1101/gr.098822.109 
UL http://genome.cshlp.org/content/20/2/190.abstract 
AB In eukaryotes, many chromatin proteins together regulate gene expression. Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example, by recruitment or competition mechanisms. The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a Bayesian network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we found that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-binding factors, including GAGA factor, JRA, and SU(VAR)3-7. Our network model provides a global view of the targeting interplay among dozens of chromatin components.