Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors
- Equal contributors
1 Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA
2 Program in Computational Biology and Bioinformatics, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA
3 Department of Computer Science and Engineering, The Chinese University of Hong Kong, Rm 1006, Ho Sin-Hang Engineering Bldg, Shatin, New Territories, Hong Kong
4 Department of Computer Science, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA
Genome Biology 2011, 12:R111 doi:10.1186/gb-2011-12-11-r111Published: 7 November 2011
We propose a method to predict yeast transcription factor targets by integrating histone modification profiles with transcription factor binding motif information. It shows improved predictive power compared to a binding motif-only method. We find that transcription factors cluster into histone-sensitive and -insensitive classes. The target genes of histone-sensitive transcription factors have stronger histone modification signals than those of histone-insensitive ones. The two classes also differ in tendency to interact with histone modifiers, degree of connectivity in protein-protein interaction networks, position in the transcriptional regulation hierarchy, and in a number of additional features, indicating possible differences in their transcriptional regulation mechanisms.