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Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

Chao Cheng1, Chong Shou2, Kevin Y Yip13 and Mark B Gerstein124*

Author Affiliations

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

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Genome Biology 2011, 12:R111  doi:10.1186/gb-2011-12-11-r111

Published: 7 November 2011

Abstract

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.