title: Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.
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.
authors: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
authors: Chao
authors: C
authors: Cheng
authors: Chong
authors: C
authors: Shou
authors: Kevin Y
authors: KY
authors: Yip
authors: Mark B
authors: MB
authors: Gerstein
mesh_terms: D000107:Acetylation; D000465:Algorithms; D020816:Amino Acid Motifs; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006657:Histones / Q000235:genetics*; D008957:Models, Genetic; D011485:Protein Binding; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D006657:Histones; D014157:Transcription Factors