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Genome Biol. 2011 Nov 7;12(11):R111. doi: 10.1186/gb-2011-12-11-r111.

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

Author information

1
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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.

PMID:
22060676
PMCID:
PMC3334597
DOI:
10.1186/gb-2011-12-11-r111
[Indexed for MEDLINE]
Free PMC Article

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