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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.

SUBMITTER: Cheng C

PROVIDER: S-EPMC3334597 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

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

Cheng Chao C Shou Chong C Yip Kevin Y KY Gerstein Mark B MB

Genome biology 20111107 11

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 diff ...[more]

PMID: 22060676

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