Oct 8, 2014

Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling

BioRxiv : the Preprint Server for Biology
Juliane PernerHo-Ryun Chung

Abstract

Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes, or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.

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Mentioned in this Paper

Biological Neural Networks
Genome
Genes
Regulation of Biological Process
Complex (molecular entity)
Transcription, Genetic
Chromatin Immunoprecipitation
Histone Modification
Literature
Chromatin Remodeling Factor

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