Understanding the chromatin remodeling code

Abstract

Remodeling a chromatin structure enables the genetic elements stored in a genome to function in a condition-specific manner and predisposes the interactions between cis-regulatory elements and trans-acting factors. A chromatin signature can be an indicator of the activity of the underlying genetic elements. This paper reviews recent studies showing that the combination and arrangements of chromatin remodeling marks play roles as chromatin code affecting the activity of genetic elements. This paper also reviews recent studies inferring the primary DNA sequence contexts associated with chromatin remodeling that suggest interactions between genetic and epigenetic factors. We conclude that chromatin remodeling, which provides accurate models of gene expression and morphological variations, may help to find the biological marks that cannot be detected by genome-wide association study or genetic study.

Keywords: ChIP-seq; Chromatin modifications; Chromatin remodeling; Computational analysis; Epigenomics; H3K4me3; chromatin immunoprecipitation and sequencing; siRNA; small interference RNA; tri-methylations at histone H3 Lysine 4.