Quantitative analysis of genome-wide chromatin remodeling

Abstract

Recent high-throughput sequencing technologies have opened the door for genome-wide characterization of chromatin features at an unprecedented resolution. Chromatin accessibility is an important property that regulates protein binding and other nuclear processes. Here, we describe computational methods to analyze chromatin accessibility using DNaseI hypersensitivity by sequencing (DNaseI-seq). Although there are numerous bioinformatic tools to analyze ChIP-seq data, our statistical algorithm was developed specifically to identify significantly accessible genomic regions by handling features of DNaseI hypersensitivity. Without prior knowledge of relevant protein factors, one can discover genome-wide chromatin remodeling events associated with specific conditions or differentiation stages from quantitative analysis of DNaseI hypersensitivity. By performing appropriate subsequent computational analyses on a select subset of remodeled sites, it is also possible to extract information about putative factors that may bind to specific DNA elements within DNaseI hypersensitive sites. These approaches enabled by DNaseI-seq represent a powerful new methodology that reveals mechanisms of transcriptional regulation.

Fig. 1.

Example sequence tag profiles of DHS elements. (a) DNaseI hypersensitive sites (DHSs) are measured by deep sequencing of small, size-selected DNA fragments released by DNaseI treatment from regions of locally reorganized chromatin (2). (b) The DNaseI-seq data are presented as tag density profiles, summarizing the number of sequence tags that are aligned to the region. Density values can be normalized by the total number of aligned sequence tags to aid comparison of multiple samples. A DNaseI-seq profile obtained from a mammary carcinoma cell line is shown for a region in chromosome 1 (genome build: mm8). Regions of increased DNaseI sensitivity are detected by the computational algorithms as “hotspots” (DHS hotspots track). Within these hotspots are found localized peaks of hypersensitivity (DHS peaks track).