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Review
. 2014 Nov 20;7(1):33.
doi: 10.1186/1756-8935-7-33. eCollection 2014.

Chromatin accessibility: a window into the genome

Maria Tsompana  1 , Michael J Buck  2
Affiliations
Review

Chromatin accessibility: a window into the genome

Maria Tsompana et al. Epigenetics Chromatin. .

Abstract

Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.

Keywords: ATAC; Chromatin; DNase; Epigenome; FAIRE; Histone; Library; MNase; Nucleosome; Sequencing.

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Figures

Figure 1
Figure 1
Schematic diagram of current chromatin accessibility assays performed with typical experimental conditions. Representative DNA fragments generated by each assay are shown, with end locations within chromatin defined by colored arrows. Bar diagrams represent data signal obtained from each assay across the entire region. The footprint created by a transcription factor (TF) is shown for ATAC-seq and DNase-seq experiments.
Figure 2
Figure 2
Chromatin accessibility high-throughput data analysis workflow. Chromatin accessibility data analysis involves a number of stages with progressively increased level of difficulty and advanced requirements for computational and genomics expertise. All major steps of analyses, from sequence tags to data annotation/integration are shown in a comprehensive workflow format (read text for additional details).
See this image and copyright information in PMC

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