Chromatin accessibility: a window into the genome

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.Electronic supplementary materialThe online version of this article (doi:10.1186/1756-8935-7-33) contains supplementary material, which is available to authorized users.

Persistent Chromatin Modifications Induced by High Fat Diet*

“…This methodology is one of many (including DNase-seq and ATAC-seq (29)) used to identify regions of accessible chromatin. Although there are differences with these methods (30), generally, they all are able to identify active promoters and enhancers. For this study we chose FAIRE-seq, a method that does not rely on enzymatic reactions and therefore is more reproducible across conditions with low technical variability (31), and it has been pre-viously used to identify open chromatin sites in mouse liver (9).…”

High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility

“…Unlike chromatin immunoprecipitation (ChIP), FAIRE does not depend on the prior selection of a specific target. Without the need for an enzymatic processing step, FAIRE does not require the optimization (and consequent variability) associated with DNase, MNase, or Assay for Transposase-Accessible Chromatin (ATAC) (40), other techniques that explore chromatin accessibility. A specific chromatin signature associated with multiple molecular mechanisms can form the basis for an HT-FAIRE functional screen.…”

Nucleosome Positioning and Its Role in Gene Regulation in Yeast

“…Second, nucleosome occupancy was scaled by dividing the occupancy value by the average nucleosome occupancy of the whole genome; i.e., the nucleosome occupancy was expressed as the fold change of the absolute occupancy relative to the average occupancy. Reads can also be shifted 73 bp toward the 3′ direction, which represented the midpoint [60].With paired-end sequencing, it is assumed that the nucleosome midpoint is consistent with the midpoint of the forward and reverse reads. Unless the reads are from the on type cell (single cell), nucleosome positions actually represent the average positions in cell population.…”

“…Thus, the opening region may alter in diferent cells types. This can be relected in DHSs.The change of DHSs often associates one or more nucleosomes loss or formation [60].DNase-seq means the DNase I digestion followed by DNA sequencing [60]. DNase-seq has been widely used in probing cell-speciic chromatin accessibility.…”

“…Unless the reads are from the on type cell (single cell), nucleosome positions actually represent the average positions in cell population. Therefore, the overlapping reads have to be clustered over genomic regions [60].Calling nucleosomes actually is to ind the peak positions along the nucleosome proile. DANPOS is one tool that can identify nucleosome positions [37].…”