Chromatin accessibility: a window into the genome

被引：286

作者：

Tsompana, Maria ^{[1
]}

Buck, Michael J. ^{[1
,2
]}

机构：

[1] SUNY Buffalo, New York State Ctr Excellence Bioinformat & Life, Buffalo, NY 14203 USA

[2] SUNY Buffalo, Dept Biochem, Buffalo, NY 14203 USA

来源：

EPIGENETICS & CHROMATIN | 2014年 / 7卷

关键词：

Chromatin; MNase; DNase; ATAC; FAIRE; Sequencing; Library; Epigenome; Histone; Nucleosome; DNASE HYPERSENSITIVE SITES; PROTEIN-BINDING FOOTPRINTS; NUCLEOSOME CORE PARTICLE; CHIP-SEQ DATA; MICROCOCCAL NUCLEASE; REGULATORY ELEMENTS; IN-VIVO; QUANTITATIVE-ANALYSIS; MOTIF DISCOVERY; SEQUENCING DATA;

D O I：

10.1186/1756-8935-7-33

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

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