Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo

BMC Genomics

Thomas G Fazzio³  Kurtis N McCannell¹  Sarah J Hainer¹  Lihua J Zhu²  Poshen B Chen¹ 

[1] Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA;Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA;Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA

关键词: Embryonic stem cells;    Nucleosome dynamics;    Chromatin accessibility;    Restriction enzyme accessibility;    RED-seq;   

Others  :  1127308
DOI  :  10.1186/1471-2164-15-1104

 received in 2014-06-02, accepted in 2014-12-10,  发布年份 2014

【 摘 要 】

Background

Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, differences in nucleosome composition or dynamics may also regulate accessibility. Methods for mapping nucleosome positions and occupancies genome-wide (MNase-seq) have uncovered the nucleosome landscapes of many different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays.

Results

Here we probe the genome-wide accessibility of multiple cell types in an unbiased manner using restriction endonuclease digestion of chromatin coupled to deep sequencing (RED-seq). Using this method, we identified differences in chromatin accessibility between populations of cells, not only in nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the majority of the genome that is packaged into nucleosome arrays. Furthermore, we identified both large differences in chromatin accessibility in distinct cell lineages and subtle but significant changes during differentiation of mouse embryonic stem cells (ESCs). Most significantly, using RED-seq, we identified differences in accessibility among nucleosomes harboring well-studied histone variants, and show that these differences depend on factors required for their deposition.

Conclusions

Using an unbiased method to probe chromatin accessibility genome-wide, we uncover unique features of chromatin structure that are not observed using more widely-utilized methods. We demonstrate that different types of nucleosomes within mammalian cells exhibit different degrees of accessibility. These findings provide significant insight into the regulation of DNA accessibility.

【 授权许可】

   
2014 Chen et al.; licensee BioMed Central.

【 图 表 】

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