Mapping genome-wide transcription factor binding sites in frozen tissues

Epigenetics & Chromatin

Richard M Myers¹  Gregory M Cooper¹  Preti Jain¹  Jason Gertz¹  Daniel Savic¹ 

[1] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA

关键词: Tissue specificity;    Genomics;    Gene regulation;    Frozen tissues;    ChIP-seq;   

Others  :  809680
DOI  :  10.1186/1756-8935-6-30

 received in 2013-07-23, accepted in 2013-08-13,  发布年份 2013

【 摘 要 】

Background

Genome-wide maps of transcription factor binding sites in primary tissues can expand our understanding of genome function, transcriptional regulation, and genetic alterations that contribute to disease risk. However, almost all genome-wide studies of transcription factors have been in cell lines, and performing these experiments in tissues has been technically challenging and limited in throughput.

Results

Here we outline a simple strategy for mapping transcription factor binding sites in frozen tissues that utilizes dry pulverization of samples and is scalable for high-throughput analyses. We show that the method leads to accurate and reproducible chromatin immunoprecipitation next-generation sequencing (ChIP-seq) data, and is highly sensitive, identifying high-quality transcription factor binding sites from chromatin corresponding to only 5 mg of liver tissue.

Conclusions

The enhanced reproducibility, robustness, and sensitivity of the dry pulverization method, in addition to the ease of implementation and scalability, makes ChIP-seq in primary tissues a widely accessible assay.

【 授权许可】

   
2013 Savic et al.; licensee BioMed Central Ltd.

【 图 表 】

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