In silico analysis identifies novel restriction enzyme combinations that expand reduced representation bisulfite sequencing CpG coverage

BMC Research Notes

Vassilios Papadopoulos²  Sunghoon Lee¹  Daniel B Martinez-Arguelles³ 

[1] Departments of Biochemistry, McGill University, Montreal, QC, Canada;Departments of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada;Department of Medicine, McGill University, Montreal, QC, Canada

关键词: Next-generation sequencing;    Restriction enzyme;    Epigenetics;    DNA methylation;    RRBS;   

Others  :  1130429
DOI  :  10.1186/1756-0500-7-534

 received in 2014-04-29, accepted in 2014-08-12,  发布年份 2014

【 摘 要 】

Background

Epigenetics is the study of gene expression changes that are not caused by changes in the deoxyribonucleic acid (DNA) sequence. DNA methylation is an epigenetic mark occurring in C–phosphate–G sites (CpGs) that leads to local or regional gene expression changes. Reduced-representation bisulfite sequencing (RRBS) is a technique that is used to ascertain the DNA methylation of millions of CpGs at single-nucleotide resolution. The genomic coverage of RRBS is given by the restriction enzyme combination used during the library preparation and the throughput capacity of the next-generation sequencer, which is used to read the generated libraries. The four-nucleotide cutters, MspI and TaqαI, are restriction enzymes commonly used in RRBS that, when combined, achieve ~12% genomic coverage. The increase in throughput of next-generation sequencers allows for novel combinations of restriction enzymes that provide higher CpG coverage.

Results

We performed a near-neighbor analysis of the four nucleotide sequences most frequently found within 50 nt of all genomic CpGs. This resulted in the identification of seven methylation-insensitive restriction enzymes (AluI, BfaI, HaeIII, HpyCH4V, MluCI, MseI, and MspI) that shared similar restriction conditions suitable for RRBS library preparation. We report that the use of two or three enzyme combinations increases the theoretical epigenome coverage to almost half of the human genome.

Conclusions

We provide the enzyme combinations that are more likely to increase the CpG coverage in human, rat, and mouse genomes.

【 授权许可】

   
2014 Martinez-Arguelles et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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