COBRA-Seq: Sensitive and Quantitative Methylome Profiling
AbstractCombined Bisulfite Restriction Analysis (COBRA) quantifies DNA methylation at a specific locus. It does so via digestion of PCR amplicons produced from bisulfite-treated DNA, using a restriction enzyme that contains a cytosine within its recognition sequence, such as TaqI. Here, we introduce COBRA-seq, a genome wide reduced methylome method that requires minimal DNA input (0.1–1.0 mg) and can either use PCR or linear amplification to amplify the sequencing library. Variants of COBRA-seq can be used to explore CpG-depleted as well as CpG-rich regions in vertebrate DNA. The choice of enzyme influences enrichment for specific genomic features, such as CpG-rich promoters and CpG islands, or enrichment for less CpG dense regions such as enhancers. COBRA-seq coupled with linear amplification has the additional advantage of reduced PCR bias by producing full length fragments at high abundance. Unlike other reduced representative methylome methods, COBRA-seq has great flexibility in the choice of enzyme and can be multiplexed and tuned, to reduce sequencing costs and to interrogate different numbers of sites. Moreover, COBRA-seq is applicable to non-model organisms without the reference genome and compatible with the investigation of non-CpG methylation by using restriction enzymes containing CpA, CpT, and CpC in their recognition site. View Full-Text
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Varinli, H.; Statham, A.L.; Clark, S.J.; Molloy, P.L.; Ross, J.P. COBRA-Seq: Sensitive and Quantitative Methylome Profiling. Genes 2015, 6, 1140-1163.
Varinli H, Statham AL, Clark SJ, Molloy PL, Ross JP. COBRA-Seq: Sensitive and Quantitative Methylome Profiling. Genes. 2015; 6(4):1140-1163.Chicago/Turabian Style
Varinli, Hilal; Statham, Aaron L.; Clark, Susan J.; Molloy, Peter L.; Ross, Jason P. 2015. "COBRA-Seq: Sensitive and Quantitative Methylome Profiling." Genes 6, no. 4: 1140-1163.