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2015 ; 6
(4
): 1140-63
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COBRA-Seq: Sensitive and Quantitative Methylome Profiling
#MMPMID26512698
Varinli H
; Statham AL
; Clark SJ
; Molloy PL
; Ross JP
Genes (Basel)
2015[Oct]; 6
(4
): 1140-63
PMID26512698
show ga
Combined 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.