Friday, April 13, 2012

A novel transposase-based, low-input methyl-seq method

The role of DNA methylation in gene regulation and epigenetics is of ever-increasing interest. Until now, investigating DNA methylation has been crippled either by: i) the necessity for microgram quantities of input DNA for whole-genome bisulfite sequencing (WGBS); or ii) incomplete  interrogation of the methylome in the case of reduced-representation bisulfite sequencing (RRBS).

In a recent publication, Adey and Shendure report a transposon-based in vitro library construction method to demonstrate that a highly complex bisulfite sequencing library may be obtained from as little as 10 ng of genomic DNA. The authors describe the use of a custom-loaded transposase for "tagmentation" (tagging and fragmentation of the DNA) that contained an unmethylated transposon sequence. After an oligonucleotide replacement procedure, in which (methylated) adaptors were ligated to each end of the tagmented genomic DNA, standard bisulfite treatment was used. The library was amplified by PCR and sequenced on an Illumina® MiSeq using a single-end, 100-bp run. Over 100 million aligned reads were obtained at high complexity with >96% of CpG and >98% of non-CpG cytosines covered for the genome. The necessity to have part of the transposon DNA unmethylated served as an internal control and demonstrated that the conversion rate of the bisulfite treatment was >99%. The method described will allow for whole-methylome interrogation where DNA sample is limiting (biopsy samples, microdissected tissues, etc.) and may also allow for the utilization of poor-quality or degraded DNA samples.

ResearchBlogging.orgAdey, A., & Shendure, J. (2012). Ultra-low-input, tagmentation-based whole genome bisulfite sequencing Genome Research DOI: 10.1101/gr.136242.111

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