Here’s another great advance in methylome sequencing. You all know about bisulfite sequencing, the “gold standard” method. Unfortunately it’s expensive. It also requires a lot of sample, due to DNA degradation. There are enrichment methods, like MeDIP-seq, that are relatively cheap. However, there is the drawback of CpG density bias. Excitingly, there is a new enzyme based enrichment method, called TamC-Seq that requires less sample, less money, and provides excellent coverage for genome-wide profiling. The devlopers are from the He group, University of Chicago. The paper is Liang Zhang et al. Tet-mediated covlent labelling of 5-methylctosine for its genome-wide detection and sequencing. (2013) Nature Communications, (4) 1517
So how does it work? Their protocol uses mouse Tet (Ten-eleven translocation)-1, (or mTet1) enzyme expressed in a baculovirus system. First 5hmC is protected with a glucose using Beta-GT. Next, in a “One pot” procedure, the mTet1 converts 5hmC from 5mC, which is then immediately glycoslated by Beta-GT with a modified glucose moiety(6-N3-glucose) . Then all the original 5mC is labeled with biotin via click chemistry. Time for affinity biotin/streptavidin purification, followed by sequencing.
The researchers used mouse embryotic stem cells, as well as human breast cancer cell lines, to compare methylome data with other methods. TamC-Seq was efficient at providing more methylation site coverage than MeDIP-Seq. TamC-Seq captured a wider range of CpGs, showing less density bias than MeDIP-Seq. The TamC-Seq data was concordant with Bisulfite-Seq data.
The same research group is also working on RNA epigenetics. Interesting! Check out their web site.
Zhang L, Szulwach KE, Hon GC, Song CX, Park B, Yu M, Lu X, Dai Q, Wang X, Street CR, Tan H, Min JH, Ren B, Jin P, & He C (2013). Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature communications, 4 PMID: 23443545