Introduction
2015-09-15Chengqi YiBisulfite-free, base-resolution analysis of 5-formylcytosine at whole-genome scale
Center of Life Sciences' research team lead by Dr. Chengqi Yi published their work entitled "Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale" in Nature Methods on September 7th, 2015. In this study, the team reported fC-CET—a selective chemical labelling and pull-down method—to identify the genome-wide, base-resolution 5-formylcytosine (5fC) DNA modification in mouse embryonic stem cells.
Discovery of the ten-eleven translocation (TET)-dependent generation and removal of oxidized derivatives of 5mC, namely, 5hmC, 5fC and 5caC, revealed a new paradigm of active DNA demethylation in mammalian genomes. A major challenge is the lack of a selective and sensitive sequencing method for the genome-wide identification of this newly discovered DNA modification. In this study, the team presents fC-CET (cyclization-enabled C-to-T transition of 5fC), a bisulfite-free method for whole-genome analysis of 5fC based on selective chemical labeling of 5fC and subsequent C-to-T transition during PCR. Base-resolution 5fC maps showed limited overlap with 5hmC, with 5fC-marked regions more active than 5hmC-marked ones. Because fC-CET demonstrates no noticeable DNA degradation, fC-CET also has potential for analyses of precious DNA including clinical samples.
Prof. Chengqi Yi from Peking University and Prof. Chuan He from University of Chicago are co-corresponding authors of the study; Bo Xia (PKU), Dali Han, Xingyu Lu (U of Chicago) are co-first authors. The study was supported by the Ministry of Science and Technology, the National Natural Science Foundation of China, and Peking-Tsinghua Center for Life Sciences.
Web link of the paper:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3569.html#affil-auth
