title: Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements.
abstract: Although non-CG methylations are abundant in several mammalian cell types, their biological significance is sparsely characterized. We gathered 51 human and mouse DNA methylomes from brain neurons, embryonic stem cells and induced pluripotent stem cells, primordial germ cells and oocytes. We utilized an unbiased sub-motif prediction method and reported CW as the representative non-CG methylation context, which is distinct from CC methylation in terms of sequence context and genomic distribution. A two-dimensional comparison of non-CG methylations across cell types and species was performed. Unambiguous studies of sequence preferences and genomic region enrichment showed that CW methylation is cell-type specific and is also conserved between humans and mice. In brain neurons, it was found that active long interspersed nuclear element-1 (LINE-1) lacked CW methylations but not CG methylations. Coincidentally, both human Alu and mouse B1 elements preferred high CW methylations at specific loci during their respective evolutionary development. Last, the strand-specific distributions of CW methylations in introns and long interspersed nuclear elements are also cell-type specific and conserved. In summary, our results illustrate that CW methylations are highly conserved among species, are dynamically regulated in each cell type, and are potentially involved in the evolution of transposon elements.
authors: The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, People's Republic of China.
authors: Weilong
authors: W
authors: Guo
authors: Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, United States of America.|Bioinformatics Division, TNLIST and Center for Synthetic &Systems Biology, Tsinghua University, Beijing, People's Republic of China.
authors: Michael Q
authors: MQ
authors: Zhang
authors: The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, People's Republic of China.
authors: Hong
authors: H
authors: Wu
mesh_terms: D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D051379:Mice; D009928:Organ Specificity / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements