二倍体和四倍体泥鳅全基因组DNA甲基化的比较

以二倍体和四倍体泥鳅为研究对象,采用甲基化修饰依赖性内切酶测序技术(MethylRAD-Seq)在全基因组水平上分析泥鳅的DNA甲基化特点及倍性间的DNA甲基化变异。测序结果共得到302 111 684条Methyl-RAD序列标签。与参考基因组比对结果显示,泥鳅的甲基化位点主要分布在基因体区(gene body),其次为内含子区(intron)和基因间区(intergenic),而在其他功能元件上的分布较少。四倍体泥鳅的整体甲基化水平比二倍体高,尤其是在第一外显子区(1st Exon)和转录起始位点上游1 500bp至200bp区(TSS1500),且倍性间差异极显著(P0.01)。但在启动子区,四倍体泥鳅的甲基化水平略低于二倍体。在二倍体和四倍体泥鳅间共筛选到1 268个差异甲基化CmCGG位点和14个差异甲基化CmCWGG位点,这些位点主要分布于内含子、基因体和基因间区。比较各基因的甲基化水平,共得到684个倍性间差异甲基化基因。KEGG分析结果显示,倍性间差异甲基化基因主要富集到与生长发育、免疫及错配修复等相关通路上。     

Genome-wide DNA methylation of palate embryonic tissue in process of embryonic mouse cleft palate formation

AIM:To analyze genome-wide DNA differential methylation site-related genes and genomic diffe-rential methylation levels involved in embryonic mouse cleft palate formation. METHODS:MethylRAD-Seq was performed on the gestational day 13.5 (GD13.5), GD14.5 and GD16.5 in experimental group and control group, which is a method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes. A comparison was made to process the different location of the methylation site and the methylation level differential genes among genome-wide different functional components (3'-untranslated region, 5'-untranslated region, TSS2000, intron, exon, and intergenic region). The genome-wide DNA differential methylation site-related genes and methylation differential genes were analyzed using GO function enrichment and KEGG pathway enrichment. RESULTS:(1) The peak number and peak value of methylation sites in different components of DNA did not change significantly in the control group, and the methylation level of the experimental group decreased gradually over time. (2) GO function enrichment analysis and KEGG pathway enrichment ana-lysis were performed to process methylation level differential genes and genome-wide DNA differential methylation site-rela-ted genes, among which there were 6 genes (Fgf16, Jarid2, Kdm6a, Nr3c1, Tbx22 and Trp53) involved in embryonic mouse cleft palate formation. (3) MAPK, Wnt, TGF-β and other signaling pathways were found to participate in the formation of cleft palate. CONCLUSION:DNA methylation plays an important regulatory role in the process of cleft palate formation.