Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Genome Biol. 2011 Jul 6;12(7):R62. doi: 10.1186/gb-2011-12-7-r62.
We performed a comparative analysis of the genome-wide DNA methylation profiles from three human embryonic stem cell (HESC) lines. It had previously been shown that HESC lines had significantly higher non-CG methylation than differentiated cells, and we therefore asked whether these sites were conserved across cell lines.
We find that heavily methylated non-CG sites are strongly conserved, especially when found within the motif TACAG. They are enriched in splice sites and are more methylated than other non-CG sites in genes. We next studied the relationship between allele-specific expression and allele-specific methylation. By combining bisulfite sequencing and whole transcriptome shotgun sequencing (RNA-seq) data we identified 1,020 genes that show allele-specific expression, and 14% of CG sites genome-wide have allele-specific methylation. Finally, we asked whether the methylation state of transcription factor binding sites affects the binding of transcription factors. We identified variations in methylation levels at binding sites and found that for several transcription factors the correlation between the methylation at binding sites and gene expression is generally stronger than in the neighboring sequences.
These results suggest a possible but as yet unknown functional role for the highly methylated conserved non-CG sites in the regulation of HESCs. We also identified a novel set of genes that are likely transcriptionally regulated by methylation in an allele-specific manner. The analysis of transcription factor binding sites suggests that the methylation state of cis-regulatory elements impacts the ability of factors to bind and regulate transcription.
我们对三个人类胚胎干细胞（HESC）系的全基因组 DNA 甲基化谱进行了比较分析。先前已经表明，HESC 系的非 CG 甲基化程度明显高于分化细胞，因此我们询问这些位点是否在细胞系之间保守。
我们发现高度甲基化的非 CG 位点具有很强的保守性，尤其是在 TACAG 基序内发现时。它们在剪接位点中富集，并且在基因中的其他非 CG 位点中更甲基化。我们接下来研究了等位基因特异性表达与等位基因特异性甲基化之间的关系。通过结合亚硫酸氢盐测序和全转录组鸟枪法测序（RNA-seq）数据，我们鉴定出 1020 个表现出等位基因特异性表达的基因，并且全基因组中有 14%的 CG 位点具有等位基因特异性甲基化。最后，我们询问转录因子结合位点的甲基化状态是否影响转录因子的结合。我们确定了结合位点处甲基化水平的变化，并发现对于几个转录因子，结合位点处的甲基化与基因表达之间的相关性通常比邻近序列更强。
这些结果表明，高度甲基化的保守非 CG 位点在 HESC 的调控中可能具有未知的功能作用。我们还鉴定出了一组可能以等位基因特异性方式受甲基化转录调控的新基因。转录因子结合位点的分析表明，顺式调节元件的甲基化状态会影响因子结合和调节转录的能力。
