Zeschnigk Michael, Martin Marcel, Betzl Gisela, Kalbe Andreas, Sirsch Caroline, Buiting Karin, Gross Stephanie, Fritzilas Epameinondas, Frey Bruno, Rahmann Sven, Horsthemke Bernhard
Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany.
Hum Mol Genet. 2009 Apr 15;18(8):1439-48. doi: 10.1093/hmg/ddp054. Epub 2009 Feb 17.
Methylation of CpG islands (CGIs) plays an important role in gene silencing. For genome-wide methylation analysis of CGIs in female white blood cells and in sperm, we used four restriction enzymes and a size selection step to prepare DNA libraries enriched with CGIs. The DNA libraries were treated with sodium bisulfite and subjected to a modified 454/Roche Genome Sequencer protocol. We obtained 163 034 and 129 620 reads from blood and sperm, respectively, with an average read length of 133 bp. Bioinformatic analysis revealed that 12 358 (7.6%) blood library reads and 10 216 (7.9%) sperm library reads map to 6167 and 5796 different CGIs, respectively. In blood and sperm DNA, we identified 824 (13.7%) and 482 (8.5%) fully methylated autosomal CGIs, respectively. Differential methylation, which is characterized by the presence of methylated and unmethylated reads of the same CGI, was observed in 53 and 52 autosomal CGIs in blood and sperm DNA, respectively. Remarkably, methylation of X-chromosomal CGIs in female blood cells was most often incomplete (25-75%). Such incomplete methylation was mainly found on the X-chromosome, suggesting that it is linked to X-chromosome inactivation.
CpG岛（CGIs）的甲基化在基因沉默中起重要作用。为了对女性白细胞和精子中的CGIs进行全基因组甲基化分析，我们使用了四种限制性内切酶和一个大小选择步骤来制备富含CGIs的DNA文库。DNA文库用亚硫酸氢钠处理，并采用改良的454/罗氏基因组测序仪方案。我们分别从血液和精子中获得了163034条和129620条读数，平均读数长度为133 bp。生物信息学分析显示，血液文库读数中的12358条（7.6%）和精子文库读数中的10216条（7.9%）分别映射到6167个和5796个不同的CGIs。在血液和精子DNA中，我们分别鉴定出824个（13.7%）和482个（8.5%）完全甲基化的常染色体CGIs。在血液和精子DNA中，分别在53个和52个常染色体CGIs中观察到以同一CGI存在甲基化和未甲基化读数为特征的差异甲基化。值得注意的是，女性血细胞中X染色体CGIs的甲基化大多是不完全的（25%-75%）。这种不完全甲基化主要在X染色体上发现，表明它与X染色体失活有关。
