Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete

被引：26

作者：

Zeschnigk, Michael ^{[1
]}

Martin, Marcel ^{[2
]}

Betzl, Gisela ^{[3
]}

Kalbe, Andreas ^{[3
]}

Sirsch, Caroline ^{[3
]}

Buiting, Karin ^{[1
]}

Gross, Stephanie ^{[1
]}

Fritzilas, Epameinondas ^{[4
]}

Frey, Bruno ^{[3
]}

Rahmann, Sven ^{[2
]}

Horsthemke, Bernhard ^{[1
]}

机构：

[1] Univ Klinikum Essen, Inst Humangenet, D-45122 Essen, Germany

[2] TU Dortmund, Bioinformat High Throughput Technol, D-44221 Dortmund, Germany

[3] Roche Diagnost GmbH, D-82377 Penzberg, Germany

[4] Univ Bielefeld, Int NRW Grad Sch Bioinformat & Genome Res, D-33594 Bielefeld, Germany

来源：

HUMAN MOLECULAR GENETICS | 2009年 / 18卷 / 08期

关键词：

COMPREHENSIVE ANALYSIS; IMPRINTED GENES; GENOME; PROMOTER; CELLS; WIDE; PLURIPOTENT; IDENTIFY; MAPS; PCR;

D O I：

10.1093/hmg/ddp054

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1439 / 1448

页数：10

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