title: Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete.
abstract: 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.
authors.affiliation: Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany. michael.zeschnigk@uni-due.de
authors.forename: Michael
authors.initials: M
authors.lastname: Zeschnigk
authors.forename: Marcel
authors.initials: M
authors.lastname: Martin
authors.forename: Gisela
authors.initials: G
authors.lastname: Betzl
authors.forename: Andreas
authors.initials: A
authors.lastname: Kalbe
authors.forename: Caroline
authors.initials: C
authors.lastname: Sirsch
authors.forename: Karin
authors.initials: K
authors.lastname: Buiting
authors.forename: Stephanie
authors.initials: S
authors.lastname: Gross
authors.forename: Epameinondas
authors.initials: E
authors.lastname: Fritzilas
authors.forename: Bruno
authors.initials: B
authors.lastname: Frey
authors.forename: Sven
authors.initials: S
authors.lastname: Rahmann
authors.forename: Bernhard
authors.initials: B
authors.lastname: Horsthemke
mesh_terms: D001773:Blood Cells / Q000737:chemistry; D018899:CpG Islands; D004247:DNA / Q000302:isolation & purification; D019175:DNA Methylation; D005260:Female; D015894:Genome, Human; D006801:Humans; D008297:Male; D017422:Sequence Analysis, DNA; D013094:Spermatozoa / Q000737:chemistry; D049951:X Chromosome Inactivation
chemical_list: D004247:DNA