Genome Wide Methylation Patterns in Holstein Leukocytes

The objective of this research was to describe genome-wide DNA methylation patterns in leukocytes from 8 Holstein cows with variable phenotypes. Following DNA extraction from peripheral blood leukocytes, methylated DNA fragments were captured via methylated DNA immunoprecipitation (MeDIP) and paired-end 49 -bp reads were sequenced.  The number of reads covering each nucleotide was extracted and the geometric mean number of reads (GMR) across cows was determined. GMR were merged with details for 13,677 genes available from Ensembl. The majority (78.4%) of CpG sites were sequenced at least once and repetitive element reads were primarily mapped to satellite (36.4%), SINE (29.1%), and LINE (23.7%) regions. GMR were lower at the centromeric ends than for the remainder of most chromosomes. There were significant variations at a chromosome level with the lowest DNA methylation for X and highest for BTA 19. Genomic regions with more annotated genes generally had higher GMR; however, partially methylated domains in gene-rich areas were evident. GMR were lower in upstream than in intra-genic and downstream regions, with the nadir GMR occurring ~100 bp upstream of the transcription start site. GMR were relatively low over the first exon when compared with later exons, whereas GMR were high near intron-exon junctions and lower in the center of introns. DNA methylation levels varied across the genome and tended to be highest in gene-rich regions. DNA methylation was lower upstream and across initial gene exons, corresponding to regions controlling gene transcription levels.