DNA Methylation patterns of L1Md_Tf (L1), major satellites (mSat), and IAPLTR1 (IAP) in germ cells and three pronuclear stages (PN) of mouse zygotes. (A) DNA methylation patterns, Bars are the sum of the DNA methylation status of all CpG dyads. The map next to the bar represents the distribution of methylated sites. Each column shows neighbored CpG dyads, and each line represents one sequence read. The reads in the map are sorted first by fully methylated sites and then by hemimethylated CpG dyads. Red, fully methylated CpG dyads; light green and dark green, hemimethylated CpG dyads on the upper and lower strand; blue, unmethylated CpG dyads; white, mutated or not analyzable. As 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) cannot be discriminated by bisulfite sequencing, "mC" should be considered to mean 5mC or 5hmC throughout the paper, and equally "C" (cytosine) should be considered to mean C, 5-formylcytosine (5fC), or 5-carboxycytosine (5caC). (B) Absolute DNA methylation level and percentage of hemimethylated CpG dyads in relation to all methylated CpG dyads. DNA Methylation patterns of L1, mSat and IAP were analyzed in germ cells (oocytes and sperm) and different PN stages (PN1 and early PN3 are before replication, PN4 to PN5 are after replication) using deep hairpin bisulfite sequencing (DHBS). DNA methylation pattern changes can be observed following the first DNA replication after fertilization; in all elements an increasing amount of hemimethylated CpG dyads can be seen, and for L1 DNA demethylation can also be observed.