Schematic representation of (A) EDSB-PCR and (B) L1-EDSB methylation status. (A) Red lines, blue arrows and parallel vertical bars represent genomic DNAs, LINE-1 sequences and EDSB ends, respectively. First, LMPCR linkers, yellow arrow and green line, are ligated to EDSB ends. Yellow arrows are primer sequences. On the left, there is no EDSB and only COBRA-L1 yields a positive amplicon. On the right, only an EDSB end located nearby LINE-1 sequence is detected as L1-EDSB-LMPCR or COBRA-L1-EDSB (1). (B) The two red lines represent the same chromosomes of two different cells. Methylation levels of the LINE-1s are distinct among loci, but methylation levels between nearby LINE-1s are closely correlated (2). Blue arrows represent LINE-1 sequences, in which methylation levels of the dark blue LINE-1s are higher. Two parallel vertical lines represent EDSB ends. Detectable EDSBs can only be found rarely (from EDSB PCR data) and randomly (from variable EDSB PCR amplicon sizes (data not shown)); however, they are found preferentially near hypermethylated LINE-1s (1).