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. Author manuscript; available in PMC: 2011 Jan 2.
Published in final edited form as: Cell. 2010 Jun 25;141(7):1159–1170. doi: 10.1016/j.cell.2010.05.021

Figure 1. A strategy for identifying dimorphic L1Hs elements in individual human genomes.

Figure 1

In silico comparison of the fosmid end sequences (red squares) from individual genomic libraries (blue horizontal line) and the HGR (pink horizontal line) enables the detection of fosmids that may contain insertions or deletions with respect to the HGR (see dashed lines). Insertion fosmids were screened by allele specific oligonucleotide hybridization to detect characters that are present in the 5′ UTR of newer L1 elements (one discriminating character utilized, a deletion of the G residue at bp 74 in recent L1s, is indicated in maroon). Putative L1Hs-containing fosmids were analyzed by Southern blotting with a 5′ UTR probe (blue arrow). A representative digest and Southern blot is shown. The ~6kb band is diagnostic for the full-length L1. The additional hybridizing band (~1.3kb band liberated from the L1 5′ flank in this Southern blot example) serves to distinguish individual fosmids. ATLAS and/or DNA sequencing confirmed the presence of a dimorphic, full-length L1Hs insertion.