Fig. 1

Mapping transposable element (TE) insertion sites. a. A schematic illustrating the sequential steps of Transposon Insertion Profiling by microarray (TIP-chip). (1) An interval of double stranded genomic DNA with two TE insertions (boxes) oriented on opposing strands is shown; (2) the DNA is digested in parallel restriction enzyme reactions and ligated to vectorette oligonucleotides; (3) oligonucleotides complementary to the TE insertions prime first strand synthesis; (4) the elongating strands form reverse complements of the vectorette sequence; (5) there is exponential amplification of insertion site fragments; (6) these amplicons are labeled and hybridized to genomic tiling microarrays; and (7) ‘peaks’ of fluorescence intensity across several probes corresponding to contiguous genomic positions indicate a TE insertion. b. An example of a polymorphic Alu peak in two leukemia cell lines (SR and MOLT-4) in the third intron of the TCOF1 (Treacher Collins-Franceschetti syndrome 1) gene on chromosome 5. The upper panels show TIP-chip data for the insertion, which is present in the SR line and not the MOLT-4 cells. The Alu insertion is a minus (-) strand insertion to the right of the probe with the greatest intensity; an arrow is drawn to indicate its position and orientation, but the arrow is not drawn to scale. Alu insertions approximate 300 bp, and the width of the peak in this case is 5 kb. c. Peaks were recognized using a sliding window algorithm which identified adjacent probes above a threshold fluorescence intensity value. The threshold value was progressively lowered to identify peaks in a rank order. The graphs show the number of reference insertions identified verses peak rank for a representative LINE-1 and Alu TIP-chip. The cut-off for defining a candidate insertion was established using the inflection points (red arrows) of these plots