Transposon insertion site profiling chip (TIP-chip)

Wheelan et al. 10.1073/pnas.0605450103.

Supporting Information

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Fig. 5. Virtual overlay of GRF167 and L27-10 arrays, color-coded to display concordance between the arrays. Yellow signals are seen in GRF167 only and blue signals in L27-10 only; overlapping signals are colored red. Many spots are red, which is to be expected, as GRF167 is the parent strain for L27-10. Many more lines appear in blue, indicating that there are many transposons in the L27-10 strain not found in GRF167. A few features appear in yellow; these are transposons that are new in GRF167 or are lost in L27-10.

Fig. 6. The diagram shows the structure of the tE(UUC)L locus in the sequenced strain (S288C derivative) as reported on Aug. 31, 2006 by SGD. Note the presence of a truncated 5' delta (Ty1 LTR; boxed truncated triangle) as is typically found near many tRNA genes. A similar sequence is found in the L27-10 strain, reflecting its derivation from strain GRF167, a strain related but not identical to S288C. The most prominent difference is an insertion of 193 bp in the middle of the delta sequence. This sequence is a 100% match to the sequence of an internally deleted tau element (Ty4 LTR; shown above the delta) plus four bp of unknown origin at the left end. There is no target site duplication associated with this Tau event, suggesting a complex history and that this part of the GRF167 genome has evolved independently of the S288C genome for some time. The lines on the bottom represent the sequenced segments and the fractions indicated the identical bases/total bases sequenced to the left and right of the Tau insertion. The 6 digit numbers are SGD coordinates from chromosome XII.

Fig. 7. Comparison of the yeast-only FY2 hybridization to the yeast-plus-human FY2 hybridization. The top panel, a, is a TIP-chip hybridization with FY2 yeast genomic DNA. The bottom panel, b, shows a hybridization, done in parallel, of exactly the same amount of FY2 yeast DNA but in the presence of a 100-fold excess of human genomic DNA (by weight). The human genomic DNA was added to the yeast FY2 DNA at the first step; the digests, ligation, PCR, and hybridization were performed on the combined yeast-human hybrid sample.