Interrogating the transgenic genome: development of an interspecies tiling array

Abstract

A single expressing copy of the human protamine domain was randomly inserted into an intron of Cyp2c38. The transgenic locus was shown to recapitulate the level of expression observed in normal human testis while not perturbing endogenous protamine expression. The development of an interspecies tiling array was pursued to enable direct comparison of the orthologous protamine domains in a single experiment. Probe design was adapted to generate species-specific high resolution probe sets that would tolerate repetitive elements. Results from competitive hybridizations demonstrate that interspecies tiling arrays are a valuable tool for parallel analysis of highly similar DNA sequences. This approach provides a rapid and reliable means of interrogating samples prior to deep sequencing analysis. These arrays should readily compliment most DNA isolation and analysis techniques such as ChIP, nuclease sensitivity and nuclear matrix association assays.

Keywords:

• protamine
• tiling array
• transgenic

Acknowledgments

This work is supported in part by the NIH grant HD36512. GDJ is supported by a Wayne State School of Medicine graduate fellowship. The authors would like to thank Frédéric Leduc for his review of this manuscript.