Strategies of kinetoplastid cryptogene discovery and analysis

The experimental approach to revealing the genetic information hidden in kinetoplastid cryptogenes and expressed through the posttranscriptional mRNA processing of U-insertion/deletion editing proceeds in reverse to the informational flow of the RNA editing process itself. While the editing integrates the informational content of maxicircle-encoded cryptogenes with that of minicircle-encoded gRNAs to produce functional edited mRNAs, the cryptogene analysis utilizes a comparison of the mature mRNA sequence with the cryptogene sequence to deduce the locations of edited sites and editing patterns, and a comparison of that mRNA sequence with the minicircle (or minicircle equivalent) sequences to identify the corresponding guide RNAs. Although a "direct" approach (prediction of a fully edited sequence pattern based on the analysis of cryptogene and minicircle sequences) seems to be theoretically possible, it proved to be not practically feasible. The major steps of the procedures utilized to decipher editing in a broad range of kinetoplastid species are presented in this chapter.