My dissertation extends the understanding about the impact of Alternative Transpositions (AT) on maize genome in three aspects: 1) Novel chromosomal rearrangements and structures; 2) new genes; 3) novel regulation on Ac/Ds.

First, my dissertation described several AT alleles that derived from three types of termini configurations including Reversed Ends Transposition (RET) with termini in reversed orientation, Sister Chromatid Transposition (SCT) from direct oriented ends on sister chromatids, and Macrotransposon (MTn) engaging the external 5' and 3' termini from nearby Ac/Ds. In Chapter 2 we isolated 10 excision and reinsertion events from MTn, revealing the features of MTn transposition in maize; In Chapter 3, we identified one translocation allele, and 11 duplication alleles derived from RET at p1 locus, showing duplication-induced exon shuffling and novel gene creation; In Chapter 4, we characterized two alleles that carry both inverted duplications (ID) and composite insertions (CI) from SCT-induced DNA re-replication. All the alleles described above further support the activity of AT and the impact on maize genome.

Second, we demonstrated how the AT-induced segmental duplications shuffle exons and generate new genes in the maize genome. From the 11 RET-induced duplication alleles, we isolated the chimeric transcript carrying p1 exon 1 - 2 and p2 exon 3, explaining the new phenotype observed. Moreover, we identified one possible fusion gene in maize B73 genome, suggesting that the RET induced duplication actually made new genes during evolution.

Third, we described the AT-induced RNAi regulation on Ac/Ds activity. We isolated two SCT-induced DNA re-replication alleles carry both ID and CI. The CI is composed of fAc fragments in inverted orientation. The transcription of CI produces dsRNA serving as the precursor of siRNA. We detected dsRNA and siRNA, demonstrating the RNAi pathway and explaining the in-trans and stable repression associated with the structural changes. The study is the first evidence of the RNAi on Ac/Ds regulation. Also, the study implies an AT-induced self-repression mechanism on Ac/Ds.