Transposons in ciliated protozoa

Ciliated protozoa carry two types of nuclei in each cell. One is an undifferentiated "germline" micronucleus; the other is a nucleus that has undergone a complete terminal differentiation resulting in a macronucleus specialized for high levels of transcription. Differentiation results in elimination of noncoding DNA and amplification of coding DNA. The evolution of a macronucleus has allowed many ciliates to maintain large cell sizes. My work has encompassed steps in the differentiation of the macronucleus from a normal diploid nucleus. Early work addressed nuclear events that lead to designating and differentiating a macronucleus. Later work dealt with a particular type of DNA elimination in macronuclear differentiation, namely the precise removal or excision of DNA sequences internal to macronucleus-destined sequences. This requires excision of the internal sequence and rejoining of the flanking sequences retained in the macronucleus. Many of these internal eliminated sequences are transposons. Thus, this work has included characterization of the excised transposon families, as well as the mechanism of their elimination. It has resulted in a better understanding of the structure and evolution of internal eliminated transposons and the mechanism of their elimination. My work has helped to invalidate a popular hypothesis explaining transposon excision and may help to bring us closer to a new model of how transposons (and internal eliminated sequences of ciliates in general) are excised from the differentiating macronucleus. Experimental results and my attempts to model excision have made it clear that a number of different recombination mechanisms could effect transposon excision as we now understand it. Identifying on the likely mechanism will require further characterization of transposon excision intermediates and a more thorough exploration of possible excision mechanisms.