The transposon content of S. pombe.

Since the process of integration has the potential to compromise the fitness of the host, we wish to understand the balance between the ability of the transposon to insert into the host genome verses the efforts of the host to maintain its viability. The recently completed sequence of the S. pombe genome has allowed us to ask whether Tf1 integration results in the disruption of host genes. Much of what is know about the insertion sites of LTR-retrotransposons indicate that the process of integration is specifically controlled to avoid the disruption of host genes. In fact, all 5 transposons of Saccharomyces cerevisiae select sites for integration that lack coding sequences for host genes. Ty1, Ty2, Ty3, and Ty4 integrate into gene poor regions associated with the 5' ends of tRNA genes (2, 6). Ty5 avoids the disruption of host genes by selecting regions of silent chromatin for its integration (8). Much less is known about the interactions between the genome of S. pombe and its transposons. The recent completion of the genome sequence of S. pombe allowed us to study the full set of transposon sequences and their relationship to the host genes.

We conducted a comprehensive search of the genome sequence of S. pombe for transposon related sequences. Surprisingly, the only transposons found in the genome were related to the Tf1/Tf2 family of LTR retrotransposons. No complete copies of Tf1 were found and just 13 full-length copies of Tf2 were identified. These together with 202 single LTRs, constitute the 1.1% of the pombe genome that was derived from transposons. Single LTRs result from the removal of full-length elements by homologous recombination. As a result, the single LTRs provide important information about the transposon history of the host genome. A phylogenetic analysis of the LTRs identified several classes of Tf transpsons.

In all cases, the positions of the Tf LTRs were in the intergenic spaces between coding sequences. Since 60.2% of the genome of S. pombe is coding sequence, the positions of the LTRs was strongly biased.

On a larger scale, the LTRs were found to be widely distributed throughout each of the three chromosomes of S. pombe. However, it was particularly surprising that the concentration of LTRs on the three chromosomes varied significantly.