Paramecium, as all ciliates, has the fascinating property of displaying separate germ and somatic lines in the same cytoplasmic unit. It possesses two nuclei: a germ nucleus (micronucleus), responsible for the transmission of genetic information through sexual processes, and a somatic nucleus (macronucleus) which ensures the expression of this information. During each sexual event, a new somatic nucleus is built through programmed rearrangements of the germinal genome.

Post-transcriptional gene silencing is a defense mechanism of genomes against parasitic nucleic acids. This mechanism, also known as RNA interference, is present in Paramecium and conserved in eukaryotic evolution. In Paramecium, it can be experimentally triggered by the introduction of a transgene or double-stranded RNA into the cell, in particular by feeding paramecia with bacteria expressing double stranded RNA corresponding to the target sequence. RNA interference leads to the degradation of all homologous messenger RNAs in the cell. RNA interference is also involved in the development of the somatic nucleus of Paramecium, a fact that can explain non-Mendelian transmission of certain traits in this ciliate. Paramecium is a very good organism to study such epigenetic phenomena, because they are easily amenable to experimentation. The biological role of epigenetic phenomena in the development of multicellular organisms is not well understood.

In order to investigate the organization of a Paramecium somatic chromosome, the largest macronuclear chromosome of P. tetraurelia (the one-megabase chromosome) was isolated, sequenced and annotated. In a pilot study of the P. tetraurelia global gene expression pattern we performed an analysis of the transcription profile of the 460 genes annotated on the megabase chromosome. We have concentrated on changes in gene transcription levels during autogamy.

DNA microarrays carrying PCR fragments representative for the 460 genes were prepared and hybridized with fluorescently labelled cDNA from cells isolated at different stages of the sexual cycle. For two genes we observed cell death within 48 hours of vegetative growth in the feeding medium. The knock down of three genes showed strong phenotypic defects, leading to cell death after autogamy. Out of these, one gene showing no similarity to known proteins results in a delay in meiosis and totally inhibits the formation of new macronuclei.

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