Sequencing of genomic DNA and sRNAs from a Paramecium tetraurelia gene knockdowns. Paramecium tetraurelia strain:51

In eukaryotes small RNAs (sRNAs), such as microRNAs and Piwi-interacting RNAs, have key roles in development, by regulation of gene expression and by maintenance of genome integrity. In ciliated protozoa, development of the somatic genome from the germline genome requires extensive processing, resulting in elimination of the bulk of non-coding DNA. In the ciliate Paramecium, a class of germline, Piwi-interacting sRNAs, called scanRNAs, enables comparison of the maternal and zygotic genomes. This epigenetic trans-nuclear comparison mechanism is employed in a system that ensures reproducible DNA elimination and genome organization over sexual generations. We have discovered a novel class of sRNAs originating from the excised portion of the germline genome, which we propose is involved in targeted DNA elimination. By studying major proteins responsible for the production and interaction of specific Paramecium sRNA classes with the developing genome, we provide new insights into the mechanism of maternal control of genome development