Research My lab focuses on the mechanisms of RNA-mediated epigenetic inheritance in eukaryotic cells. One of the most wonderful epigenetic phenomena known to researchers are those accompanying the whole-genome scale developmental DNA rearrangements in ciliated protozoans. This involves a comparison of the developing zygotic genome with the maternal somatic genome in an extraordinarily massive and precise manner. In ciliates, germline and somatic functions are ensured by two different kinds of nuclei, the diploid micronucleus and a DNA rich macronucleus. Sexual events are initiated by meiosis of the micronucleus, and following fertilization, the parental macronucleus is lost and replaced by a new one that develops from the zygotic nucleus. The development of a new macronucleus involves extensive rearrangements of the germline genome, including elimination of transposons and other repeated sequences and the precise excision of numerous single-copy Internal Eliminated Sequences (IESs) from coding and non-coding sequences. Genome-wide rearrangements discard nearly all non-genic DNA, resulting in streamlined gene-rich genomes (in Paramecium for instance, ~40,000 genes in only 72 Mb). In some cases, for example in the ciliate Oxytricha, rearrangement of the remaining somatic DNA segments (Macronucleus Destined Segments, or MDSs) also occurs by reordering or inversion (the so-called “scrambled genes”). The amazingly high degree of specificity and reproducibility suggests a role for some general mechanism of programming of rearrangements, assuring its absolute accuracy and recurrence. The parental ciliate cell must provide sufficient amount of information in order to produce a fully functional new macronucleus. The mechanisms, which allow the cell to perfectly recognize hundreds of thousands of DNA sequences destined for elimination remains largely unknown. However, the discovery of homology-dependent maternal effects that can modify rearrangements patterns has shed some light on the molecular basis of the programming process. It now seems clear that epigenetic phenomena play a central role in the mechanism of programming of developmental genome rearrangements in ciliates. The developing genome reproduces the rearrangements present in the parental nucleus through an RNA-mediated trans-nuclear comparison of genomes (see figures 1 and 2). Figure 1. Scan RNA model – programming of developmental DNA deletions in Paramecium and Tetrahymena. Parental somatic genome (MAC DNA) is entirely transcribed during sexual process (A). Meiotic micronucleus produces short, 25-30-nt dsRNA, so-called scnRNA that correspond to the entire germline genome (B), and are subsequently transported to the parental nucleus (C). Pairing between RNA copy of the parental genome and scnRNA takes place prior new MAC development, allowing selection of unpaired MIC-specific scnRNA (D). MIC-specific scnRNA target deletions of homologous DNA deletions in the developing MAC (E), leading to a mature new MAC. Blue boxes represent MAC-destined DNA, which in the MIC are separated from each other by germline-specific sequences (red boxes) like IESs or transposons. Figure 2. Model for RNA guiding of genome rearrangements during macronuclear development in Oxytricha. Bidirectional RNA transcription of all DNA nanochromosomes in the old, maternal macronucleus (MAC) before its degradation (A). Transport of these RNA transcripts to the newly developing macronucleus (B), where they may act as scaffolds to guide rearrangements (deletion, permutation and inversion) of corresponding micronuclear (MIC) DNA sequences (C). In this illustration, segments 2 and 3 are switched and segment 5 is inverted (number upside down).