In ciliates, massive genome reorganization occurs during autogamy where superfluous DNA such as Internal Eliminated Sequences (IESs), transposons, minisatellites and other repetitive sequences are eliminated from the developing macronucleus producing a streamlined functional somatic genome. Here we describe our current analyses of a novel Paramecium tetraurelia protein, SDCP, which is significantly differentially expressed during autogamy. SDCP contains an ATPase, a helicase domain, a SANT domain and a SLIDE domain. This architecture is characteristic of the conserved ISWI protein family. The domains of ISWI proteins are known to play multiple roles, regulating transcription, chromosome organization and DNA replication. This makes SDCP an interesting protein to study its putative role in the genome reorganization during sexual reproduction (autogamy).
Knockdown of SDCP during autogamy in Paramecium tetraurelia is lethal and affects both precise and imprecise DNA excision leading to the retention of maternally and non-maternally controlled IESs, and transposons. MAC genome sequencing data following SDCP knockdown shows substantial retention of IESs and a modest correlation between IESs retained following either Nowa1 or TFIIS4 silencing, two other genes involved in IES excision (Nowacki, 2005 & Maliszewska-Olejniczak, 2015). SDCP knockdown leads to similar IES end base frequency variation relative to IES retention in a similar manner to that seen for the other genes (Swart & Denby Wilkes, 2014). Interestingly, IES retention scores seem to peak at a regular base length interval corresponding to the size of the nucleosomes. Since the C-terminal of the protein contains a SLIDE domain, that is known to regulate ATP-dependent repositioning of the nucleosomes, we wished to determine, firstly whether SDCP is involved in nucleosome positioning, and secondly if the nucleosome position around an IES is important for its precise excision. To assess these possible roles for SDCP, we are therefore sequencing nucleosome-bound DNA from post-autogamous cultures.