ISWI complex proteins facilitate developmental genome editing in Paramecium

Chromatin remodeling is required for essential cellular processes, including DNA replication, DNA repair, and transcription regulation. Here, we describe a chromatin remodeling complex contributing to the precise excision of DNA during genome reorganization. The ciliate germline and soma are partitioned into two distinct nuclei within the same cell. During a massive editing process for somatic genome formation, ciliates eliminate thousands of DNA sequences from a copy of the MIC genome in the form of internal eliminated sequences (IESs) and transposons. Recently we showed that the chromatin remodeler ISWI1 is required for the development of the somatic genome in the ciliate Paramecium tetraurelia. In this study, we describe two paralogous proteins, ICOP1 and ICOP2, that form a complex with ISWI1, and which are essential for DNA elimination and excision precision. ICOP1 and ICOP2 are highly divergent, and the only domain detected was a distant homolog to the WSD motif. Both ICOP1 and ICOP2 interact with ISWI1 and are essential for DNA elimination and excision precision. Furthermore, upon ICOP knockdown, changes in nucleosome densities on IESs are similar to those observed for ISWI1 knockdown. We thus propose that a complex comprising ISWI1 and either or both ICOP1 and ICOP2 are needed for chromatin remodeling and accurate DNA excision.