With its nuclear dimorphism, the ciliate Paramecium tetraurelia provides an original model to study the dynamics of transposable elements (TEs) within their host genome. The germline genome, hosted in the transcriptionally silent micronuclei (MIC), has been colonized by TEs, including in coding regions. At each sexual generation, TEs and thousands of related sequences are removed from the somatic genome, when the macronucleus (MAC), dedicated to gene expression, develops from a copy of the MIC. Several components of the programmed DNA elimination (PDE) machinery are known, including the PiggyMac (Pgm) endonuclease and its five Pgm-like partners (PgmL1 to PgmL5). However, how the DNA cleavage activity of Pgm is controlled during PDE has remained elusive.

In this study, a TurboID screen uncovered the presence of two condensin I subunits, Smc2 and CapD2.3, in the proximal proteomes of Pgm and PgmL4. Condensin is a conserved pentameric complex known for its role in chromosome compaction and segregation during mitosis and meiosis. A combination of transcriptome analyses and tandem immunoprecipitation experiments from Paramecium nuclear extracts allowed us to identify a developmental condensin I complex, formed by the association of three development-specific subunits, Smc4.2, CapD2.3 and CapH.3, with two constitutive subunits, Smc2 and CapG. We report that Smc4.2 and CapD2.3 localize exclusively in the developing MACs, and that SMC4.2, CAPD2.3 or CAPH.3 knockdowns block PDE, leading to death of sexual progeny. Moreover, depleting cells of any of the three developmental subunits destabilizes the localization of Pgm and its partners within the developing MAC, by the time PDE takes place. CapD2.3 immunoprecipitation experiments further showed a physical interaction between the condensin I and the endonuclease complexes. Our results indicate that the developmental condensin complex assists the Pgm endonuclease during PDE in P. tetraurelia, highlighting a non-canonical role of a eukaryotic condensin in a non-mitotic process.