Transcriptional reprogramming and epigenetic regulation in Paramecium caudatum: a new model for studying extreme...

Metazoans suppress transposons via small RNA-mediated silencing mechanisms, whereas ciliates have evolved a unique repressed strategy by physically eliminating transposons during somatic macronuclear genome development, offering unique models for transposon regulation and programmed DNA rearrangement. The ciliate Paramecium caudatum exhibits the most extreme known DNA elimination among eukaryotes, removing > 98% of its germline genome, yet its molecular basis and underlying mechanisms remain unknown. Here we present a high-quality, near-chromosome-level somatic macronuclear genome assembly, which is exceptionally compact, with ultra-short untranslated regions, and high gene density. Comprehensive transcriptome analysis across 15 life cycle stages reveals extensive transcriptional reprogramming during sexual reproduction. A total of 8260 genes are identified as developmentally regulated, forming 10 co-regulated clusters. While the core DNA elimination machinery appears to be conserved, many regulatory genes exhibit divergent expression patterns compared to related species. We further demonstrate that the histone methyltransferases Ezl1 and Ezl3 deposit the repressive marks H3K9me3/H3K27me3 in a nuclear-specific manner, showing functional specialization distinct from those previously reported in other ciliates. Our findings establish P. caudatum as an exceptional model for studying extreme genome rearrangement and provide new insights into the evolution of epigenetic mechanisms controlling transposon silencing and genome stability in eukaryotes.