Epigenetic Regulation of Programmed Genomic Rearrangements in Paramecium aurelia1

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Abstract
In ciliates, development of the polyploid somatic macronucleus after sexual events involves extensive and reproducible rearrangements of the germ‐line genome, including chromosome fragmentation and precise excision of numerous internal sequence elements. In Paramecium aurelia, alternative macronuclear versions of the same germ‐line genome can be maternally inherited across sexual generations, showing that rearrangement patterns are not strictly determined by the germ‐line sequence. Homology‐dependent maternal effects can be evidenced by transformation of the vegetative macronucleus with cloned macronuclear sequences: new fragmentation patterns or internal deletions are specifically induced during differentiation of a new macronucleus, in sexual progeny of transformed clones. Furthermore, transformation of the maternal macronucleus with germ‐line sequences containing internal eliminated sequences (short single‐copy elements) can result in a specific inhibition of the excision of the same elements in the zygotic macronucleus. These experiments show that the processing of many germ‐line sequences in the developing macronucleus is sensitive to the structure and copy number of homologous sequences in the maternal macronucleus. The generality and sequence specificity of this trans‐nuclear, epigenetic regulation of rearrangements suggest that it is mediated by pairing interactions between germ‐line sequences and sequences imported from the maternal macronucleus.