Homology-Dependent Maternal Inhibition of Developmental Excision of Internal Eliminated Sequences in Paramecium tetraurelia

ABSTRACT

Thousands of single-copy internal eliminated sequences (IESs) are excised from the germ line genome of ciliates during development of the polygenomic somatic macronucleus, following sexual events.Paramecium IESs are short, noncoding elements that frequently interrupt coding sequences. No absolutely conserved sequence element, other than flanking 5′-TA-3′ direct repeats, has been identified among sequenced IESs; the mechanisms of their specific recognition and precise elimination are unknown. Previous work has revealed the existence of an epigenetic control of excision. It was shown that the presence of one IES in the vegetative macronucleus results in a specific inhibition of the excision of the same element during the development of a new macronucleus, in the following sexual generation. We have assessed the generality and sequence specificity of this transnuclear maternal control by studying the effects of macronuclear transformation with 13 different IESs. We show that at least five of them can be maintained in the new macronuclear genome; sequence specificity is complete both between genes and between different IESs in the same gene. In all cases, the degree of excision inhibition correlates with the copy number of the maternal IES, but each IES shows a characteristic inhibition efficiency. Short internal IES-like segments were found to be excised from two of the IESs when excision between normal boundaries was inhibited. Available data suggest that the sequence specificity of these maternal effects is mediated by pairing interactions between homologous nucleic acids.

ACKNOWLEDGMENTS

We thank J. R. Preer, Jr., for the gift of the λ library of micronuclear DNA and J. D. Forney for the gift of phage λSA1.

This work was supported by grant no. 22/95 from the Groupement de Recherches et d’Etudes sur les Génomes, BP25, 91193 Gif-sur-Yvette Cedex, France; grant no. 1374 from the Association pour la Recherche sur le Cancer, 94800 Villejuif, France; and grant no. 97N63/0016 from the Centre National de la Recherche Scientifique. S. Duharcourt was the recipient of doctoral fellowships from the Association pour la Recherche sur le Cancer and from the Fondation pour la Recherche Médicale.