Transgenerational function of Tetrahymena Piwi protein Twi8p at distinctive noncoding RNA loci

Abstract

Transgenerational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of transgenerational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of transgenerational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated transgenerational regulation to include unique noncoding RNA loci. Ciliates such as have a phenotypically silent germline micronucleus and an expressed somatic macronucleus, which is differentiated anew from a germline genome copy in sexual reproduction. We show that the nuclear-localized Piwi protein Twi8p shuttles from parental to zygotic macronuclei. Genetic elimination of Twi8p has no phenotype for cells in asexual growth. On the other hand, cells lacking Twi8p arrest in sexual reproduction with zygotic nuclei that retain the germline genome structure, without the DNA elimination and fragmentation required to generate a functional macronucleus. Twi8p-bound small RNAs originate from long-noncoding RNAs with a terminal hairpin, which become detectable in the absence of Twi8p. Curiously, the loci that generate Twi8p-bound small RNAs are essential for asexual cell growth, even though Twi8 RNPs are essential only in sexual reproduction. Our findings suggest the model that Twi8 RNPs act on silent germline chromosomes to permit their conversion to expressed macronuclear chromosomes. Overall this work reveals that a Piwi protein carrying small RNAs from long-noncoding RNA loci has transgenerational function in establishing zygotic nucleus competence for gene expression.

Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs

“…5 b). In Tetrahymena , piRNAs that are derived from noncoding RNA loci bind to Tetrahymena PIWI protein Twi8p and its target lncRNAs, which leads to a decrease in the level of the targeted lncRNAs [ 102 ]. These roles are similar to what has been found in mammalian systems.…”

Disruption of a ∼23–24 nucleotide small RNA pathway elevates DNA damage responses in Tetrahymena thermophila

“…Of the two Twis most highly expressed during growth, a knockout strain lacking cytoplasmically localized Twi2 fully phenocopies RDN2 in its altered sRNA profiles (Couvillion et al, 2009). In contrast, Twi8, which localizes predominantly to the macronucleus (Couvillion et al, 2009;Farley and Collins, 2017), contributes to the accumulation of a subset of the sRNAs classes perturbed…”

“…Sequencing of these sRNAs revealed alignment to a number of discrete sites in the MAC genome. The most abundant sRNAs mapped in clusters to processed pseudogene-like loci, widely dispersed high-copy repeats, and intergenic loci yielding long ncRNAs with predicted 3' hairpins (Lee and Collins, 2006;Couvillion et al, 2009;Farley and Collins, 2017). In addition, a subset of sRNAs mapped to a limited number of putative protein-coding loci predicted to generate transcripts that form extensive secondary structure, correspond to paralogous gene clusters, or undergo convergent transcription (Couvillion et al, 2009).…”

Diversity of RNA interference pathways in regulation of endogenous and exogenous sequences expression in ciliates Tetrahymena and Paramecium

“…Гены белков Twi2, Twi8 и Twi12 активно экспрессируются во время вегетативного роста. Было показано, что белки Twi2 и Twi12 локализуются в цитоплазме, а Twi8 -в МАК [28,31]. Ни один из белков Twi не был обнаружен в транскрипционно неактивном МИК.…”