Small-RNA-Mediated Genome-wide trans -Recognition Network in Tetrahymena DNA Elimination

Abstract

SummarySmall RNAs are used to silence transposable elements (TEs) in many eukaryotes, which use diverse evolutionary solutions to identify TEs. In ciliated protozoans, small-RNA-mediated comparison of the germline and somatic genomes underlies identification of TE-related sequences, which are then eliminated from the soma. Here, we describe an additional mechanism of small-RNA-mediated identification of TE-related sequences in the ciliate Tetrahymena. We show that a limited set of internal eliminated sequences (IESs) containing potentially active TEs produces a class of small RNAs that recognize not only the IESs from which they are derived, but also other IESs in trans. This trans recognition triggers the expression of yet another class of small RNAs that identify other IESs. Therefore, TE-related sequences in Tetrahymena are robustly targeted for elimination by a genome-wide trans-recognition network accompanied by a chain reaction of small RNA production.

Dynamic distributions of long double-stranded RNA in Tetrahymena during nuclear development and genome rearrangements

“…Recent findings in scnRNA characterization have revealed a second class of scnRNAs that are produced specifically at late stages, presumably from new MACs, and the production of them is enhanced by early scnRNAs in trans (Noto et al, 2015). Our findings implicate a possible role of new MAC dsRNAs in the biogenesis of late scnRNAs that requires early scnRNAs.…”

“…Deep sequencing revealed their origins from both strands of IESs and some MAC-destined sequences (MDSs, sequences that are not deleted from new MACs) (Schoeberl et al, 2012). These small RNAs are bound by the piwi-related Tetrahymena argonaute proteins Twi1p and Twi11p (Mochizuki et al, 2002;Couvillion et al, 2009;Noto et al, 2015) and are thought to guide heterochromatin targeting through homology recognition, though the targeting mechanism is still unknown. The targeted regions are modified with silencing marks, including specific histone modifications and chromodomain proteins (Taverna et al, 2002;Liu et al, 2004Liu et al, , 2007Yao and Chao, 2005), leading to their excision using a domesticated piggyBac transposase, Tpb2p (Cheng et al, 2010;Chalker and Yao, 2011).…”

Phosphorylation of an HP1-like protein is a prerequisite for heterochromatin body formation in Tetrahymena DNA elimination

“…S5E); (iv) WT and MUT26 showed similar affinity to RNA in vitro (Fig. S5F), which we previously suggested to be essential for heterochromatin body formation (25); and (v) Pdd1p-dependent production of Late-scnRNA (22) occurred normally in the cells expressing MUT26 (see Phosphorylation of Pdd1p Is Dispensable for Late-scnRNA Production). Altogether, we conclude that, to form functional heterochromatin bodies for DNA elimination, certain numbers of Ser/Thr residues, or at least a few particular residues, need to be accumulatively phosphorylated.…”

“…methylation at histone H3 lysine 27 (H3K27me), and the Pdd1p that binds to these methylated histones (20,21) nucleates heterochromatin. Then, another class of small RNAs, which are also ∼29 nt in length and are called Late-scnRNAs, are produced from IESs in the new MAC in an Ezl1p-and Pdd1p-dependent manner, and they reinforce robust heterochromatin formation on IESs (22). The heterochromatinized IESs are eventually excised by the domesticated transposase Tpb2p (23,24).…”

Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

“…While the distantly related ciliates Paramecium and Tetrahymena use PIWI-associated "scnRNAs" to mark regions of the MIC for elimination (Mochizuki et al 2002;Lepère et al 2008) and other small RNAs that may facilitate IES removal (Sandoval et al 2014;Noto et al 2015), Oxytricha uses PIWI-associated RNAs (piRNAs) to mark segments of the MIC genome for retention rather than elimination (Fang et al 2012;Zahler et al 2012). These 27-nt piRNAs derive from both strands and show peak expression between 18 and 24 h after the beginning of conjugation (Fang et al 2012;Zahler et al 2012).…”