In recent years, the Piwi pathway has been shown to regulate the silencing of mobile genetic elements. However, we know little about how Piwi pathways impose silencing and even less about trans-generational stability of Piwi-induced silencing. We demonstrate that the Caenorhabditis elegans Piwi protein PRG-1 can initiate an extremely stable form of gene silencing on a transgenic, single-copy target. This type of silencing is faithfully maintained over tens of generations in the absence of a functional Piwi pathway. Interestingly, RNAi can also trigger permanent gene silencing of a single-copy transgene and the phenomenon will be collectively referred to as RNA-induced epigenetic silencing (RNAe). RNAe can act in trans and is dependent on endogenous RNAi factors. The involvement of factors known to act in nuclear RNAi and the fact that RNAe is accompanied by repressive chromatin marks indicate that RNAe includes a transcriptional silencing component. Our results demonstrate that, at least in C. elegans, the Piwi pathway can impose a state of gene silencing that borders on 'permanently silent'. Such a property may be more widely conserved among Piwi pathways in different animals.

No abstract

Selfish genetic elements, like transposable elements or viruses, are a threat to genomic stability. A variety of processes, including small RNA-based RNA interference (RNAi)-like pathways, has evolved to counteract these elements. Amongst these, endogenous small interfering RNA and Piwi-interacting RNA (piRNA) pathways were implicated in silencing selfish genetic elements in a variety of organisms. Nematodes have several incredibly specialized, rapidly evolving endogenous RNAi-like pathways serving such purposes. Here, we review recent research regarding the RNAi-like pathways of Caenorhabditis elegans as well as those of other nematodes, to provide an evolutionary perspective. We argue that multiple nematode RNAi-like pathways share piRNA-like properties and together form a broad nematode toolkit that allows for silencing of foreign genetic elements.

Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Gtsf1 homolog, named it and characterized it in the context of the sRNA pathways of We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying mutants. We show, both and , that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities.

11Endogenous small RNAs (sRNAs) and Argonaute proteins are ubiquitous regulators of gene 12 expression in germline and somatic tissues. sRNA-Argonaute complexes are often expressed in 13 gametes and are consequently inherited by the next generation upon fertilization. In Caenorhabditis 14 elegans, 26G-RNAs are primary endogenous sRNAs that trigger the expression of downstream 15 secondary sRNAs. Two subpopulations of 26G-RNAs exist, each of which displaying strongly 16 compartmentalized expression: one is expressed in the spermatogenic gonad and associates with the 17 Argonautes ALG-3/4; plus another expressed in oocytes and in embryos, which associates with the 18 Argonaute ERGO-1. The determinants and dynamics of gene silencing elicited by 26G-RNAs are 19 largely unknown. Here, we provide diverse new insights into these endogenous sRNA pathways of C. 20 elegans. Using genetics and deep sequencing, we dissect a maternal effect of the ERGO-1 branch 21 sRNA pathway. We find that maternal primary sRNAs can trigger the production of zygotic secondary 22 sRNAs that are able to silence targets, even in the absence of zygotic primary triggers. Thus, the 23 interaction of maternal and zygotic sRNA populations, assures target gene silencing throughout 24 Author Summary 31Small RNAs (sRNAs) and their partner Argonaute proteins regulate the expression of target 32RNAs. When sperm and egg meet upon fertilization, a diverse set of proteins and RNA, including 33 sRNA-Argonaute complexes, is passed on to the developing progeny. Thus, these two players are 34 important to initiate specific gene expression programs in the next generation. The nematode 35Caenorhabditis elegans expresses several classes of sRNAs. 26G-RNAs are a particular class of sRNAs 36 that are divided into two subpopulations: one expressed in the spermatogenic gonad and another 37 expressed in oocytes and in embryos. In this work, we describe the dynamics whereby oogenic 26G-38RNAs setup gene silencing in the next generation. We also show several ways that spermatogenic 39 26G-RNAs and their partner Argonautes, ALG-3 and ALG-4, use to regulate their targets. Finally, we 40show that ALG-3 and ALG-4 are fine-tuning their own expression, a rare role of Argonaute proteins. 41Overall, we provide new insights into how sRNAs and Argonautes are regulating gene expression. 42 (TEs). 48MicroRNA (miRNA), Piwi-interacting RNA (piRNA) and endogenous small interfering RNA 49 (endo-siRNA) pathways are the better described RNAi-like pathways, which differ in their biogenesis 50 and specialized cofactors. MicroRNAs are commonly found in many, if not all, tissues and broadly 51 regulate gene expression throughout development (1). piRNAs are typically, but not exclusively, 52 expressed in the metazoan germline, where they assume a central function in TE control (2-5). Endo-53 siRNA pathways comprise varied classes of sRNAs expressed in the soma and germline that can, for 54 example, control TEs, protein-coding genes and direct heterochromatin formation (6-8). A key 55 commonali...

In every domain of life, Argonaute proteins and their associated small RNAs regulate gene expression. Despite great conservation of Argonaute proteins throughout evolution, many proteins acting in small RNA pathways are not widely conserved. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured, acidic C-terminal tail, are conserved in animals and act in small RNA pathways. In fly and mouse, they are required for fertility and have been shown to interact with Piwi clade Argonautes. We identified T06A10.3 as the Caenorhabditis elegans Gtsf1 homolog and named it gtsf-1. Given its conserved nature and roles in Piwi-mediated gene silencing, we sought out to characterize GTSF-1 in the context of the small RNA pathways of C. elegans. Like its homologs, GTSF-1 is required for normal fertility. Surprisingly, we report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show strong depletion of a class of endogenous small RNAs, known as 26G-RNAs, and fully phenocopy mutants lacking RRF-3, the RNA-dependent RNA Polymerase that synthesizes 26G-RNAs. We show, both in vivo and in vitro, that GTSF-1 specifically and robustly interacts with RRF-3 via its tandem CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex, also known as ERIC, thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may similarly act to drive the assembly of larger complexes that subsequently act in small RNA production and/or in imposing small RNA-mediated silencing activities.

Graphical abstract

Telomeres are bound by dedicated proteins, which protect them from DNA damage and regulate telomere length homeostasis. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to identify TEBP-1 and TEBP-2, two paralogs expressed in the germline and embryogenesis that associate to telomeres in vitro and in vivo. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp-2 mutants display shorter telomeres and a Mortal Germline. Notably, tebp-1;tebp-2 double mutant animals have synthetic sterility, with germlines showing signs of severe mitotic and meiotic arrest. Furthermore, we show that POT-1 forms a telomeric complex with TEBP-1 and TEBP-2, which bridges TEBP-1/-2 with POT-2/MRT-1. These results provide insights into the composition and organization of a telomeric protein complex in C. elegans.