An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

Function and Evolution of Nematode RNAi Pathways

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.

Intergenerational and transgenerational epigenetic inheritance in animals

Animals transmit not only DNA but also other molecules, such as RNA, proteins and metabolites, to their progeny via gametes. It is currently unclear to what extent these molecules convey information between generations and whether this information changes according to their physiological state and environment. Here, we review recent work on the molecular mechanisms by which 'epigenetic' information is transmitted between generations over different timescales, and the importance of this information for development and physiology.

Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms

Complementary sequences in cellular transcripts base-pair to form double-stranded RNA (dsRNA) structures. Because transposon-derived repeats often give rise to self-complementary sequences, dsRNA structures are prevalent in eukaryotic genomes, typically occurring in gene introns and untranslated regions (UTRs). However, the regulatory impact of double-stranded structures within genes is not fully understood. We used three independent methods to define loci in Caenorhabditis elegans predicted to form dsRNA and correlated these structures with patterns of gene expression, gene essentiality, and genome organization. As previously observed, dsRNA loci are enriched on distal arms of C. elegans autosomes, where genes typically show less conservation and lower overall expression. In contrast, we find that dsRNAs are associated with essential genes on autosome arms, and dsRNA-associated genes exhibit higher-than-expected expression and histone modification patterns associated with transcriptional elongation. Genes with significant repetitive sequence content are also highly expressed, and, thus, observed gene expression trends may relate either to dsRNA structures or to repeat content. Our results raise the possibility that as-yet-undescribed mechanisms promote expression of loci that produce dsRNAs, despite their well-characterized roles in gene silencing.

A New Tool for Inducible Gene Expression in Caenorhabditis elegans

Controlling protein activity and localization is a key tool in modern biology. Mammalian steroid receptor ligand-binding domain (LBD) fusions have been used in a range of organisms and cell types to inactivate proteins of interest until the cognate steroid ligand is applied. Here, we demonstrate that the glucocorticoid receptor LBD confers ligand-gated control of a heterologous gene expression system (Q system) and the DAF-16 transcription factor in Caenorhabditis elegans These experiments provide a powerful tool for temporal control of protein activity, and will bolster existing tools used to modulate gene expression and protein activity in this animal.

C. elegans Heterochromatin Factor SET-32 Plays an Essential Role in Transgenerational Establishment of Nuclear RNAi-Mediated Epigenetic Silencing

The dynamic process by which nuclear RNAi engages a transcriptionally active target, before the repressive state is stably established, remains largely a mystery. Here, we found that the onset of exogenous dsRNA-induced nuclear RNAi in C. elegans is a transgenerational process, and it requires a putative histone methyltransferase (HMT), SET-32. By developing a CRISPR-based genetic approach, we found that silencing establishment at the endogenous targets of germline nuclear RNAi also requires SET-32. Although SET-32 and two H3K9 HMTs, MET-2 and SET-25, are dispensable for the maintenance of silencing, they do contribute to transcriptional repression in mutants that lack the germline nuclear Argonaute protein HRDE-1, suggesting a conditional role of heterochromatin in the maintenance phase. Our study indicates that (1) establishment and maintenance of siRNA-guided transcriptional repression are two distinct processes with different genetic requirements and (2) the rate-limiting step of the establishment phase is a transgenerational, chromatin-based process.

Optogenetic dissection of mitotic spindle positioning in vivo

The position of the mitotic spindle determines the plane of cell cleavage, and thereby daughter cell location, size, and content. Spindle positioning is driven by dynein-mediated pulling forces exerted on astral microtubules, which requires an evolutionarily conserved complex of Gα∙GDP, GPR-1/2^Pins/LGN, and LIN-5^Mud/NuMA proteins. To examine individual functions of the complex components, we developed a genetic strategy for light-controlled localization of endogenous proteins in C. elegans embryos. By replacing Gα and GPR-1/2 with a light-inducible membrane anchor, we demonstrate that Gα∙GDP, Gα∙GTP, and GPR-1/2 are not required for pulling-force generation. In the absence of Gα and GPR-1/2, cortical recruitment of LIN-5, but not dynein itself, induced high pulling forces. The light-controlled localization of LIN-5 overruled normal cell-cycle and polarity regulation and provided experimental control over the spindle and cell-cleavage plane. Our results define Gα∙GDP–GPR-1/2^Pins/LGN as a regulatable membrane anchor, and LIN-5^Mud/NuMA as a potent activator of dynein-dependent spindle-positioning forces.

A cell about to divide must decide where exactly to cut itself in two. Split right down the middle, and the two daughter cells will be identical; offset the cleavage plane to one side, and the resulting siblings will have different sizes, places and fates.

In animals, the splitting of cells is dictated by the location of the spindle, a structure that forms when cable-like microtubules stretch from the cell membrane to attach to the chromosomes. At the membrane, a group of proteins tugs on the microtubules to bring the spindle into the correct position. One of these proteins, dynein, is a motor that uses microtubules as its track to pull the spindle into place. What the other parts of the complex do is still unclear, but a general assumption is that they may be serving as an anchor for dynein.

To test this model, Fielmich, Schmidt et al. removed one or more proteins from the complex in the developing embryos of the nematode worm Caenorhabditis elegans. A light-activated system then linked the remaining proteins to the membrane by tying them to an artificial anchor. Two of the proteins in the complex could be replaced with the artificial anchor, but pulling forces were absent when dynein was artificially tied to the membrane. This indicates that the motor being anchored at the edge of the cell is not enough for it to pull on microtubules. Instead, the experiments showed that dynein needs to be activated by another component of the complex, a protein called LIN-5. This suggests that individual proteins in the complex have specialized roles that go beyond simply tethering dynein. In fact, steering where LIN-5 was attached on the membrane helped to control the location of the spindle, and therefore of the cleavage plane.

As mammals have a protein similar to LIN-5, dissecting the roles of the components involved in positioning the spindle in C. elegans could help to understand normal and abnormal human development. In addition, these results demonstrate that creating artificial interactions between proteins using light is a powerful technique to study biological processes.

Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans

Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations. We focus on the intricate interactions between heritable small RNAs and histone modifications, deposited on specific loci. A trace of heritable chromatin marks, in particular trimethylation of histone H3 lysine 9, is deposited on RNAi-targeted loci. However, how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.

Rapid Integration of Multi-copy Transgenes Using Optogenetic Mutagenesis in Caenorhabditis elegans

Stably transmitted transgenes are indispensable for labeling cellular components and manipulating cellular functions. In Caenorhabditis elegans, transgenes are generally generated as inheritable multi-copy extrachromosomal arrays, which can be stabilized in the genome through a mutagenesis-mediated integration process. Standard methods to integrate extrachromosomal arrays primarily use protocols involving ultraviolet light plus trimethylpsoralen or gamma- or X-ray irradiation, which are laborious and time-consuming. Here, we describe a one-step integration method, following germline-mutagenesis induced by mini Singlet Oxygen Generator (miniSOG). Upon blue light treatment, miniSOG tagged to histone (Histone-miniSOG) generates reactive oxygen species (ROS) and induces heritable mutations, including DNA double-stranded breaks. We demonstrate that we can bypass the need to first establish extrachromosomal transgenic lines by coupling microinjection of desired plasmids with blue light illumination on Histone-miniSOG worms to obtain integrants in the F₃ progeny. We consistently obtained more than one integrant from 12 injected animals in two weeks. This optogenetic approach significantly reduces the amount of time and labor for transgene integration. Moreover, it enables to generate stably expressed transgenes that cause toxicity in animal growth.

piRNA Rules of Engagement

piRNAs are known to silence transposable elements, but not all piRNAs match transposon sequences. Recent studies from Shen et al. (2018) and Zhang et al. (2018) identify rules for piRNA target recognition in Caenorhabditis elegans. Permissive pairing rules allow targeting of essentially all germline mRNAs, while protective mechanisms prevent silencing self-genes.

A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans

In metazoans, Piwi-related Argonaute proteins engage piRNAs (Piwi-interacting small RNAs) to defend the genome against invasive nucleic acids, such as transposable elements. Yet many organisms-including worms and humans-express thousands of piRNAs that do not target transposons, suggesting that piRNA function extends beyond genome defense. Here, we show that the X chromosome-derived piRNA 21ux-1 downregulates XOL-1 (XO Lethal), a master regulator of X chromosome dosage compensation and sex determination in Caenorhabditis elegans. Mutations in 21ux-1 and several Piwi-pathway components sensitize hermaphrodites to dosage compensation and sex determination defects. We show that the piRNA pathway also targets xol-1 in C. briggsae, a nematode species related to C. elegans. Our findings reveal physiologically important piRNA-mRNA interactions, raising the possibility that piRNAs function broadly to ensure robust gene expression and germline development.

The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes

Piwi-interacting RNAs (piRNAs) silence transposons to safeguard genome integrity in animals. However, the functions of the many piRNAs that do not map to transposons remain unknown. Here, we show that piRNA targeting in Caenorhabditis elegans can tolerate a few mismatches but prefer perfect pairing at the seed region. The broad targeting capacity of piRNAs underlies the germline silencing of transgenes in C. elegans Transgenes engineered to avoid piRNA recognition are stably expressed. Many endogenous germline-expressed genes also contain predicted piRNA targeting sites, and periodic An/Tn clusters (PATCs) are an intrinsic signal that provides resistance to piRNA silencing. Together, our study revealed the piRNA targeting rules and highlights a distinct strategy that C. elegans uses to distinguish endogenous from foreign nucleic acids.

Broad Chromatin Domains: An Important Facet of Genome Regulation

Chromatin composition differs across the genome, with distinct compositions characterizing regions associated with different properties and functions. Whereas many histone modifications show local enrichment over genes or regulatory elements, marking can also span large genomic intervals defining broad chromatin domains. Here we highlight structural and functional features of chromatin domains marked by histone modifications, with a particular emphasis on the potential roles of H3K27 methylation domains in the organization and regulation of genome activity in metazoans.

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription

Small RNAs play a crucial role in genome defense against transposable elements and guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. However, the molecular basis of this process remains unknown. Here, we identify the conserved RNA helicase Aquarius/EMB-4 as a direct and essential link between small RNA pathways and the transcriptional machinery in Caenorhabditis elegans. Aquarius physically interacts with the germline Argonaute HRDE-1. Aquarius is required to initiate small-RNA-induced heritable gene silencing. HRDE-1 and Aquarius silence overlapping sets of genes and transposable elements. Surprisingly, removal of introns from a target gene abolishes the requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene silencing. We conclude that Aquarius allows small RNA pathways to compete for access to nascent transcripts undergoing co-transcriptional splicing in order to detect and silence transposable elements. Thus, Aquarius and HRDE-1 act as gatekeepers coordinating gene expression and genome defense.

Identification of regulators of germ stem cell enwrapment by its niche in C. elegans

Many stem cell niches contain support cells that increase contact with stem cells by enwrapping them in cellular processes. One example is the germ stem cell niche in C. elegans, which is composed of a single niche cell termed the distal tip cell (DTC) that extends cellular processes, constructing an elaborate plexus that enwraps germ stem cells. To identify genes required for plexus formation and to explore the function of this specialized enwrapping behavior, a series of targeted and tissue-specific RNAi screens were performed. Here we identify genes that promote stem cell enwrapment by the DTC plexus, including a set that specifically functions within the DTC, such as the chromatin modifier lin-40/MTA1, and others that act within the germline, such as the 14-3-3 signaling protein par-5. Analysis of genes that function within the germline to mediate plexus development reveal that they are required for expansion of the germ progenitor zone, supporting the emerging idea that germ stem cells signal to the niche to stimulate enwrapping behavior. Examination of wild-type animals with asymmetric plexus formation and animals with reduced DTC plexus elaboration via loss of two candidates including lin-40 indicate that cellular enwrapment promotes GLP-1/Notch signaling and germ stem cell fate. Together, our work identifies novel regulators of cellular enwrapment and suggests that reciprocal signaling between the DTC niche and the germ stem cells promotes enwrapment behavior and stem cell fate.

Sequence-Modified Antibiotic Resistance Genes Provide Sustained Plasmid-Mediated Transgene Expression in Mammals

Conventional plasmid vectors are incapable of achieving sustained levels of transgene expression in vivo even in quiescent mammalian tissues because the transgene expression cassette is silenced. Transcriptional silencing results from the presence of the bacterial plasmid backbone or virtually any DNA sequence of >1 kb in length placed outside of the expression cassette. Here, we show that transcriptional silencing can be substantially forestalled by increasing the An/Tn sequence composition in the plasmid bacterial backbone. Increasing numbers of An/Tn sequences increased sustained transcription of both backbone sequences and adjacent expression cassettes. In order to recapitulate these expression profiles in compact and portable plasmid DNA backbones, we engineered the standard kanamycin or ampicillin antibiotic resistance genes, optimizing the number of An/Tn sequence without altering the encoded amino acids. The resulting vector backbones yield sustained transgene expression from mouse liver, providing generic DNA vectors capable of sustained transgene expression without additional genes or mammalian regulatory elements.

The synaptonemal complex has liquid crystalline properties and spatially regulates meiotic recombination factors

The synaptonemal complex (SC) is a polymer that spans ~100 nm between paired homologous chromosomes during meiosis. Its striated, periodic appearance in electron micrographs led to the idea that transverse filaments within this structure ‘crosslink’ the axes of homologous chromosomes, stabilizing their pairing. SC proteins can also form polycomplexes, three-dimensional lattices that recapitulate the periodic structure of SCs but do not associate with chromosomes. Here we provide evidence that SCs and polycomplexes contain mobile subunits and that their assembly is promoted by weak hydrophobic interactions, indicative of a liquid crystalline phase. We further show that in the absence of recombination intermediates, polycomplexes recapitulate the dynamic localization of pro-crossover factors during meiotic progression, revealing how the SC might act as a conduit to regulate chromosome-wide crossover distribution. Properties unique to liquid crystals likely enable long-range signal transduction along meiotic chromosomes and underlie the rapid evolution of SC proteins.

DOI:http://dx.doi.org/10.7554/eLife.21455.001

The genetic information in cells is encoded within long molecules of DNA called chromosomes. In most human cells, the two copies of each chromosome – the one inherited from our mother and the one from our father – are physically separated and behave independently. However, in the reproductive cells that give rise to eggs or sperm, each chromosome must pair with its partner. Pairing first occurs at one or more positions along each chromosome. This triggers a protein-based polymer called the “synaptonemal complex” to assemble between the paired chromosomes, and then spread along the interface between the partners until they are fully lined up side-by-side. Chromosomes in reproductive cells must pair in this particular way to exchange genetic information and generate new combinations of traits.

The synaptonemal complex was first observed over 60 years ago, but it remains enigmatic. Though its structure is highly ordered and looks very similar in different organisms from yeast to humans, little is known about how this polymer forms or what it does between chromosomes. Some evidence has suggested that the synaptonemal complex helps to regulate how much information can be transferred between each pair of chromosomes, but not all studies have supported this conclusion.

Several lines of evidence suggest that the synaptonemal complex might be fundamentally different from other protein-based polymers, such as those that form filamentous skeletal structures within cells, namely actin filaments and microtubules. Now, Rog et al. have tested the idea that the synaptonemal complex might actually have liquid-like properties, despite its highly ordered appearance.

The experiments showed that the proteins that make up the synaptonemal complex in yeast, worms and fruit flies are weakly bound to each other and can move around within the assembled structure. These are considered to be defining properties that distinguish liquids from solid materials. Together with its regular, repetitive organization, these findings indicate that the synaptonemal complex behaves like a liquid crystal. This intriguing class of materials has properties between those of conventional liquids and those of solid crystals, and is particularly sensitive to environmental conditions.

Rog et al. believe that this discovery helps to explain how signals are transmitted along the length of chromosomes to regulate the transfer of genetic information. In support of this idea, further experiments showed that proteins that are required for this recombination process were also found within the synaptonemal complex. As reproductive cells transition from one stage of their development to the next, these proteins abruptly move to a new location, indicating that a switch-like signal rapidly spreads throughout the synaptonemal complex.

Together the findings suggest that the liquid crystal-like properties of the synaptonemal complex allow signals to be transmitted along the interface between pairs of chromosomes. The next challenges are to understand what triggers these signals and to explore whether they are based upon physical or chemical changes within the synaptonemal complex. Further research is also needed to uncover how this information is propagated along the length of a chromosome.

DOI:http://dx.doi.org/10.7554/eLife.21455.002