Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes

Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium

The clearance of untranslated mRNAs by Argonaute proteins is essential for embryonic development in metazoans. However, it is currently unknown whether similar processes exist in unicellular eukaryotes. The ciliate Paramecium tetraurelia harbors a vast array of PIWI-clade Argonautes involved in various small RNA (sRNA) pathways, many of which have not yet been investigated. Here, we investigate the function of a PIWI protein, Ptiwi08, whose expression is limited to a narrow time window during development, concomitant with the start of zygotic transcription. We show that Ptiwi08 acts in an endogenous small interfering RNA (endo-siRNA) pathway involved in the clearance of untranslated mRNAs. These endo-siRNAs are found in clusters that are strictly antisense to their target mRNAs and are a subset of siRNA-producing clusters (SRCs). Furthermore, the endo-siRNAs are 2'-O-methylated by Hen1 and require Dcr1 for their biogenesis. Our findings suggest that sRNA-mediated developmental mRNA clearance extends beyond metazoans and may be a more widespread mechanism than previously anticipated.

Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements

Noncoding RNAs (ncRNAs) make up to ∼98% percent of the transcriptome of a given organism. In recent years, one relatively new class of ncRNAs, long noncoding RNAs (lncRNAs), were shown to be more than mere by-products of gene expression and regulation. The unicellular eukaryote Paramecium tetraurelia is a member of the ciliate phylum, an extremely heterogeneous group of organisms found in most bodies of water across the globe. A hallmark of ciliate genetics is nuclear dimorphism and programmed elimination of transposons and transposon-derived DNA elements, the latter of which is essential for the maintenance of the somatic genome. Paramecium and ciliates in general harbor a plethora of different ncRNA species, some of which drive the process of large-scale genome rearrangements, including DNA elimination, during sexual development. Here, we identify and validate the first known functional lncRNAs in ciliates to date. Using deep-sequencing and subsequent bioinformatic processing and experimental validation, we show that Paramecium expresses at least 15 lncRNAs. These candidates were predicted by a highly conservative pipeline, and informatic analyses hint at differential expression during development. Depletion of two lncRNAs, lnc1 and lnc15, resulted in clear phenotypes, decreased survival, morphological impairment, and a global effect on DNA elimination.

Paramecium epigenetics in development and proliferation

The term epigenetics is used for any layer of genetic information aside from the DNA base-sequence information. Mammalian epigenetic research increased our understanding of chromatin dynamics in terms of cytosine methylation and histone modification during differentiation, aging, and disease. Instead, ciliate epigenetics focused more on small RNA-mediated effects. On the one hand, these do concern the transport of RNA from parental to daughter nuclei, representing a regulated transfer of epigenetic information across generations. On the other hand, studies of Paramecium, Tetrahymena, Oxytricha, and Stylonychia revealed an almost unique function of transgenerational RNA. Rather than solely controlling chromatin dynamics, they control sexual progeny's DNA content quantitatively and qualitatively. Thus epigenetics seems to control genetics, at least genetics of the vegetative macronucleus. This combination offers ciliates, in particular, an epigenetically controlled genetic variability. This review summarizes the epigenetic mechanisms that contribute to macronuclear heterogeneity and relates these to nuclear dimorphism. This system's adaptive and evolutionary possibilities raise the critical question of whether such a system is limited to unicellular organisms or binuclear cells. We discuss here the relevance of ciliate genetics and epigenetics to multicellular organisms.

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics, including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin, our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression, and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy, suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Because of a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different from that of other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data imply that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.

Two Piwis with Ago-like functions silence somatic genes at the chromatin level

Most sRNA biogenesis mechanisms involve either RNAse III cleavage or ping-pong amplification by different Piwi proteins harbouring slicer activity. Here, we follow the question why the mechanism of transgene-induced silencing in the ciliate Paramecium needs both Dicer activity and two Ptiwi proteins. This pathway involves primary siRNAs produced from non-translatable transgenes and secondary siRNAs from targeted endogenous loci. Our data does not indicate any signatures from ping-pong amplification but Dicer cleavage of long dsRNA. Ptiwi13 and 14 prefer different sub-cellular localizations and different preferences for primary and secondary siRNAs but do not load them mutually exclusive. Both Piwis enrich for antisense RNAs and show a general preference for uridine-rich sRNAs along the entire sRNA length. In addition, Ptiwi14-loaded siRNAs show a 5´-U signature. Our data indicates both Ptiwis and 2´-O-methylation contributing to strand selection of Dicer cleaved siRNAs. This unexpected function of the two distinct vegetative Piwis extends the increasing knowledge of the diversity of Piwi functions in diverse silencing pathways. We describe an unusual mode of action of Piwi proteins extending not only the great variety of Piwi-associated RNAi pathways but moreover raising the question whether this could have been the primordial one.

Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium

Supply of exogenous dsRNA (exo-dsRNA), either by injection or by feeding, is a fast and powerful alternative to classical knockout studies. The biotechnical potential of feeding techniques is evident from the numerous studies focusing on oral administration of dsRNA to control pests and viral infection in crops/animal farming. We aimed to dissect the direct and indirect effects of exo-dsRNA feeding on the endogenous short interfering RNA (endo-siRNA) populations of the free-living ciliate Paramecium. We introduced dsRNA fragments against Dicer1 (DCR1), involved in RNA interference (RNAi) against exo- and few endo-siRNAs, and an RNAi unrelated gene, ND169. Any feeding, even the control dsRNA, diminishes genome wide the accumulation of endo-siRNAs and mRNAs. This cannot be explained by direct off-target effects and suggests mechanistic overlaps of the exo- and endo-RNAi mechanisms. Nevertheless, we observe a stronger down-regulation of mRNAs in DCR1 feeding compared with ND169 knockdown. This is likely due to the direct involvement of DCR1 in endo-siRNA accumulation. We further observed a cis-regulatory effect on mRNAs that overlap with phased endo-siRNAs. This interference of exo-dsRNA with endo-siRNAs warrants further investigations into secondary effects in target species/consumers, risk assessment of dsRNA feeding applications, and environmental pollution with dsRNA.

Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium

Extensive research has characterized distinct exogenous RNAi pathways interfering in gene expression during vegetative growth of the unicellular model ciliate Paramecium. However, role of RNAi in endogenous transcriptome regulation, and environmental adaptation is unknown. Here, we describe the first genome-wide profiling of endogenous sRNAs in context of different transcriptomic states (serotypes). We developed a pipeline to identify, and characterize 2602 siRNA producing clusters (SRCs). Our data show no evidence that SRCs produce miRNAs, and in contrast to other species, no preference for strand specificity of siRNAs. Interestingly, most SRCs overlap coding genes and a separate group show siRNA phasing along the entire open reading frame, suggesting that the mRNA transcript serves as a source for siRNAs. Integrative analysis of siRNA abundance and gene expression levels revealed surprisingly that mRNA and siRNA show negative as well as positive associations. Two RNA-dependent RNA Polymerase mutants, RDR1 and RDR2, show a drastic loss of siRNAs especially in phased SRCs accompanied with increased mRNA levels. Importantly, most SRCs depend on both RDRs, reminiscent to primary siRNAs in the RNAi against exogenous RNA, indicating mechanistic overlaps between exogenous and endogenous RNAi contributing to flexible transcriptome adaptation.

Programmed Chromosome Deletion in the Ciliate Oxytricha trifallax

The ciliate Oxytricha trifallax contains two nuclei: a germline micronucleus and a somatic macronucleus. These two nuclei diverge significantly in genomic structure. The micronucleus contains approximately 100 chromosomes of megabase scale, while the macronucleus contains 16,000 gene-sized, high ploidy "nanochromosomes." During its sexual cycle, a copy of the zygotic germline micronucleus develops into a somatic macronucleus via DNA excision and rearrangement. The rearrangement process is guided by multiple RNA-based pathways that program the epigenetic inheritance of sequences in the parental macronucleus of the subsequent generation. Here, we show that the introduction of synthetic DNA molecules homologous to a complete native nanochromosome during the rearrangement process results in either loss or heavy copy number reduction of the targeted nanochromosome in the macronucleus of the subsequent generation. This phenomenon was tested on a variety of nanochromosomes with different micronuclear structures, with deletions resulting in all cases. Deletion of the targeted nanochromosome results in the loss of expression of the targeted genes, including gene knockout phenotypes that were phenocopied using alternative knockdown approaches. Further investigation of the chromosome deletion showed that, although the full length nanochromosome was lost, remnants of the targeted chromosome remain. We were also able to detect the presence of telomeres on these remnants. The chromosome deletions and remnants are epigenetically inherited when backcrossed to wild type strains, suggesting that an undiscovered mechanism programs DNA elimination and cytoplasmically transfers to both daughter cells during conjugation. Programmed deletion of targeted chromosomes provides a novel approach to investigate genome rearrangement and expands the available strategies for gene knockout in Oxytricha trifallax.

Automated analysis of small RNA datasets with RAPID

Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2.

Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis

Adult expression of IMP2 is often associated with several types of disease and cancer. The RNA binding protein IMP2 binds and stabilizes the IGF2 mRNA as well as hundreds of other transcripts during development. To gain insight into the molecular action of IMP2 and its contribution to disease in context of adult cellular metabolism, we analyze transgenic overexpression of IMP2 in mouse livers, which has been shown to induce a steatosis-like phenotype and enhanced risk to develop hepatocellular carcinoma (HCC). Our data show up-regulation of several HCC marker genes and miRNAs (miR438-3p and miR151-5p). To characterize the impact of miRNAs to their targets, integrative analysis of transcriptome-and miRNAome-dynamics in combination with IMP2 target prediction was carried out. Our analyses show that targets of expressed miRNAs become accumulated in the case that these transcripts have positive IMP2 binding prediction. Therefore, our data indicates that overexpression of IMP2 alters the regulatory capacity of many miRNAs and we conclude that IMP2 competes with miRNAs for binding sites on thousands of transcripts. As a result, our data implicates that overexpression of IMP2 has distinct effects to the regulatory capacity of miRNAs with yet unknown consequences for translational efficiency.

Two Sets of Piwi Proteins Are Involved in Distinct sRNA Pathways Leading to Elimination of Germline-Specific DNA

Piwi proteins and piRNAs protect eukaryotic germlines against the spread of transposons. During development in the ciliate Paramecium, two Piwi-dependent sRNA classes are involved in the elimination of transposons and transposon-derived DNA: scan RNAs (scnRNAs), associated with Ptiwi01 and Ptiwi09, and iesRNAs, whose binding partners we now identify as Ptiwi10 and Ptiwi11. scnRNAs derive from the maternal genome and initiate DNA elimination during development, whereas iesRNAs continue DNA targeting until the removal process is complete. Here, we show that scnRNAs and iesRNAs are processed by distinct Dicer-like proteins and bind Piwi proteins in a mutually exclusive manner, suggesting separate biogenesis pathways. We also demonstrate that the PTIWI10 gene is transcribed from the developing nucleus and that its transcription depends on prior DNA excision, suggesting a mechanism of gene expression control triggered by the removal of short DNA segments interrupting the gene.

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Identification of two Piwi proteins (Ptiwi10/11) associated with iesRNAs

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Piwi proteins bind Dicer-produced sRNAs and remove passenger strands

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Ptiwi10 is expressed from the new somatic macronucleus

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DNA elimination activates gene transcription

Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation

Genes or alleles can interact by small RNAs in a homology dependent manner meaning that short interfering (siRNAs) can act in trans at the chromatin level producing stable and heritable silencing phenotypes. Because of the puzzling data on endogenous paramutations, their impact contributing to adaptive evolution in a Lamarckian manner remains unknown. An increasing number of studies characterizes the underlying siRNA accumulation pathways using transgene experiments. Also in the ciliate Paramecium tetraurelia, we induce trans silencing on the chromatin level by injection of truncated transgenes. Here, we characterize the efficiency of this mechanism at different temperatures showing that silencing of the endogenous genes is temperature dependent. Analyzing different transgene constructs at different copy numbers, we dissected whether silencing efficiency is due to varying precursor RNAs or siRNA accumulation. Our data shows that silencing efficiency correlates with more efficient accumulation of primary siRNAs at higher temperatures rather than higher expression of precursor RNAs. Due to higher primary levels, secondary siRNAs also show temperature dependency and interestingly increase their relative proportion to primary siRNAs. Our data shows that efficient trans silencing on the chromatin level in P. tetraurelia depends on environmental parameters, thus being an important epigenetic factor limiting regulatory effects of siRNAs.