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1.  An RIG-I-Like RNA Helicase Mediates Antiviral RNAi Downstream of Viral siRNA Biogenesis in Caenorhabditis elegans 
PLoS Pathogens  2009;5(2):e1000286.
Dicer ribonucleases of plants and invertebrate animals including Caenorhabditis elegans recognize and process a viral RNA trigger into virus-derived small interfering RNAs (siRNAs) to guide specific viral immunity by Argonaute-dependent RNA interference (RNAi). C. elegans also encodes three Dicer-related helicase (drh) genes closely related to the RIG-I-like RNA helicase receptors which initiate broad-spectrum innate immunity against RNA viruses in mammals. Here we developed a transgenic C. elegans strain that expressed intense green fluorescence from a chromosomally integrated flock house virus replicon only after knockdown or knockout of a gene required for antiviral RNAi. Use of the reporter nematode strain in a feeding RNAi screen identified drh-1 as an essential component of the antiviral RNAi pathway. However, RNAi induced by either exogenous dsRNA or the viral replicon was enhanced in drh-2 mutant nematodes, whereas exogenous RNAi was essentially unaltered in drh-1 mutant nematodes, indicating that exogenous and antiviral RNAi pathways are genetically distinct. Genetic epistatic analysis shows that drh-1 acts downstream of virus sensing and viral siRNA biogenesis to mediate specific antiviral RNAi. Notably, we found that two members of the substantially expanded subfamily of Argonautes specific to C. elegans control parallel antiviral RNAi pathways. These findings demonstrate both conserved and unique strategies of C. elegans in antiviral defense.
Author Summary
The genome of Caenorhabditis elegans encodes three Dicer-related helicases (DRHs) highly homologous to the DExD/H box helicase domain found in two distinct families of virus sensors, Dicer ribonucleases and RIG-I-like helicases (RLRs). Dicer initiates the specific, RNAi-mediated viral immunity in plants, fungi and invertebrates by producing virus-derived small interfering RNAs (siRNAs). By contrast, mammalian RLRs trigger interferon production and broad-spectrum viral immunity, although one of the three RLRs may act as both a negative and positive regulator of viral immunity. In this study we developed a transgenic C. elegans strain for high-throughput genetic screens and identified 35 genes including drh-1 that are required for RNAi-mediated viral immunity. Genetic epistatic analyses demonstrate that drh-1 mediates RNAi immunity downstream of the production of viral siRNAs. Notably, we found that drh-2 functions as a negative regulator of the viral immunity. Thus, both nematode DRHs and mammalian RLRs participate in antiviral immune responses. Unlike mammalian RLRs, however, nematode DRH-1 employs an RNAi effector mechanism and is unlikely to be involved in direct virus sensing.
PMCID: PMC2629121  PMID: 19197349
2.  Characterizing the role of RNA silencing components in Cryptococcus neoformans 
Fungal genetics and biology : FG & B  2010;47(12):1070-1080.
The RNA interference (RNAi) mediated by homology-dependent degradation of the target mRNA with small RNA molecules plays a key role in controlling transcription and translation processes in a number of eukaryotic organisms. The RNAi machinery is also evolutionarily conserved in a wide variety of fungal species, including pathogenic fungi. To elucidate the physiological functions of the RNAi pathway in Cryptococcus neoformans that causes fungal meningitis, here we performed genetic analyses for genes encoding Argonaute (AGO1 and AGO2), RNA-dependent RNA polymerase (RDP1), and Dicers (DCR1 and DCR2) in both serotype A and D C. neoformans. The present study shows that Ago1, Rdp1, and Dcr2 are the major components of the RNAi process occurring in C. neoformans. However, the RNAi machinery is not involved in regulation of production of two virulence factors (capsule and melanin), sexual differentiation, and diverse stress response. Comparative transcriptome analysis of the serotype A and D RNAi mutants revealed that only modest changes occur in the genome-wide transcriptome profiles when the RNAi process was perturbed. Notably, the serotype D rdp1Δ mutants showed an increase in transcript abundance of active retrotransposons and transposons, such as T2 and T3, the latter of which is a novel serotype D-specific transposon of C. neoformans. In a wild type background both T2 and T3 were found to be weakly active mobile elements, although we found no evidence of Cnl1 retrotransposon mobility. In contrast, all three transposable elements exhibited enhanced mobility in the rdp1Δ mutant strain. In conclusion, the RNAi pathway plays an important role in controlling transposon activity and genome integrity of C. neoformans.
PMCID: PMC3021383  PMID: 21067947
RNA interference; RNA-dependent RNA polymerase; Dicer; Argonaute; Transposon
3.  Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection 
PLoS Pathogens  2013;9(8):e1003579.
In Drosophila, post-transcriptional gene silencing occurs when exogenous or endogenous double stranded RNA (dsRNA) is processed into small interfering RNAs (siRNAs) by Dicer-2 (Dcr-2) in association with a dsRNA-binding protein (dsRBP) cofactor called Loquacious (Loqs-PD). siRNAs are then loaded onto Argonaute-2 (Ago2) by the action of Dcr-2 with another dsRBP cofactor called R2D2. Loaded Ago2 executes the destruction of target RNAs that have sequence complementarity to siRNAs. Although Dcr-2, R2D2, and Ago2 are essential for innate antiviral defense, the mechanism of virus-derived siRNA (vsiRNA) biogenesis and viral target inhibition remains unclear. Here, we characterize the response mechanism mediated by siRNAs against two different RNA viruses that infect Drosophila. In both cases, we show that vsiRNAs are generated by Dcr-2 processing of dsRNA formed during viral genome replication and, to a lesser extent, viral transcription. These vsiRNAs seem to preferentially target viral polyadenylated RNA to inhibit viral replication. Loqs-PD is completely dispensable for silencing of the viruses, in contrast to its role in silencing endogenous targets. Biogenesis of vsiRNAs is independent of both Loqs-PD and R2D2. R2D2, however, is required for sorting and loading of vsiRNAs onto Ago2 and inhibition of viral RNA expression. Direct injection of viral RNA into Drosophila results in replication that is also independent of Loqs-PD. This suggests that triggering of the antiviral pathway is not related to viral mode of entry but recognition of intrinsic features of virus RNA. Our results indicate the existence of a vsiRNA pathway that is separate from the endogenous siRNA pathway and is specifically triggered by virus RNA. We speculate that this unique framework might be necessary for a prompt and efficient antiviral response.
Author Summary
The RNA interference (RNAi) pathway utilizes small non-coding RNAs to silence gene expression. In insects, RNAi regulates endogenous genes and functions as an RNA-based immune system against viral infection. Here we have uncovered details of how RNAi is triggered by RNA viruses. Double-stranded RNA (dsRNA) generated as a replication intermediate or from transcription of the RNA virus can be used as substrate for the biogenesis of virus-derived small interfering RNAs (vsiRNAs). Unlike other dsRNAs, virus RNA processing involves Dicer but not its canonical partner protein Loqs-PD. Thus, vsiRNA biogenesis is mechanistically different from biogenesis of endogenous siRNAs or siRNAs derived from other exogenous RNA sources. Our results suggest a specialization of the pathway dedicated to silencing of RNA viruses versus other types of RNAi silencing. The understanding of RNAi mechanisms during viral infection could have implications for the control of insect-borne viruses and the use of siRNAs to treat viral infections in humans.
PMCID: PMC3757037  PMID: 24009507
4.  RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells 
PLoS Genetics  2013;9(11):e1003791.
In most mouse tissues, long-interspersed elements-1 (L1s) are silenced via methylation of their 5′-untranslated regions (5′-UTR). A gradual loss-of-methylation in pre-implantation embryos coincides with L1 retrotransposition in blastocysts, generating potentially harmful mutations. Here, we show that Dicer- and Ago2-dependent RNAi restricts L1 accumulation and retrotransposition in undifferentiated mouse embryonic stem cells (mESCs), derived from blastocysts. RNAi correlates with production of Dicer-dependent 22-nt small RNAs mapping to overlapping sense/antisense transcripts produced from the L1 5′-UTR. However, RNA-surveillance pathways simultaneously degrade these transcripts and, consequently, confound the anti-L1 RNAi response. In Dicer−/− mESC complementation experiments involving ectopic Dicer expression, L1 silencing was rescued in cells in which microRNAs remained strongly depleted. Furthermore, these cells proliferated and differentiated normally, unlike their non-complemented counterparts. These results shed new light on L1 biology, uncover defensive, in addition to regulatory roles for RNAi, and raise questions on the differentiation defects of Dicer−/− mESCs.
Author Summary
A basal network of gene regulation orchestrates the processes ensuring maintenance of genome integrity. Eukaryotic small RNAs generated by the RNAse-III Dicer have emerged as central players in this network, by mediating gene silencing at the transcriptional or post-transcriptional level via RNA interference (RNAi). To gain insight into their potential developmental functions in mammals, we have characterized small RNA expression profiles during mouse Embryonic Stem Cell (mESCs) differentiation, a model for early mammalian development. Long interspersed elements 1 (L1) are non-long-terminal-repeat retrotransposons that dominate the mouse genomic landscape, and are expressed in germ cells or during early development and mESCs. Based on clear precedents in plants and fission yeast, we investigated a role for RNAi and other RNA-based pathways in the regulation of L1 transcription and mobilization. Our work uncovered the existence of small (s)RNAs that map to active L1 elements. Some have characteristics of cognate siRNA produced by Dicer, while others display strand biases and length heterogeneity that evoke their biogenesis through RNA surveillance pathways, in a Dicer-independent manner. Furthermore, genetic ablation of DICER or of ARGONAUTE proteins has complex and profound consequences on L1 transcription and mobilization, indicating that endogenous RNAi do indeed maintain genomic integrity against L1 proliferation.
PMCID: PMC3820764  PMID: 24244175
5.  Comparative Genomics Reveals Two Novel RNAi Factors in Trypanosoma brucei and Provides Insight into the Core Machinery 
PLoS Pathogens  2012;8(5):e1002678.
The introduction ten years ago of RNA interference (RNAi) as a tool for molecular exploration in Trypanosoma brucei has led to a surge in our understanding of the pathogenesis and biology of this human parasite. In particular, a genome-wide RNAi screen has recently been combined with next-generation Illumina sequencing to expose catalogues of genes associated with loss of fitness in distinct developmental stages. At present, this technology is restricted to RNAi-positive protozoan parasites, which excludes T. cruzi, Leishmania major, and Plasmodium falciparum. Therefore, elucidating the mechanism of RNAi and identifying the essential components of the pathway is fundamental for improving RNAi efficiency in T. brucei and for transferring the RNAi tool to RNAi-deficient pathogens. Here we used comparative genomics of RNAi-positive and -negative trypanosomatid protozoans to identify the repertoire of factors in T. brucei. In addition to the previously characterized Argonaute 1 (AGO1) protein and the cytoplasmic and nuclear Dicers, TbDCL1 and TbDCL2, respectively, we identified the RNA Interference Factors 4 and 5 (TbRIF4 and TbRIF5). TbRIF4 is a 3′-5′ exonuclease of the DnaQ superfamily and plays a critical role in the conversion of duplex siRNAs to the single-stranded form, thus generating a TbAGO1-siRNA complex required for target-specific cleavage. TbRIF5 is essential for cytoplasmic RNAi and appears to act as a TbDCL1 cofactor. The availability of the core RNAi machinery in T. brucei provides a platform to gain mechanistic insights in this ancient eukaryote and to identify the minimal set of components required to reconstitute RNAi in RNAi-deficient parasites.
Author Summary
RNA interference (RNAi), a naturally-occurring pathway whereby the presence of double-stranded RNA in a cell triggers the degradation of homologous mRNA, has been harnessed in many organisms as an invaluable molecular biology tool to interrogate gene function. Although this technology is widely used in the protozoan parasite Trypanosoma brucei, other parasites of considerable public health significance, such as Trypanosoma cruzi, Leishmania major, and Plasmodium falciparum do not perform RNAi. Since RNAi has recently been introduced into budding yeast, this opens up the possibility that RNAi can be reconstituted in these pathogens. The key to this is getting a handle on the essential RNAi factors in T. brucei. By applying comparative genomics we identified five genes that are present in the RNAi-proficient species, but not in RNAi-deficient species: three previously identified RNAi factors, and two novel ones, which are described here. This insight into the core T. brucei RNAi machinery represents a major step towards transferring this pathway to RNAi-deficient parasites.
PMCID: PMC3359990  PMID: 22654659
6.  Retention and Loss of RNA Interference Pathways in Trypanosomatid Protozoans 
PLoS Pathogens  2010;6(10):e1001161.
RNA interference (RNAi) pathways are widespread in metaozoans but the genes required show variable occurrence or activity in eukaryotic microbes, including many pathogens. While some Leishmania lack RNAi activity and Argonaute or Dicer genes, we show that Leishmania braziliensis and other species within the Leishmania subgenus Viannia elaborate active RNAi machinery. Strong attenuation of expression from a variety of reporter and endogenous genes was seen. As expected, RNAi knockdowns of the sole Argonaute gene implicated this protein in RNAi. The potential for functional genetics was established by testing RNAi knockdown lines lacking the paraflagellar rod, a key component of the parasite flagellum. This sets the stage for the systematic manipulation of gene expression through RNAi in these predominantly diploid asexual organisms, and may also allow selective RNAi-based chemotherapy. Functional evolutionary surveys of RNAi genes established that RNAi activity was lost after the separation of the Leishmania subgenus Viannia from the remaining Leishmania species, a divergence associated with profound changes in the parasite infectious cycle and virulence. The genus Leishmania therefore offers an accessible system for testing hypothesis about forces that may select for the loss of RNAi during evolution, such as invasion by viruses, changes in genome plasticity mediated by transposable elements and gene amplification (including those mediating drug resistance), and/or alterations in parasite virulence.
Author Summary
RNAi interference pathways play fundamental roles in eukaryotes and provide important methods for the analysis of gene function. Occasionally RNAi has been lost, precluding its use as a tool, as well as raising the question of what forces could lead to loss of such a key pathway. Genomic and functional studies previously showed that within trypanosomatids protozoans RNAi was absent in both Leishmania major and Trypanosoma cruzi. The genome of L. braziliensis, a member of the early diverging Leishmania subgenus Viannia, retained key genes required for RNAi such as an Argonaute. We demonstrated that in fact L. braziliensis shows strong RNAi activity with reporter and endogenous genes affecting flagellar function. These data suggest that RNAi may be productively applied for functional genomic studies in L. braziliensis. We mapped the evolutionary point at which RNAi was lost in lineage leading to Leishmania and Crithidia, and establish that RNAi must have been lost at least twice in the trypanosomatids, once on the lineage leading to T. cruzi and independently following the divergence of the Viannia subgenus from other Leishmania species. Lastly, we discuss hypotheses concerning the forces leading to the loss of RNAi in Leishmania evolution, including viral invasion, increased genome plasticity, and altered virulence.
PMCID: PMC2965760  PMID: 21060810
7.  Small regulatory RNAs inhibit RNA Polymerase II during the elongation phase of transcription 
Nature  2010;465(7301):1097-1101.
Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defense against parasitic nucleic acids, and genome rearrangement. Many small regulatory RNAs are thought to function in nuclei 1-2. For instance, in plants and fungi siRNAs associate with nascent transcripts and direct chromatin and/or DNA modifications 1-2. To further understand the biological roles of small regulatory RNAs, we conducted a genetic screen to identify factors required for RNA interference (RNAi) in C. elegans nuclei 3. Here we show that nrde-2 encodes an evolutionarily conserved protein that is required for small interfering (si)RNA-mediated silencing in nuclei. NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNAi. We find that nuclear-localized siRNAs direct a NRDE-2-dependent silencing of pre-mRNAs 3’ to sites of RNAi, a NRDE-2-dependent accumulation of RNA Polymerase (RNAP) II at genomic loci targeted by RNAi, and NRDE-2-dependent decreases in RNAP II occupancy and RNAP II transcriptional activity 3’ to sites of RNAi. These results define NRDE-2 as a component of the nuclear RNAi machinery and demonstrate that metazoan siRNAs can silence nuclear-localized RNAs co-transcriptionally. In addition, these results establish a novel mode of RNAP II regulation; siRNA-directed recruitment of NRDE factors that inhibit RNAP II during the elongation phase of transcription.
PMCID: PMC2892551  PMID: 20543824
8.  RNA Interference: Biology, Mechanism, and Applications 
Double-stranded RNA-mediated interference (RNAi) is a simple and rapid method of silencing gene expression in a range of organisms. The silencing of a gene is a consequence of degradation of RNA into short RNAs that activate ribonucleases to target homologous mRNA. The resulting phenotypes either are identical to those of genetic null mutants or resemble an allelic series of mutants. Specific gene silencing has been shown to be related to two ancient processes, cosuppression in plants and quelling in fungi, and has also been associated with regulatory processes such as transposon silencing, antiviral defense mechanisms, gene regulation, and chromosomal modification. Extensive genetic and biochemical analysis revealed a two-step mechanism of RNAi-induced gene silencing. The first step involves degradation of dsRNA into small interfering RNAs (siRNAs), 21 to 25 nucleotides long, by an RNase III-like activity. In the second step, the siRNAs join an RNase complex, RISC (RNA-induced silencing complex), which acts on the cognate mRNA and degrades it. Several key components such as Dicer, RNA-dependent RNA polymerase, helicases, and dsRNA endonucleases have been identified in different organisms for their roles in RNAi. Some of these components also control the development of many organisms by processing many noncoding RNAs, called micro-RNAs. The biogenesis and function of micro-RNAs resemble RNAi activities to a large extent. Recent studies indicate that in the context of RNAi, the genome also undergoes alterations in the form of DNA methylation, heterochromatin formation, and programmed DNA elimination. As a result of these changes, the silencing effect of gene functions is exercised as tightly as possible. Because of its exquisite specificity and efficiency, RNAi is being considered as an important tool not only for functional genomics, but also for gene-specific therapeutic activities that target the mRNAs of disease-related genes.
PMCID: PMC309050  PMID: 14665679
9.  Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe 
Strand-specific RNA sequencing of S. pombe reveals a highly structured programme of ncRNA expression at over 600 loci. Functional investigations show that this extensive ncRNA landscape controls the complex programme of sexual differentiation in S. pombe.
The model eukaryote S. pombe features substantial numbers of ncRNAs many of which are antisense regulatory transcripts (ARTs), ncRNAs expressed on the opposing strand to coding sequences.Individual ARTs are generated during the mitotic cycle, or at discrete stages of sexual differentiation to downregulate the levels of proteins that drive and coordinate sexual differentiation.Antisense transcription occurring from events such as bidirectional transcription is not simply artefactual ‘chatter', it performs a critical role in regulating gene expression.
Regulation of the RNA profile is a principal control driving sexual differentiation in the fission yeast Schizosaccharomyces pombe. Before transcription, RNAi-mediated formation of heterochromatin is used to suppress expression, while post-transcription, regulation is achieved via the active stabilisation or destruction of transcripts, and through at least two distinct types of splicing control (Mata et al, 2002; Shimoseki and Shimoda, 2001; Averbeck et al, 2005; Mata and Bähler, 2006; Xue-Franzen et al, 2006; Moldon et al, 2008; Djupedal et al, 2009; Amorim et al, 2010; Grewal, 2010; Cremona et al, 2011).
Around 94% of the S. pombe genome is transcribed (Wilhelm et al, 2008). While many of these transcripts encode proteins (Wood et al, 2002; Bitton et al, 2011), the majority have no known function. We used a strand-specific protocol to sequence total RNA extracts taken from vegetatively growing cells, and at different points during a time course of sexual differentiation. The resulting data redefined existing gene coordinates and identified additional transcribed loci. The frequency of reads at each of these was used to monitor transcript abundance.
Transcript levels at 6599 loci changed in at least one sample (G-statistic; False Discovery Rate <5%). 4231 (72.3%), of which 4011 map to protein-coding genes, while 809 loci were antisense to a known gene. Comparisons between haploid and diploid strains identified changes in transcript levels at over 1000 loci.
At 354 loci, greater antisense abundance was observed relative to sense, in at least one sample (putative antisense regulatory transcripts—ARTs). Since antisense mechanisms are known to modulate sense transcript expression through a variety of inhibitory mechanisms (Faghihi and Wahlestedt, 2009), we postulated that the waves of antisense expression activated at different stages during meiosis might be regulating protein expression.
To ask whether transcription factors that drive sense-transcript levels influenced ART production, we performed RNA-seq of a pat1.114 diploid meiosis in the absence of the transcription factors Atf21 and Atf31 (responsible for late meiotic transcription; Mata et al, 2002). Transcript levels at 185 ncRNA loci showed significant changes in the knockout backgrounds. Although meiotic progression is largely unaffected by removal of Atf21 and Atf31, viability of the resulting spores was significantly diminished, indicating that Atf21- and Atf31-mediated events are critical to efficient sexual differentiation.
If changes to relative antisense/sense transcript levels during a particular phase of sexual differentiation were to regulate protein expression, then the continued presence of the antisense at points in the differentiation programme where it would normally be absent should abolish protein function during this phase. We tested this hypothesis at four loci representing the three means of antisense production: convergent gene expression, improper termination and nascent transcription from an independent locus. Induction of the natural antisense transcripts that opposed spo4+, spo6+ and dis1+ (Figures 3 and 7) in trans from a heterologous locus phenocopied a loss of function of the target protein. ART overexpression decreased Dis1 protein levels. Antisense transcription opposing spk1+ originated from improper termination of the sense ups1+ transcript on the opposite strand (Figure 3B, left locus). Expression of either the natural full-length ups1+ transcript or a truncated version, restricted to the portion of ups1+ overlapping spk1+ (Figure 3, orange transcripts) in trans from a heterologous locus phenocopied the spk1.Δ differentiation deficiency. Convergent transcription from a neighbouring gene on the opposing strand is, therefore, an effective mechanism to generate RNAi-mediated (below) silencing in fission yeast. Further analysis of the data revealed, for many loci, substantial changes in UTR length over the course of meiosis, suggesting that UTR dynamics may have an active role in regulating gene expression by controlling the transcriptional overlap between convergent adjacent gene pairs.
The RNAi machinery (Grewal, 2010) was required for antisense suppression at each of the dis1, spk1, spo4 and spo6 loci, as antisense to each locus had no impact in ago1.Δ, dcr1.Δ and rdp1.Δ backgrounds. We conclude that RNAi control has a key role in maintaining the fidelity of sexual differentiation in fission yeast. The histone H3 methyl transferase Clr4 was required for antisense control from a heterologous locus.
Thus, a significant portion of the impact of ncRNA upon sexual differentiation arises from antisense gene silencing. Importantly, in contrast to the extensively characterised ability of the RNAi machinery to operate in cis at a target locus in S. pombe (Grewal, 2010), each case of gene silencing generated here could be achieved in trans by expression of the antisense transcript from a single heterologous locus elsewhere in the genome.
Integration of an antibiotic marker gene immediately downstream of the dis1+ locus instigated antisense control in an orientation-dependent manner. PCR-based gene tagging approaches are widely used to fuse the coding sequences of epitope or protein tags to a gene of interest. Not only do these tagging approaches disrupt normal 3′UTR controls, but the insertion of a heterologous marker gene immediately downstream of an ORF can clearly have a significant impact upon transcriptional control of the resulting fusion protein. Thus, PCR tagging approaches can no longer be viewed as benign manipulations of a locus that only result in the production of a tagged protein product.
Repression of Dis1 function by gene deletion or antisense control revealed a key role this conserved microtubule regulator in driving the horsetail nuclear migrations that promote recombination during meiotic prophase.
Non-coding transcripts have often been viewed as simple ‘chatter', maintained solely because evolutionary pressures have not been strong enough to force their elimination from the system. Our data show that phenomena such as improper termination and bidirectional transcription are not simply interesting artifacts arising from the complexities of transcription or genome history, but have a critical role in regulating gene expression in the current genome. Given the widespread use of RNAi, it is reasonable to anticipate that future analyses will establish ARTs to have equal importance in other organisms, including vertebrates.
These data highlight the need to modify our concept of a gene from that of a spatially distinct locus. This view is becoming increasingly untenable. Not only are the 5′ and 3′ ends of many genes indistinct, but that this lack of a hard and fast boundary is actively used by cells to control the transcription of adjacent and overlapping loci, and thus to regulate critical events in the life of a cell.
Strand-specific RNA sequencing of S. pombe revealed a highly structured programme of ncRNA expression at over 600 loci. Waves of antisense transcription accompanied sexual differentiation. A substantial proportion of ncRNA arose from mechanisms previously considered to be largely artefactual, including improper 3′ termination and bidirectional transcription. Constitutive induction of the entire spk1+, spo4+, dis1+ and spo6+ antisense transcripts from an integrated, ectopic, locus disrupted their respective meiotic functions. This ability of antisense transcripts to disrupt gene function when expressed in trans suggests that cis production at native loci during sexual differentiation may also control gene function. Consistently, insertion of a marker gene adjacent to the dis1+ antisense start site mimicked ectopic antisense expression in reducing the levels of this microtubule regulator and abolishing the microtubule-dependent ‘horsetail' stage of meiosis. Antisense production had no impact at any of these loci when the RNA interference (RNAi) machinery was removed. Thus, far from being simply ‘genome chatter', this extensive ncRNA landscape constitutes a fundamental component in the controls that drive the complex programme of sexual differentiation in S. pombe.
PMCID: PMC3738847  PMID: 22186733
antisense; meiosis; ncRNA; S. pombe; siRNA
10.  MicroRNA–Directed siRNA Biogenesis in Caenorhabditis elegans 
PLoS Genetics  2010;6(4):e1000903.
RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi–related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.
Author Summary
Due to its intrinsic characteristics, RNA interference (RNAi) has become one of the most widely used tools in cell biology and has revolutionized approaches to elucidate gene function. The process, also known as RNA silencing, is triggered by dsRNA molecules that are cleaved by Dicer proteins into small interfering RNAs (siRNAs). The rde-1 gene from Caenorhabditis elegans was one of the first genes found in association with this mechanism and encodes the only Argonaute protein in worms, which is by itself essential for the classical RNAi pathway triggered by exogenously introduced dsRNA. However, little is known about endogenous functions of RDE-1. Here we show that RDE-1 binds to many classes of small RNAs, including microRNAs. We show that miR-243 is efficiently bound by RDE-1 and triggers regular RNAi on an endogenous target, implying that many RNA species, including miRNAs, are constantly being screened against the transcriptome using the canonical exogenous RNAi pathway.
PMCID: PMC2851571  PMID: 20386745
11.  Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins 
BMC Genomics  2014;15(1):775.
RNA interference (RNAi) leads to sequence specific knock-down of gene expression and has emerged as an important tool to analyse gene functions, pathway analysis and gene therapy. Although RNAi is a conserved cellular process involving common elements and factors, species-specific differences have been observed among different eukaryotes. Identification of components for RNAi pathway is pursued intensively and successful genome-wide screens have been performed for components of RNAi pathways in various organisms. Functional comparative genomics analysis offers evolutionary insight that forms basis of discoveries of novel RNAi-factors within related organisms. Keeping in view the academic and commercial utility of insect derived cell-line from Spodoptera frugiperda, we pursued the identification and functional analysis of components of RNAi-machinery of Sf21 cell-line using genome-wide application.
The genome and transcriptome of Sf21 was assembled and annotated. In silico application of comparative genome analysis among insects allowed us to identify several RNAi factors in Sf21 line. The candidate RNAi factors from assembled genome were validated by knockdown analysis of candidate factors using the siRNA screens on the Sf21-gfp reporter cell-line. Forty two (42) potential factors were identified using the cell based assay. These include core RNAi elements including Dicer-2, Argonaute-1, Drosha, Aubergine and auxiliary modules like chromatin factors, RNA helicases, RNA processing module, signalling allied proteins and others. Phylogenetic analyses and domain architecture revealed that Spodoptera frugiperda homologs retained identity with Lepidoptera (Bombyx mori) or Coleoptera (Tribolium castaneum) sustaining an evolutionary conserved scaffold in post-transcriptional gene silencing paradigm within insects.
The database of RNAi-factors generated by whole genome association survey offers comprehensive outlook about conservation as well as specific differences of the proteins of RNAi machinery. Understanding the interior involved in different phases of gene silencing also offers impending tool for RNAi-based applications.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-775) contains supplementary material, which is available to authorized users.
PMCID: PMC4247154  PMID: 25199785
RNA interference; siRNA screening; Sf21 cells; Genome-wide screening; Insect RNAi; Spodoptera frugiperda
12.  Convergent Evolution of Argonaute-2 Slicer Antagonism in Two Distinct Insect RNA Viruses 
PLoS Pathogens  2012;8(8):e1002872.
RNA interference (RNAi) is a major antiviral pathway that shapes evolution of RNA viruses. We show here that Nora virus, a natural Drosophila pathogen, is both a target and suppressor of RNAi. We detected viral small RNAs with a signature of Dicer-2 dependent small interfering RNAs in Nora virus infected Drosophila. Furthermore, we demonstrate that the Nora virus VP1 protein contains RNAi suppressive activity in vitro and in vivo that enhances pathogenicity of recombinant Sindbis virus in an RNAi dependent manner. Nora virus VP1 and the viral suppressor of RNAi of Cricket paralysis virus (1A) antagonized Argonaute-2 (AGO2) Slicer activity of RNA induced silencing complexes pre-loaded with a methylated single-stranded guide strand. The convergent evolution of AGO2 suppression in two unrelated insect RNA viruses highlights the importance of AGO2 in antiviral defense.
Author Summary
Multi-cellular organisms require a potent immune response to ensure survival under the ongoing assault by microbial pathogens. Co-evolution of virus and host shapes the genome of both pathogen and host. Using Drosophila melanogaster as a model, we study virus-host interactions in infections by Nora virus, a non-lethal natural pathogen of fruit flies. Insects depend on the RNA interference (RNAi) pathway for antiviral defense. A hallmark of the antiviral RNAi response is the production of viral small RNAs during infection. We detected Nora virus small RNAs during infection of Drosophila, demonstrating that Nora virus is a target of the antiviral RNAi pathway. Furthermore, we show that Nora virus viral protein 1 (VP1) inhibits the catalytic activity of Argonaute-2, a key protein of the RNAi pathway. The 1A protein of Cricket paralysis virus suppresses RNAi via a similar mechanism. Importantly, whereas Nora virus persistently infects Drosophila, Cricket paralysis virus induces a lethal infection. Our findings thus indicate that two distantly related viruses independently evolved an RNAi suppressor protein that targets the Argonaute-2 protein. Altogether, our results emphasize the critical role of Argonaute-2 in insect antiviral defense, both in lethal and persistent infections.
PMCID: PMC3420963  PMID: 22916019
13.  On the origin and functions of RNA-mediated silencing: from protists to man 
Current genetics  2006;50(2):81-99.
Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways. We have examined the taxonomic distribution and the phylogenetic relationship of key components of the RNA interference (RNAi) machinery in members of five eukaryotic supergroups. On the basis of the parsimony principle, our analyses suggest that a relatively complex RNAi machinery was already present in the last common ancestor of eukaryotes and consisted, at a minimum, of one Argonaute-like polypeptide, one Piwi-like protein, one Dicer, and one RNA-dependent RNA polymerase. As proposed before, the ancestral (but non-essential) role of these components may have been in defense responses against genomic parasites such as transposable elements and viruses. From a mechanistic perspective, the RNAi machinery in the eukaryotic ancestor may have been capable of both small-RNA-guided transcript degradation as well as transcriptional repression, most likely through histone modifications. Both roles appear to be widespread among living eukaryotes and this diversification of function could account for the evolutionary conservation of duplicated Argonaute-Piwi proteins. In contrast, additional RNAi-mediated pathways such as RNA-directed DNA methylation, programmed genome rearrangements, meiotic silencing by unpaired DNA, and miRNA-mediated gene regulation may have evolved independently in specific lineages.
PMCID: PMC2583075  PMID: 16691418
RNA interference; Transposon silencing; Heterochromatin; RNAi phylogenetics
14.  New Developments of RNAi in Paracoccidioides brasiliensis: Prospects for High-Throughput, Genome-Wide, Functional Genomics 
The Fungal Genome Initiative of the Broad Institute, in partnership with the Paracoccidioides research community, has recently sequenced the genome of representative isolates of this human-pathogen dimorphic fungus: Pb18 (S1), Pb03 (PS2) and Pb01. The accomplishment of future high-throughput, genome-wide, functional genomics will rely upon appropriate molecular tools and straightforward techniques to streamline the generation of stable loss-of-function phenotypes. In the past decades, RNAi has emerged as the most robust genetic technique to modulate or to suppress gene expression in diverse eukaryotes, including fungi. These molecular tools and techniques, adapted for RNAi, were up until now unavailable for P. brasiliensis.
Methodology/Principal Findings
In this paper, we report Agrobacterium tumefaciens mediated transformation of yeast cells for high-throughput applications with which higher transformation frequencies of 150±24 yeast cell transformants per 1×106 viable yeast cells were obtained. Our approach is based on a bifunctional selective marker fusion protein consisted of the Streptoalloteichus hindustanus bleomycin-resistance gene (Shble) and the intrinsically fluorescent monomeric protein mCherry which was codon-optimized for heterologous expression in P. brasiliensis. We also report successful GP43 gene knock-down through the expression of intron-containing hairpin RNA (ihpRNA) from a Gateway-adapted cassette (cALf) which was purpose-built for gene silencing in a high-throughput manner. Gp43 transcript levels were reduced by 73.1±22.9% with this approach.
We have a firm conviction that the genetic transformation technique and the molecular tools herein described will have a relevant contribution in future Paracoccidioides spp. functional genomics research.
Author Summary
Diverse eukaryotes, including various fungi, utilize RNA interference (RNAi) pathways to regulate genome-wide gene expression. Since the initial characterization of these pathways and the demonstration of its artificial induction in the filamentous ascomycete Neurospora crassa, RNAi has emerged as the most robust reverse-genetic technique to scrutinize the function of genes and has been increasingly adopted in high-throughput functional genomics in search of new insights into fungal pathobiology. Herein, we have developed appropriate molecular tools and straightforward techniques to streamline the generation of stable loss-of-function phenotypes for the human-pathogen Paracoccidioides brasiliensis, which is phylogenetically related to Blastomyces dermatitidis, Coccidioides immitis and Histoplasma capsulatum. Likewise these thermo-dimorphic fungi, P. brasiliensis infection in immunocompetent or immunocompromised individuals ensue in a life-threatening systemic mycosis known as Paracoccidioidomycosis.
PMCID: PMC4183473  PMID: 25275433
15.  The miR-35-41 Family of MicroRNAs Regulates RNAi Sensitivity in Caenorhabditis elegans 
PLoS Genetics  2012;8(3):e1002536.
RNA interference (RNAi) utilizes small interfering RNAs (siRNAs) to direct silencing of specific genes through transcriptional and post-transcriptional mechanisms. The siRNA guides can originate from exogenous (exo–RNAi) or natural endogenous (endo–RNAi) sources of double-stranded RNA (dsRNA). In Caenorhabditis elegans, inactivation of genes that function in the endo–RNAi pathway can result in enhanced silencing of genes targeted by siRNAs from exogenous sources, indicating cross-regulation between the pathways. Here we show that members of another small RNA pathway, the mir-35-41 cluster of microRNAs (miRNAs) can regulate RNAi. In worms lacking miR-35-41, there is reduced expression of lin-35/Rb, the C. elegans homolog of the tumor suppressor Retinoblastoma gene, previously shown to regulate RNAi responsiveness. Genome-wide microarray analyses show that targets of endo–siRNAs are up-regulated in mir-35-41 mutants, a phenotype also displayed by lin-35/Rb mutants. Furthermore, overexpression of lin-35/Rb specifically rescues the RNAi hypersensitivity of mir-35-41 mutants. Although the mir-35-41 miRNAs appear to be exclusively expressed in germline and embryos, their effect on RNAi sensitivity is transmitted to multiple tissues and stages of development. Additionally, we demonstrate that maternal contribution of miR-35-41 or lin-35/Rb is sufficient to reduce RNAi effectiveness in progeny worms. Our results reveal that miRNAs can broadly regulate other small RNA pathways and, thus, have far reaching effects on gene expression beyond directly targeting specific mRNAs.
Author Summary
RNA interference (RNAi) has become a widely used approach for silencing genes of interest. This tool is possible because endogenous RNA silencing pathways exist broadly across organisms, including humans, worms, and plants. The general RNAi pathway utilizes small ∼21-nucleotide RNAs to target specific protein-coding genes through base-pairing interactions. Since RNAs from exogenous sources require some of the same factors as endogenous small RNAs to silence gene expression, there can be competition between the pathways. Thus, perturbations in the endogenous RNAi pathway can result in enhanced silencing efficiency by exogenous small RNAs. MicroRNAs (miRNAs) comprise another endogenous small RNA pathway, but their biogenesis and mechanism of gene silencing are distinct in many ways from RNAi pathways. Here we show that a family of miRNAs regulates the effectiveness of RNAi in Caenorhabditis elegans. Loss of mir-35-41 results in enhanced RNAi by exogenous RNAs and reduced silencing of endogenous RNAi targets. The embryonic miR-35-41 miRNAs regulate the sensitivity to RNAi through lin-35/Rb, a homolog of the human Retinoblastoma tumor suppressor gene previously shown to regulate RNAi effectiveness in C. elegans. Additionally, we show that this sensitivity can be passed on to the next generation of worms, demonstrating a far-reaching effect of the miR-35-41 miRNAs on gene regulation by other small RNA pathways.
PMCID: PMC3297572  PMID: 22412382
16.  A Double-Stranded-RNA Response Program Important for RNA Interference Efficiency▿  
Molecular and Cellular Biology  2007;27(11):3995-4005.
When recognized by the RNA interference (RNAi) pathway, double-stranded RNA (dsRNA) produced in eukaryotic cells results in posttranscriptional gene silencing. In addition, dsRNA can trigger the interferon response as part of the immune response in vertebrates. In this study, we show that dsRNA, but not short interfering RNA (siRNA), induces the expression of qde-2 (an Argonaute gene) and dcl-2 (a Dicer gene), two central components of the RNAi pathway in the filamentous fungus Neurospora crassa. The induction of QDE-2 by dsRNA is required for normal gene silencing, indicating that this is a regulatory mechanism that allows the optimal function of the RNAi pathway. In addition, we demonstrate that Dicer proteins (DCLs) regulate QDE-2 posttranscriptionally, suggesting a role for DCLs or siRNA in QDE-2 accumulation. Finally, a genome-wide search revealed that additional RNAi components and homologs of antiviral and interferon-stimulated genes are also dsRNA-activated genes in Neurospora. Together, our results suggest that the activation of the RNAi components is part of a broad ancient host defense response against viral and transposon infections.
PMCID: PMC1900031  PMID: 17371837
17.  Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei 
Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in China and Southeast Asia. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less well studied and their potential roles in fungal dimorphism were largely unknown. Based on P. marneffei genome sequence, we hypothesize that miRNA-like RNAs (milRNAs) may be expressed in the dimorphic fungus.
Methodology/Principal Findings
We attempted to identify milRNAs in P. marneffei in both mycelial and yeast phase using high-throughput sequencing technology. Small RNAs were more abundantly expressed in mycelial than yeast phase. Sequence analysis revealed 24 potential milRNA candidates, including 17 candidates in mycelial and seven in yeast phase. Two genes, dcl-1 and dcl-2, encoding putative Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were identified in P. marneffei. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp., suggesting the co-evolution of dcl-2 among the thermal dimorphic fungi. Moreover, dcl-2 demonstrated higher mRNA expression levels in mycelial than yeast phase by 7 folds (P<0.001). Northern blot analysis confirmed the expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase. Using dcl-1KO, dcl-2KO, dclDKO and qde-2KO deletion mutants, we showed that the biogenesis of both milRNAs were dependent on dcl-2 but not dcl-1 or qde-2. The mRNA expression levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1KD, supporting regulatory function of milRNAs.
Our findings provided the first evidence for differential expression of milRNAs in different growth phases of thermal dimorphic fungi and shed light on the evolution of fungal proteins involved in milRNA biogenesis and possible role of post-transcriptional control in governing thermal dimorphism.
Author Summary
Penicillium marneffei is the most important thermal dimorphic pathogenic fungus in Southeast Asia. Despite findings on diverse genes and mechanisms involved in dimorphic switching, the key to signally pathways governing the switch is still unknown. Since miRNAs are important regulatory molecules in eukaryotes, we attempt to define if miRNAs are expressed in different growth phases of P. marneffei. Using high-throughput sequencing, we identified 24 potential milRNA candidates in P. marneffei, which were more abundantly expressed in mycelial than yeast phase. Two genes, dcl-1 and dcl-2, encoding Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were also identified. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp.. dcl-2 demonstrated higher mRNA levels in mycelial than yeast phase. Northern blot analysis confirmed expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase, whose expression was dependent on dcl-2 but not dcl-1 or qde-2. The mRNA levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1KD, supporting its regulatory function. This study represents the first discovery of milRNAs in thermal dimorphic fungi, with differential expression in different growth phases.
PMCID: PMC3749987  PMID: 23991243
18.  MicroRNAs that interfere with RNAi 
Worm  2013;2(1):e21835.
A recent study by Massirer et al. in the nematode C. elegans has shown that a family of microRNAs (miRNAs), miR-35-41, regulates the efficiency of RNA interference (RNAi), revealing a new connection between these small RNA pathways. In this commentary, we discuss the potential mechanisms for cross regulation in the miRNA and RNAi pathways and the implications for gene expression. While miRNAs are genetically encoded, the small interfering RNAs (siRNAs) that function in RNAi can originate from processing of exogenous dsRNA (exo-RNAi) or from the production of siRNAs from endogenous transcripts (endo-RNAi). These small RNA pathways involve Dicer and Argonaute proteins and typically use antisense base pairing to target mRNAs for downregulated expression. The discovery that loss of miR-35–41 results in enhanced exo-RNAi sensitivity and reduced endo-RNAi effectiveness suggests that these miRNAs normally help balance the RNAi pathways. The effect of mir-35–41 on RNAi is largely through lin-35, the C. elegans homolog of the tumor suppressor Retinoblastoma (Rb) gene. lin-35/Rb previously has been shown to regulate RNAi sensitivity through unclear mechanisms and the new finding that accumulation of LIN-35/Rb protein is dependent on miR-35–41 adds another layer of complexity to this process. The utilization of miRNAs to control the responsiveness of RNAi exemplifies the cross-regulation embedded in small RNA-directed pathways.
PMCID: PMC3670461  PMID: 24058860
C. elegans; RNAi; lin-35; miR-35-41; miRNA; retinoblastoma (Rb)
19.  RNA-Interference Components Are Dispensable for Transcriptional Silencing of the Drosophila Bithorax-Complex 
PLoS ONE  2013;8(6):e65740.
Beyond their role in post-transcriptional gene silencing, Dicer and Argonaute, two components of the RNA interference (RNAi) machinery, were shown to be involved in epigenetic regulation of centromeric heterochromatin and transcriptional gene silencing. In particular, RNAi mechanisms appear to play a role in repeat induced silencing and some aspects of Polycomb-mediated gene silencing. However, the functional interplay of RNAi mechanisms and Polycomb group (PcG) pathways at endogenous loci remains to be elucidated.
Principal Findings
Here we show that the endogenous Dicer-2/Argonaute-2 RNAi pathway is dispensable for the PcG mediated silencing of the homeotic Bithorax Complex (BX-C). Although Dicer-2 depletion triggers mild transcriptional activation at Polycomb Response Elements (PREs), this does not induce transcriptional changes at PcG-repressed genes. Moreover, Dicer-2 is not needed to maintain global levels of methylation of lysine 27 of histone H3 and does not affect PRE-mediated higher order chromatin structures within the BX-C. Finally bioinformatic analysis, comparing published data sets of PcG targets with Argonaute-2-bound small RNAs reveals no enrichment of these small RNAs at promoter regions associated with PcG proteins.
We conclude that the Dicer-2/Argonaute-2 RNAi pathway, despite its role in pairing sensitive gene silencing of transgenes, does not have a role in PcG dependent silencing of major homeotic gene cluster loci in Drosophila.
PMCID: PMC3681981  PMID: 23785447
20.  Targeting of Dicer-2 and RNA by a Viral RNA Silencing Suppressor in Drosophila Cells 
Journal of Virology  2012;86(10):5763-5773.
RNA interference (RNAi) is a eukaryotic gene-silencing mechanism that functions in antiviral immunity in diverse organisms. To combat RNAi-mediated immunity, viruses encode viral suppressors of RNA silencing (VSRs) that target RNA and protein components in the RNAi machinery. Although the endonuclease Dicer plays key roles in RNAi immunity, little is known about how VSRs target Dicer. Here, we show that the B2 protein from Wuhan nodavirus (WhNV), the counterpart of Flock House virus (FHV), suppresses Drosophila melanogaster RNAi by directly interacting with Dicer-2 (Dcr-2) and sequestering double-stranded RNA (dsRNA) and small interfering RNA (siRNA). Further investigations reveal that WhNV B2 binds to the RNase III and Piwi-Argonaut-Zwille (PAZ) domains of Dcr-2 via its C-terminal region, thereby blocking the activities of Dcr-2 in processing dsRNA and incorporating siRNA into the RNA-induced silencing complex (RISC). Moreover, we uncover an interrelationship among diverse activities of WhNV B2, showing that RNA binding enhances the B2–Dcr-2 interaction by promoting B2 homodimerization. Taken together, our findings establish a model of suppression of Drosophila RNAi by WhNV B2 targeting both Dcr-2 and RNA and provide evidence that an interrelationship exists among diverse activities of VSRs to antagonize RNAi.
PMCID: PMC3347268  PMID: 22438534
21.  Endogenous RNA interference is driven by copy number 
eLife  2014;3:e01581.
A plethora of non-protein coding RNAs are produced throughout eukaryotic genomes, many of which are transcribed antisense to protein-coding genes and could potentially instigate RNA interference (RNAi) responses. Here we have used a synthetic RNAi system to show that gene copy number is a key factor controlling RNAi for transcripts from endogenous loci, since transcripts from multi-copy loci form double stranded RNA more efficiently than transcripts from equivalently expressed single-copy loci. Selectivity towards transcripts from high-copy DNA is therefore an emergent property of a minimal RNAi system. The ability of RNAi to selectively degrade transcripts from high-copy loci would allow suppression of newly emerging transposable elements, but such a surveillance system requires transcription. We show that low-level genome-wide pervasive transcription is sufficient to instigate RNAi, and propose that pervasive transcription is part of a defense mechanism capable of directing a sequence-independent RNAi response against transposable elements amplifying within the genome.
eLife digest
Genes contain the codes that are needed to make the proteins used by cells. This code is transcribed to make a messenger RNA molecule that is then translated to make a protein. However, other types of RNA called non-coding RNA molecules can disrupt this process by binding to messenger RNA molecules, with matching sequences, before translation begins. This phenomenon, which is known as RNA interference, involves enzymes called Dicer and Argonaute.
Many cells contain large numbers of non-coding RNA molecules—so called because they are not translated to produce proteins—and many of these are capable of starting the process of RNA interference. However, most do not, and the reasons for this are not understood. Now, work by Cruz and Houseley has provided new insight into this phenomenon by showing that it is related to the number of copies of the gene encoding such RNAs in the genome.
Yeast cells normally do not have the genes for RNA interference, but Cruz and Houseley used genetically engineered yeast cells containing Dicer and Argonaute. Although most of the messenger RNA molecules in these cells showed no change, the expression of some genes with high ‘copy numbers’ was reduced. Further experiments that involved adding more and more copies of other genes showed that RNA interference could selectively target messenger RNA molecules produced from genes with an increased copy number—particularly if the copies of the genes were clustered in one location in the genome.
RNA interference is also used to defend against DNA sequences that invade and multiply within a genome, such as viruses and other ‘genetic parasites’. As such, the effect observed by Cruz and Houseley could explain why entire genomes are often continuously copied to RNA at low levels. This activity would allow the monitoring of the genome for the invasion of any genetic parasites that had multiplied to high numbers. Following on from this work, the next challenge will be to understand how gene copy number and location are balanced to achieve a selective RNA interference system.
PMCID: PMC3918874  PMID: 24520161
RNA interference; non-coding RNA; pervasive transcription; copy number; S. cerevisiae
22.  RNAi triggered by specialized machinery silences developmental genes and retrotransposons 
Nature  2012;493(7433):557-560.
RNAi is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats1,2. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. In the absence of the exosome, transcripts are processed preferentially by the RNAi machinery, revealing siRNA clusters and corresponding increase in heterochromatin modifications across large domains containing genes and retrotransposons. We show that the generation of siRNAs and heterochromatin assembly by RNAi is triggered by a mechanism involving the canonical poly(A) polymerase Pla1 and an associated RNA surveillance factor Red1, which also activate the exosome. Remarkably, siRNA production and heterochromatin modifications at these target loci are regulated by environmental growth conditions, and by developmental signals that induce gene expression during sexual differentiation. Our analyses uncover interplay between RNAi and the exosome that is conserved in higher eukaryotes, and show that differentiation signals modulate RNAi silencing to regulate developmental genes.
PMCID: PMC3554839  PMID: 23151475
23.  A Complex Small RNA Repertoire Is Generated by a Plant/Fungal-Like Machinery and Effected by a Metazoan-Like Argonaute in the Single-Cell Human Parasite Toxoplasma gondii 
PLoS Pathogens  2010;6(5):e1000920.
In RNA silencing, small RNAs produced by the RNase-III Dicer guide Argonaute-like proteins as part of RNA-induced silencing complexes (RISC) to regulate gene expression transcriptionally or post-transcriptionally. Here, we have characterized the RNA silencing machinery and exhaustive small RNAome of Toxoplasma gondii, member of the Apicomplexa, a phylum of animal- and human-infecting parasites that cause extensive health and economic damages to human populations worldwide. Remarkably, the small RNA-generating machinery of Toxoplasma is phylogenetically and functionally related to that of plants and fungi, and accounts for an exceptionally diverse array of small RNAs. This array includes conspicuous populations of repeat-associated small interfering RNA (siRNA), which, as in plants, likely generate and maintain heterochromatin at DNA repeats and satellites. Toxoplasma small RNAs also include many microRNAs with clear metazoan-like features whose accumulation is sometimes extremely high and dynamic, an unexpected finding given that Toxoplasma is a unicellular protist. Both plant-like heterochromatic small RNAs and metazoan-like microRNAs bind to a single Argonaute protein, Tg-AGO. Toxoplasma miRNAs co-sediment with polyribosomes, and thus, are likely to act as translational regulators, consistent with the lack of catalytic residues in Tg-AGO. Mass spectrometric analyses of the Tg-AGO protein complex revealed a common set of virtually all known RISC components so far characterized in human and Drosophila, as well as novel proteins involved in RNA metabolism. In agreement with its loading with heterochromatic small RNAs, Tg-AGO also associates substoichiometrically with components of known chromatin-repressing complexes. Thus, a puzzling patchwork of silencing processor and effector proteins from plant, fungal and metazoan origin accounts for the production and action of an unsuspected variety of small RNAs in the single-cell parasite Toxoplasma and possibly in other apicomplexans. This study establishes Toxoplasma as a unique model system for studying the evolution and molecular mechanisms of RNA silencing among eukaryotes.
Author Summary
Toxoplasma gondii is an important human parasite that causes life-threatening diseases in developing fetuses and in immunocompromised individuals, especially AIDS and transplant patients. Curiously, the Toxoplasma genome is deprived of most of the basic transcription factors that regulate gene expression in other eukaryotic cells. Therefore, alternative strategies must exist to modulate the many phases of the Toxoplasma complex life cycle that includes invasion of several hosts. Here, we investigate one of these strategies, by studying the repertoire of Toxoplasma silencing small RNAs (sRNAs). In eukaryotes, most of these regulatory molecules, 20–30nt-long, are produced by members of the Dicer RNase-III family, and exert their various functions through ubiquitous proteins called Argonaute (Ago). The surprising diversity of the Toxoplasma sRNAome uncovered in our study is consistent with those molecules exerting key functions during the parasite's life cycle, including, possibly, during virulent infection. The study also unravels an unsuspected level of complexity in the origin and mechanisms of action of the factors that generate and affect Toxoplasma sRNA, prompting a re-evaluation of our current views on RNA silencing in eukaryotes.
PMCID: PMC2877743  PMID: 20523899
24.  A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast 
Genome Biology  2014;15(10):481.
Heterochromatin plays important roles in the regulation and stability of eukaryotic genomes. Both heterochromatin components and pathways that promote heterochromatin assembly, including RNA interference, RNAi, are broadly conserved between the fission yeast Schizosaccharomyces pombe and humans. As a result, fission yeast has emerged as an important model system for dissecting mechanisms governing heterochromatin integrity. Thus far, over 50 proteins have been found to contribute to heterochromatin assembly at fission yeast centromeres. However, previous studies have not been exhaustive, and it is therefore likely that further factors remain to be identified.
To gain a more complete understanding of heterochromatin assembly pathways, we have performed a systematic genetic screen for factors required for centromeric heterochromatin integrity. In addition to known RNAi and chromatin modification components, we identified several proteins with previously undescribed roles in heterochromatin regulation. These included both known and newly characterised splicing-associated proteins, which are required for proper processing of centromeric transcripts by the RNAi pathway, and COP9 signalosome components Csn1 and Csn2, whose role in heterochromatin assembly can be explained at least in part by a role in the Ddb1-dependent degradation of the heterochromatin regulator Epe1.
This work has revealed new factors involved in RNAi-directed heterochromatin assembly in fission yeast. Our findings support and extend previous observations that implicate components of the splicing machinery as a platform for RNAi, and demonstrate a novel role for the COP9 signalosome in heterochromatin regulation.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0481-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4210515  PMID: 25274039
25.  Chromatin-associated RNAi components contribute to transcriptional regulation in Drosophila 
Nature  2011;480(7377):391-395.
RNAi pathways have evolved as important modulators of gene expression that act in the cytoplasm by degrading RNA target molecules via the activity of short (21-30nt) RNAs1-6 RNAi components have been reported to play a role in the nucleus as they are involved in epigenetic regulation and heterochromatin formation7-10. However, although RNAi-mediated post-transcriptional silencing (PTGS) is well documented, mechanisms of RNAi-mediated transcriptional gene silencing (TGS) and in particular the role of RNAi components in chromatin, especially in higher eukaryotes, are still elusive. Here we show that key RNAi components Dicer-2 (Dcr2) and and Argonaute-2 (AGO2) AGO2 associate with chromatin, with strong preference for euchromatic, transcriptionally active loci and interact with core transcription machinery. Notably Dcr2 and AGO2 loss of function show that transcriptional defects are accompanied by perturbation of Pol II positioning on promoters. Further, both Dcr2 and Ago2 null mutations as well as missense mutations compromising the RNAi activity impair global Pol II dynamics upon heat shock. Finally, AGO2 RIP-seq experiments reveal that, AGO2 is strongly enriched in small-RNAs encompassing promoter as well as other parts of heat shock and other gene loci on both sense and antisense, with a strong bias for antisense, particularly after heat shock. Taken together our results reveal a new scenario in which Dcr2 and AGO2 are globally associated with transcriptionally active loci and may play a pivotal role in shaping the transcriptome by controlling RNA Pol II processivity.
PMCID: PMC4082306  PMID: 22056986

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