Ribonucleoprotein complexes consisting of Argonaute-like proteins and small regulatory RNAs function in a wide range of biological processes. Many of these small regulatory RNAs are predicted to act, at least in part, within the nucleus. We conducted a genetic screen to identify factors essential for RNAi in nuclei of C. elegans and identified the Argonaute protein NRDE-3. In the absence of siRNAs NRDE-3 resides in the cytoplasm. NRDE-3 binds siRNAs generated by RNA-dependent RNA Polymerases acting upon mRNA templates in the cytoplasm and redistributes to the nucleus. Nuclear redistribution of NRDE-3 requires a functional nuclear localization signal, is required for nuclear RNAi, and results in NRDE-3 association with nuclear-localized nascent transcripts. Thus, specific Argonaute proteins can transport specific classes of small regulatory RNAs to distinct cellular compartments to regulate gene expression.To identify factors specifically required for RNAi in C. elegans nuclei, we chemically mutagenized worms and screened for mutant animals that failed to silence nuclear-localized RNAs in response to RNAi, but retained the ability to silence RNAs not localized exclusively in the nucleus (for details see Fig. S1). We identified 55 mutant alleles that were categorized into three complementation groups. Forty-six of these alleles defined a gene that we termed nuclear RNAi defective-3 (nrde-3). We mapped nrde-3 to a < 1 cM interval. Open reading frame (ORF) R04A9.2 lies within this genetic interval. R04A9.2 is predicted to encode an Argonaute-like protein containing a bipartite nuclear localization signal (NLS), a PAZ, and a PIWI domain. The PIWI domain of R04A9.2 lacks the DDH catalytic triad of amino acids considered necessary for Argonaute-based Slicer activity: the synonymous residues are EVQ in R04A9.2 (1). Sequencing of R04A9.2 from eight independent nrde-3 alleles identified seven mutations in R04A9.2 coding sequences (Fig. 1A). Three alleles are predicted to stop translation upstream of the PAZ/PIWI domains of R04A9.2 and thus are likely to reveal the null phenotype. Transformation of wild-type R04A9.2 DNA into nrde-3 mutant animals rescued phenotypes associated with nrde-3 mutant animals (Fig. 3B). Thus, R04A9.2 corresponds to nrde-3.A fusion gene between GFP and full-length NRDE-3 under control of the endogenous nrde-3 promoter (2) rescued

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.

In plants and fungi, small RNAs silence gene expression in the nucleus by establishing repressive chromatin states. The role of endogenous small RNAs in metazoan nuclei is largely unknown. Here we show that endogenous small interfering RNAs (endo-siRNAs) direct Histone H3 Lysine 9 methylation (H3K9me) in Caenorhabditis elegans. In addition, we report the identification and characterization of nuclear RNAi defective (nrde)-1 and nrde-4. Endo-siRNA–driven H3K9me requires the nuclear RNAi pathway including the Argonaute (Ago) NRDE-3, the conserved nuclear RNAi factor NRDE-2, as well as NRDE-1 and NRDE-4. Small RNAs direct NRDE-1 to associate with the pre-mRNA and chromatin of genes, which have been targeted by RNAi. NRDE-3 and NRDE-2 are required for the association of NRDE-1 with pre-mRNA and chromatin. NRDE-4 is required for NRDE-1/chromatin association, but not NRDE-1/pre-mRNA association. These data establish that NRDE-1 is a novel pre-mRNA and chromatin-associating factor that links small RNAs to H3K9 methylation. In addition, these results demonstrate that endo-siRNAs direct chromatin modifications via the Nrde pathway in C. elegans.

Introduction: The frequency of adverse events (AEs) is a widely used indicator of voluntary medical male circumcision (VMMC) programme quality. Though over 11.7 million male circumcisions (MCs) have been performed, little published data exists on the profile of AEs from mature, large-scale programmes. No published data exists on routine implementation of PrePex, a device-based MC method. Methods: The ZAZIC Consortium began implementing VMMC in Zimbabwe in 2013, supporting services at 36 facilities. Aggregate data on VMMC outputs are collected monthly from each facility. Detailed forms are completed describing the profile of each moderate and severe AE. Bivariate and multivariable analyses were conducted using log-binomial regression models. Results: From October 2014 through September 2015, 44,868 clients were circumcised with 156 clients experiencing a moderate or severe AE. 96.2% of clients had a follow-up visit within 14 days of their procedure. AEs were uncommon, with 0.3% (116/41,416) of surgical and 1.2% (40/3,452) of PrePex clients experiencing a moderate or severe AE. After adjusting for VMMC site, we found that PrePex was associated with a 3.29-fold (95% CI: 1.78–6.06) increased risk of experiencing an AE compared to surgical procedures. Device displacements, when the PrePex device is intentionally or accidentally dislodged during the 7-day placement period, accounted for 70% of PrePex AEs. The majority of device displacements were intentional self-removals. Overall, infection was the most common AE among VMMC clients. Compared to clients aged 20 and above, clients aged 10–14 were 3.07-fold (95% CI: 1.36–6.91) more likely to experience an infection and clients aged 15–19 were 1.80-fold (95% CI: 0.82–3.92) more likely to experience an infection, adjusted for site. Conclusions: This exploratory analysis found that clients receiving PrePex were more likely to experience an AE than surgical circumcision clients. This is largely attributable to the occurrence of device displacements, which require prompt access to corrective surgical MC procedures as part of their clinical management. Most device displacements were self-removals which are preventable if client behaviour could be modified through counselling interventions. We also found that infection after MC is more common among younger clients, who may benefit from additional counselling or increased parental involvement.

BackgroundRoutine Data Quality Assessments (RDQAs) were developed to measure and improve facility-level electronic medical record (EMR) data quality. We assessed if RDQAs were associated with improvements in data quality in KenyaEMR, an HIV care and treatment EMR used at 341 facilities in Kenya.MethodsRDQAs assess data quality by comparing information recorded in paper records to KenyaEMR. RDQAs are conducted during a one-day site visit, where approximately 100 records are randomly selected and 24 data elements are reviewed to assess data completeness and concordance. Results are immediately provided to facility staff and action plans are developed for data quality improvement. For facilities that had received more than one RDQA (baseline and follow-up), we used generalized estimating equation models to determine if data completeness or concordance improved from the baseline to the follow-up RDQAs.Results27 facilities received two RDQAs and were included in the analysis, with 2369 and 2355 records reviewed from baseline and follow-up RDQAs, respectively. The frequency of missing data in KenyaEMR declined from the baseline (31% missing) to the follow-up (13% missing) RDQAs. After adjusting for facility characteristics, records from follow-up RDQAs had 0.43-times the risk (95% CI: 0.32–0.58) of having at least one missing value among nine required data elements compared to records from baseline RDQAs. Using a scale with one point awarded for each of 20 data elements with concordant values in paper records and KenyaEMR, we found that data concordance improved from baseline (11.9/20) to follow-up (13.6/20) RDQAs, with the mean concordance score increasing by 1.79 (95% CI: 0.25–3.33).ConclusionsThis manuscript demonstrates that RDQAs can be implemented on a large scale and used to identify EMR data quality problems. RDQAs were associated with meaningful improvements in data quality and could be adapted for implementation in other settings.