piRNAs (Piwi-interacting small RNAs) engage Piwi Argonautes to silence transposons and promote fertility in animal germlines. Genetic and computational studies have suggested that C. elegans piRNAs ...tolerate mismatched pairing and in principle could target every transcript. Here we employ in vivo cross-linking to identify transcriptome-wide interactions between piRNAs and target RNAs. We show that piRNAs engage all germline mRNAs and that piRNA binding follows microRNA-like pairing rules. Targeting correlates better with binding energy than with piRNA abundance, suggesting that piRNA concentration does not limit targeting. In mRNAs silenced by piRNAs, secondary small RNAs accumulate at the center and ends of piRNA binding sites. In germline-expressed mRNAs, however, targeting by the CSR-1 Argonaute correlates with reduced piRNA binding density and suppression of piRNA-associated secondary small RNAs. Our findings reveal physiologically important and nuanced regulation of individual piRNA targets and provide evidence for a comprehensive post-transcriptional regulatory step in germline gene expression.
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•PIWI CLASH identifies piRNA binding sites transcriptome-wide•piRNAs engage all germline mRNAs via microRNA-like pairing rules•piRNA target sites have distinct 22G-RNA patterns on silenced and expressed mRNAs•Targeting by CSR-1 Argonaute correlates with reduced piRNA binding density
Transcriptome-wide profiling of piRNA targeting rules provides new insights into the interplay between Argonaute pathways and their physiological roles in C. elegans
Animal cells have a remarkable capacity to adopt durable and heritable gene expression programs or epigenetic states that define the physical properties and diversity of somatic cell types. The ...maintenance of epigenetic programs depends on poorly understood pathways that prevent gain or loss of inherited signals. In the germline, epigenetic factors are enriched in liquid-like perinuclear condensates called nuage. Here, we identify the deeply conserved helicase-domain protein, ZNFX-1, as an epigenetic regulator and component of nuage that interacts with Argonaute systems to balance epigenetic inheritance. Our findings suggest that ZNFX-1 promotes the 3′ recruitment of machinery that propagates the small RNA epigenetic signal and thus counteracts a tendency for Argonaute targeting to shift 5′ along the mRNA. These functional insights support the idea that recently identified subdomains of nuage, including ZNFX-1 granules or “Z-granules,” may define spatial and temporal zones of molecular activity during epigenetic regulation.
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•Genetic identification of ZNFX-1, a conserved epigenetic inheritance factor•ZNFX-1 balances the transgenerational inheritance of epigenetic information•ZNFX-1 interacts with RdRP and three distinct Argonaute systems in germline nuage•ZNFX-1 promotes balanced amplification of small RNA signals along germline mRNAs
Ishidate et al. identify ZNFX-1, a highly conserved helicase protein, as a factor required for epigenetic inheritance in C. elegans. Their findings indicate that ZNFX-1 localizes within nuage, where it interacts with Argonaute systems and RNA-dependent RNA polymerase (RdRP) to ensure balanced amplification of small RNA signals along germline mRNAs.
GCNA proteins are expressed across eukarya in pluripotent cells and have conserved functions in fertility. GCNA homologs Spartan (DVC-1) and Wss1 resolve DNA-protein crosslinks (DPCs), including ...Topoisomerase-DNA adducts, during DNA replication. Here, we show that GCNA mutants in mouse and C. elegans display defects in genome maintenance including DNA damage, aberrant chromosome condensation, and crossover defects in mouse spermatocytes and spontaneous genomic rearrangements in C. elegans. We show that GCNA and topoisomerase II (TOP2) physically interact in both mice and worms and colocalize on condensed chromosomes during mitosis in C. elegans embryos. Moreover, C. elegans gcna-1 mutants are hypersensitive to TOP2 poison. Together, our findings support a model in which GCNA provides genome maintenance functions in the germline and may do so, in part, by promoting the resolution of TOP2 DPCs.
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•gcna-1 is essential for germline immortality and integrity of the heritable genome•GCNA works in tandem with Spartan (DVC-1) to maintain genomic integrity•GCNA promotes the resolution of TOP2 DPCs in the germline and early embryo in worms and mice
DNA topoisomerases help unwind DNA but occasionally get trapped, resulting in DNA-protein crosslinks (DPCs). DPCs damage DNA and threaten genomic integrity. Dokshin et al. find that GCNA protein family complements standard DPC processing machinery in resolving topoisomerase II DPCs to ensure heritable genome stability and germline immortality.
Germline Argonautes direct transcriptome surveillance within perinuclear membraneless organelles called nuage. In C. elegans, a family of Vasa-related Germ Line Helicase (GLH) proteins localize in ...and promote the formation of nuage. Previous studies have implicated GLH proteins in inherited silencing, but direct roles in small-RNA production, Argonaute binding, or mRNA targeting have not been identified. Here we show that GLH proteins compete with each other to control Argonaute pathway specificity, bind directly to Argonaute target mRNAs, and promote the amplification of small RNAs required for transgenerational inheritance. We show that the ATPase cycle of GLH-1 regulates direct binding to the Argonaute WAGO-1, which engages amplified small RNAs. Our findings support a dynamic and direct role for GLH proteins in inherited silencing beyond their role as structural components of nuage.
Klippel-Feil syndrome (KFS) is characterized by the developmental failure of the cervical spine and has two dominantly inherited subtypes. Affected individuals who are the children of a ...consanguineous marriage are extremely rare in the medical literature, but the gene responsible for this recessive trait subtype of KFS has recently been reported.
We identified a family with the KFS phenotype in which their parents have a consanguineous marriage. Radiological examinations revealed that they carry fusion defects and numerical abnormalities in the cervical spine, scoliosis, malformations of the cranial base, and Sprengel's deformity. We applied whole genome linkage and whole-exome sequencing analysis to identify the chromosomal locus and gene mutated in this family. Whole genome linkage analysis revealed a significant linkage to chromosome 17q12-q33 with a LOD score of 4.2. Exome sequencing identified the G > A p.Q84X mutation in the MEOX1 gene, which is segregated based on pedigree status. Homozygous MEOX1 mutations have reportedly caused a similar phenotype in knockout mice.
Here, we report a truncating mutation in the MEOX1 gene in a KFS family with an autosomal recessive trait. Together with another recently reported study and the knockout mouse model, our results suggest that mutations in MEOX1 cause a recessive KFS phenotype in humans.
Background
Vaginal reflux is a functional voiding disorder seen in prepubertal girls without anatomical or neurological abnormality. When not associated with urinary tract infections (UTI), ...asymptomatic bacteriuria, post-void dribbling or daytime enuresis it may be considered a normal finding.
Objective
To review the radiographic features of vesicovaginal reflux based on multiple imaging modalities.
Materials and methods
Three girls aged 11, 13 and 5 years were referred for pelvic US for daytime incontinence, post-void dribbling, frequency and urgency. One girl also had recurrent UTIs treated with antibiotics and was investigated for vesicoureteric reflux with US and voiding cystourethrogram (VCUG). All three were examined with MRI.
Results
Imaging appearance common to all three girls was a fluid-filled mass posterior to the bladder that disappeared after voiding. A previous VCUG in one girl had shown contrast medium refluxing into the vagina which disappeared after bladder emptying. Pelvic MRI confirmed the findings in all three girls.
Conclusion
US examination of a distended bladder followed by a post-void study easily provides the correct diagnosis of vesicovaginal reflux by identifying the vagina as the fluid-filled mass. Treatment involves behavioural modifications. Though well known to urologists, this may be a perplexing pathology for the inexperienced trainee radiologist.
Pulsed-field gel electrophoresis (PFGE) is the most common genotyping method used for the typing of a number of bacterial species. Generally, investigators use their own custom-developed protocol, ...but a standardized PFGE protocol would allow the comparison of typing results between laboratories and the tracing of strains around the country. In the present study, we optimized a PFGE protocol for subtyping of Acinetobacter baumannii, Escherichia coli and Klebsiella spp., which are commonly isolated from nosocomial infections in many hospitals. Reproducibility of our PFGE procedure was studied three times at 2- to 3-week intervals. Epidemiological concordance of the optimized PFGE procedure was tested on seven isolates of A. baumannii from a previous outbreak and seven A. baumannii isolates randomly selected among the clinical isolates. The optimized PFGE procedure was evaluated on a total of 174 clinical isolates including 62 A. baumannii, 50 E. coli, and 62 Klebsiella spp. The inter-laboratory reproducibility of the optimized protocol was tested at four laboratories. The optimized procedure is completed in 28 h after culturing. It is likely to be cost-effective, due to the reduction in the time, reagent volume and enzyme concentration needed. The procedure showed high concordance with epidemiological data. There were no non-typeable isolates among the tested bacteria. It is reproducible and versatile. This protocol can be used to identify outbreaks and monitor the spreading rate of nosocomial infections caused by the tested bacterial isolates. Furthermore, due to its high intra- and inter-laboratory reproducibility, the protocol has the potential to be useful for comparing PFGE fingerprinting profiles of the isolates from different settings.
Background
Overweight and obesity were recently associated with a poor prognosis in patients with autosomal dominant polycystic kidney disease (ADPKD). Whether the metabolic consequences of obesity ...as defined by the metabolic syndrome (MS) are also linked with disease progression remains untested.
Methods
Eligible ADPKD patients with different stages of CKD (
n
= 105) and 105 non-diabetic controls matched for CKD stage were enrolled in the study. Groups were evaluated at baseline for presence of MS, blood markers of metabolism, homeostasis model assessment of insulin resistance (HOMA-IR) score, and biochemical markers of inflammation (hs-CRP, IL-1β, IL-6, TNF-α and PON-1). MS was defined according to the National Cholesterol Education Program-Adult Treatment Panel III (NCEP-ATP III). Patients were followed for 12 months and progression defined as a decrease in baseline eGFR > 10%.
Results
MS and hypertension were more prevalent amongst ADPKD patients than in the control group. Meanwhile, markers of inflammation such as hs-CRP (3.63 3.45–5.17 vs. 4.2 3.45–8.99 mg/dL;
p
= 0.014), IL-6 (21.65 14.1–27.49 vs. 24.9 16.23–39.4 pg/mL;
p
= 0.004) and IL-1β (21.33 15.8–26.4 vs. 26.78 18.22–35 pg/mL;
p
< 0.001) levels were all more elevated in ADPKD patients than in non-diabetic CKD subjects. In multivariate analysis having a truncating
PKD1
mutation predicted (OR 1.25 1.09–1.43;
p
= 0.002) fulfilling the MS criteria. Finally, ADPKD patients fulfilling MS criteria had a significantly more rapid progression during 12 months of follow-up than did those that did not (OR 3.28 1.09–9.87;
p
= 0.035).
Conclusions
Our data supports the notion that dysmetabolisms part of the ADPKD phenotype and associated with a poor outcome, especially in patients with a truncating
PKD1
mutation.
Climate changes determined the repeated connections between the Black Sea, Caspian Sea and Mediterranean Sea. The landlocked anoxic Black Sea basin was exposed to several transgressions throughout ...Quaternary by the Mediterranean Sea through the Straits of Istanbul (Bosphorus) and by the Caspian Sea through the Manych-Kerch spillway. Sedimentological records of these connections are limited mostly to the marine terrace deposits of Marine Isotope Stage (MIS) 5e while the pre-MIS 5e period remains uncertain due to a lack of robust facies and chronological data from deep-sea sedimentary sequences. Here we discuss the imprints of multiple Mediterranean transgressions during Middle Pleistocene in the Black Sea based on facies analysis and the optical age of coastal carbonate aeolianites. Contrary to today's hydro-climate of the Black Sea, the aeolianites bear witness to the transformation of the Black Sea into a warm inland sea during successive Mediterranean invasions. Prior to the onset of aeolian deposition, paleosols were formed on the Eocene-aged hardened sandy silts, suggesting strongly washed soil. This is evidenced by no calcium carbonate and a high Rb/Sr ratio, with quartz amounting to of 99.8%. According to our OSL ages, carbonates deposited on the shelf plain under higher temperature and increased evaporation conditions in MIS 15 and the later interglacial phases were transported to the coastal sand dunes during the transitional phases of MIS 15–14, MIS 13–12, MIS 11–10 and MIS 9–8. We suggest that the carbonate-rich and ooid-containing aeolianites were repeatedly formed in the multiple Mediterranean transgression stages, beginning with an increasingly severe dry phase following the Brunhes-Matuyama magnetic reversal.
•The aeolianite is a robust record for Mediterranean transgressions of the Black Sea.•The ooid-rich aeolianites was repeatedly formed in multiple transgression stages.•The aeolianites bear witness to the transformation of the Black Sea into a warmer sea.
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