RNA-Binding protein HuR and the members of miR-200 family play an unconventional role in the regulation of c-Jun mRNA

Post-transcriptional gene regulation is a fundamental step for coordinating cellular response in a variety of processes. RNA-binding proteins (RBPs) and microRNAs (miRNAs) are the most important factors responsible for this regulation. Here we report that different components of the miR-200 family are involved in c-Jun mRNA regulation with the opposite effect. While miR-200b inhibits c-Jun protein production, miR-200a tends to increase the JUN amount through a stabilization of its mRNA. This action is dependent on the presence of the RBP HuR that binds the 3′UTR of c-Jun mRNA in a region including the mir-200a binding site. The position of the binding site is fundamental; by mutating this site, we demonstrate that the effect is not micro-RNA specific. These results indicate that miR-200a triggers a microRNA-mediated stabilization of c-Jun mRNA, promoting the binding of HuR with c-Jun mRNA. This is the first example of a positive regulation exerted by a microRNA on an important oncogene in proliferating cells

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

Motivation: The discovery of CRISPR-Cas systems almost 20 years ago rapidly changed our perception of the bacterial and archaeal immune systems. CRISPR loci consist of several repetitive DNA sequences called repeats, inter-spaced by stretches of variable length sequences called spacers. This CRISPR array is transcribed and processed into multiple mature RNA species (crRNAs). A single crRNA is integrated into an interference complex, together with CRISPR-associated (Cas) proteins, to bind and degrade invading nucleic acids. Although existing bioinformatics tools can recognize CRISPR loci by their characteristic repeat-spacer architecture, they generally output CRISPR arrays of ambiguous orientation and thus do not determine the strand from which crRNAs are processed. Knowledge of the correct orientation is crucial for many tasks, including the classification of CRISPR conservation, the detection of leader regions, the identification of target sites (protospacers) on invading genetic elements and the characterization of protospacer-adjacent motifs. Results: We present a fast and accurate tool to determine the crRNA-encoding strand at CRISPR loci by predicting the correct orientation of repeats based on an advanced machine learning approach. Both the repeat sequence and mutation information were encoded and processed by an efficient graph kernel to learn higher-order correlations. The model was trained and tested on curated data comprising >4500 CRISPRs and yielded a remarkable performance of 0.95 AUC ROC (area under the curve of the receiver operator characteristic). In addition, we show that accurate orientation information greatly improved detection of conserved repeat sequence families and structure motifs. We integrated CRISPRstrand predictions into our CRISPRmap web server of CRISPR conservation and updated the latter to version 2.0. Availability: CRISPRmap and CRISPRstrand are available at http://rna.informatik.uni-freiburg.de/CRISPRmap. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Synthetic osmotic dilators (Dilapan-S) or dinoprostone vaginal inserts (Propess) for inpatient induction of labour: A UK cost-consequence model

To estimate the costs of synthetic osmotic dilators (Dilapan-S) compared to dinoprostone vaginal inserts (Propess) for inpatient induction of labour (IOL). A population-level, Markov model-based cost-consequence analysis was developed to compare the impact of using Dilapan-S versus Propess. The time horizon was modelled from admission to birth. The target population was women requiring inpatient IOL from 37 weeks with an unfavourable cervix in the UK. Mean population characteristics reflected those of the SOLVE (NCT03001661) trial. No patient data were included in this analysis. The care pathways and staff workload were modelled using data from the SOLVE trial and clinical experience. Cost and clinical inputs were sourced from the SOLVE trial and peer-reviewed literature. Costs were inflated to 2020 British pounds (GBP, £). Outcomes were reported as an average per woman for total costs and required staff time (minutes) from admission for IOL until birth. The model robustness was assessed using a probabilistic, multivariate sensitivity analysis of 2,000 simulations with results presented as the median (interquartile range, IQR). Dilapan-S was cost neutral compared to Propess. Midwife and obstetrician times were decreased by 146 min (-11%) and 11 min (-54%), respectively. Sensitivity analysis showed that in 78% of simulations, use of Dilapan-S reduced midwife time with a median of -160 min (IQR -277 to -24 min). Costs were reduced in 54% of simulations (median -£33, IQR -£319 to £282). The model indicates that adoption of Dilapan-S is likely to be cost-neutral and reduce staff workload in comparison to Propess. Results require support from real-world data and further exploration of Dilapan-S is to be encouraged. [Abstract copyright: Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections