Biology subjects

Bermudez-Barrientos, J. R.

Publications and source records attributed to Bermudez-Barrientos, J. R..

3 recordsLinked to original sources

bioRxiv2025

A non-vesicular Argonaute protein is transmitted from nematode to mouse and is important for parasite survival

Argonautes are ancient proteins with well-characterised functions in cell-autonomous gene regulation and genome defense but less clear roles in non-cell-autonomous processes. Extracellular Argonautes have been reported across plants, animals and protozoa yet their biochemical and functional properties remain elusive. Here we demonstrate that an extracellular Argonaute (exWAGO) released by the rodent-infective parasitic nematode Heligmosomoides bakeri is detectable inside mouse cells during the natural infection. We further show that exWAGO is released from H.bakeri in both vesicular and non-vesicular forms that have different resistances to proteolysis, different accessibilities to antibodies and associate with different subsets of secondary siRNAs. Using recombinant exWAGO protein we demonstrate that non-vesicular exWAGO is directly internalised by mouse cells in vitro and that immunisation of mice with exWAGO confers partial protection against subsequent H. bakeri infection and generates antibodies that block exWAGO uptake into cells. Finally, we show that properties of exWAGO are conserved across Clade V nematodes that infect humans and livestock. Together this work expands the context in which Argonautes function and illuminates an RNA-binding protein as a vaccine target for parasitic nematodes.

molecular biology↗

bioRxiv2023

Respiratory syncytial virus directly binds miR-26, miR-27, and let-7 to de-repress gene targets through canonical and non-canonical mechanisms

microRNAs (miRNAs) regulate nearly all physiological processes but our understanding of exactly how they function remains incomplete, particularly in the context of viral infections. Here we adapt a biochemical method (CLEAR-CLIP) and analysis pipeline to identify targets of miRNAs in lung cells infected with Respiratory syncytial virus (RSV). We show that RSV binds directly to miR-26 and miR-27 through seed pairing and demonstrate that these miRNAs target distinct gene networks associated with cell cycle and metabolism (miR-27) and antiviral immunity (miR-26). Many of the targets are de-repressed upon infection and we show that the miR-27 targets most sensitive to miRNA inhibition are those associated with cell cycle. Finally, we demonstrate that high confidence chimeras for miR-26 and miR-27 also map to regulatory regions. We validate that a proportion of miR-27 and Argonaute 2 (AGO2) is nuclear in infected cells and identify a long non-coding RNA (lncRNA) as a miR-27 target that is linked to transcriptional regulation of nearby genes. This work expands the target networks of miR-26 and miR-27 to include direct interactions with RSV and lncRNAs and implicate these miRNAs in regulation of key genes that impact the viral life cycle associated with cell cycle, metabolism, and antiviral immunity.

molecular biology↗

bioRxiv2019

Disentangling sRNA-Seq data to study RNA communication between species

Many organisms exchange small RNAs during their interactions, and these RNAs can target or bolster defense strategies in host-pathogen systems. Current sRNA-Seq technology can determine the small RNAs present in any symbiotic system, but there are very few bioinformatic tools available to interpret the results. We show that one of the biggest challenges comes from sequences that map equally well to the genomes of both interacting organisms. This arises due to the small size of the sRNA compared to large genomes, and because many of the produced sRNAs come from genomic regions that encode highly conserved miRNAs, rRNAs or tRNAs. Here we present strategies to disentangle sRNA-Seq data from samples of communicating organisms, developed using diverse plant and animal species that are known to exchange RNA with their parasites. We show that sequence assembly, both de novo and genome-guided, can be used for sRNA-Seq data, greatly reducing the ambiguity of mapping reads. Even confidently mapped sequences can be misleading, so we further demonstrate the use of differential expression strategies to determine the true parasitic sRNAs within host cells. Finally, we validate our methods on new experiments designed to probe the nature of the extracellular vesicle sRNAs from the parasitic nematode H. bakeri that get into mouse epithelial cells.

bioinformatics↗