Biology subjects

Edwards, J. R.

Publications and source records attributed to Edwards, J. R..

3 recordsLinked to original sources

bioRxiv2018

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome

Pericentromeric satellite repeats are enriched in 5-methylcytosine (5mC). Loss of 5mC at these sequences is common in cancer and is a hallmark of Immunodeficiency, Centromere and Facial abnormalities (ICF) syndrome. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. To address this deficiency, we generated a viable animal model of pericentromeric hypomethylation through mutation of the ICF-gene ZBTB24. Deletion of zebrafish zbtb24 caused a progressive loss of 5mC at pericentromeres and ICF-like phenotypes. Hypomethylation of these repeats triggered derepression of pericentromeric transcripts and activation of an interferon-based innate immune response. Injection of pericentromeric RNA is sufficient to elicit this response in wild-type embryos, and mutation of the MDA5-MAVS dsRNA-sensing machinery blocks the response in mutants. These findings identify activation of the innate immune system as an early consequence of pericentromeric hypomethylation, implicating derepression of pericentromeric transcripts as a trigger of autoimmunity.

molecular biology↗

bioRxiv2018

A Novel in vivo Model of Anaerobic Infection: The Investigation of Clostridium perfringens in Galleria mellonella Larvae.

ABSTRACTImportant research progress into the mechanisms of Clostridium perfringens associated diseases (CPAD) has been slowed by the lack of a reliable infection model. Wax moth larvae (Galleria mellonella) have emerged as a viable alternative to traditional mammalian organisms since they are economic, survive at 37{degrees}C and require no specialist equipment. This study aims to establish whether G. mellonella larvae can be developed as a viable model for the study of CPAD and their suitability for studying novel treatment strategies. In addition, the study demonstrates a novel time-lapse approach to data collection. Mortality and morbidity rates of larvae challenged with 105 CFU of C. perfringens isolates from various sources were observed over 72h and dose response data obtained using inoculum sizes of 10 - 105 CFU. Phenoloxidase enzyme activity was investigated as a marker for immune response and tissue burden by histopathological techniques. Results show that C. perfringens is pathogenic towards G. mellonella although potency varies between isolates. Infection activates the melanisation pathway resulting in melanin deposition but no increase in enzyme activity was observed. Efficacy of antibiotic therapy (penicillin G, bacitracin, neomycin and tetracycline) administered parenterally loosely correlates with that of in vitro analysis. The findings suggest G. mellonella can be a useful in vivo model of infection when investigating CPAD. Although they are unlikely to replace traditional mammals they may be useful as a pre-screening assay for virulence of C.perfringens strains or as a simple, cheap and rapid in vivo assay in the development and pre-clinical development of novel therapeutics.\n\nHighlightsO_LINovel in vivo model for the study of Clostridium perfringens infection.\nC_LIO_LINovel time-lapse approach to data collection.\nC_LIO_LIFirst report of the use of G. mellonella model for characterizing virulence in C. perfringens strains.\nC_LIO_LIAntibiotic therapy in the model that loosely correlates with in vitro testing.\nC_LI

microbiology↗

bioRxiv2018

Integrative analysis of 5-methyl- and 5-hydroxymethylcytosine indicates a role for 5-hydroxymethylcytosine as a repressive epigenetic mark

Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA base modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the demethylation of 5-methylcytosine (5mC) and also in reactivation of silenced regulatory elements, including promoters and enhancers. Further, weak positive correlations have been observed between gene body 5hmC and gene expression. We previously demonstrated that ME-Class, which uses a high-resolution model of whole-genome bisulfite sequencing data, is an effective tool to understand relationships between 5mC and expression. In this work, we present ME-Class2, a machine-learning based tool to perform integrative 5mCG, 5hmCG and expression analysis. Using ME-Class2 we analyze whole-genome single-base resolution 5mC and 5hmC datasets from 20 primary tissue and cell samples to uncover relationships between 5hmC and expression. The addition of 5hmC improves model performance for tissues with high-levels of 5hmC such as the brain. Our analysis further indicates that conversion of 5mC to 5hmC within 2kb of the transcription start site associates with distinct functions depending on the summed level of 5mC + 5hmC. Unchanged levels of 5mC + 5hmC (i.e. conversion from 5mC to stable 5hmC) associate with repression. Meanwhile, decreases in 5mC + 5hmC (i.e. 5hmC-mediated demethylation) associate with gene activation. As more large-scale, genome-wide, differential DNA methylation studies become available, tools such as ME-Class2 will prove invaluable to interpret epigenomic data and guide mechanistic studies into the function of 5hmC.

bioinformatics↗