Cellular labeling of endogenous virus replication (CLEVR) reveals de novo insertions of the gypsy endogenous retrovirus in cell culture and in both neurons and glial cells of aging fruit flies

Chang, Y.-H.; Keegan, R. M.; Prazak, L.; Dubnau, J.

doi:10.1101/445221

Home/Archive/bioRxiv

bioRxiv · 10.1101/445221

Cellular labeling of endogenous virus replication (CLEVR) reveals de novo insertions of the gypsy endogenous retrovirus in cell culture and in both neurons and glial cells of aging fruit flies

Chang, Y.-H.·Keegan, R. M.·Prazak, L.·Dubnau, J.

View original source ↗Export metadata ↓

Abstract

Evidence is rapidly mounting that transposable element expression and replication may impact biology more widely than previously thought. This includes potential effects on normal physiology of somatic tissues and dysfunctional impacts in diseases associated with aging such as cancer and neurodegeneration. Investigation of the biological impact of mobile elements in somatic cells will be greatly facilitated by use of donor elements that are engineered to report de novo events in vivo. In multicellular organisms, successful reporters of LINE element mobilization have been in use for some time, but similar strategies have not been developed to report Long Terminal Repeat (LTR) retrotransposons and endogenous retroviruses. We describe Cellular Labeling of Endogenous Virus Replication (CLEVR), which reports replication of the gypsy element in Drosophila. The gypsy-CLEVR reporter reveals gypsy replication both in cell culture and in individual neurons and glial cells of the aging adult fly. We also demonstrate that the gypsy-CLEVR replication rate is increased when the short interfering RNA silencing system is genetically disrupted. This CLEVR strategy makes use of universally conserved features of retroviruses and should be widely applicable to other LTR-retrotransposons, endogenous retroviruses and exogenous retroviruses.

Source connections

Published article ↗

Explore related subjects

genetics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Chang, Y.-H., Keegan, R. M., Prazak, L., Dubnau, J.. 2018-10-16. Cellular labeling of endogenous virus replication (CLEVR) reveals de novo insertions of the gypsy endogenous retrovirus in cell culture and in both neurons and glial cells of aging fruit flies. https://doi.org/10.1101/445221

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Mapping, stacking and characterization of a novel resistance haplotype against GpaVvrn-virulent Globodera pallida derived from wild potato relative Solanum brevicaule

Potato production is threatened by pests and pathogens. Among the most harmful are the potato cyst nematodes (PCN), including Globodera pallida. The major control measures are potato cultivars harbouring resistance genes. However, virulent nematode populations are breaking through the most broadly applied resistance genes, and therefore novel resistance genes are required to keep control of G. pallida. In this study we map a resistance locus in wild potato relative Solanum brevicaule to the bottom of chromosome 11 (42.83 - 42.85 Mb) using a k-mer based bulked segregant analysis and name the resistant haplotype GpaXIbrc. The presence of the GpaXIbrc marker in the potato genome significantly increases resistance against a GpaVvrn-virulent G. pallida population (AMPOP01). Furthermore, the GpaXIbrc haplotype was stacked with three other resistance haplotypes: GpaXItar, GpaVvrn, and GpaIXvrn. Stacking of the novel GpaXIbrc haplotype to these other resistance haplotypes resulted in a significant increase in resistance. The largest effect was seen in combinations with 'major' resistance haplotypes GpaVvrn + GpaIXvrn and GpaXItar + GpaXIbrc. To determine whether we are dealing with a novel allele, the resistance mechanism underlying the GpaXIbrc haplotype was described after performing an in vitro bioassay. The resistance mechanism was different from GpaXIspl as described in literature, which is also localized at the bottom of chromosome 11. Therefore, we conclude that we found a novel resistance allele originating from S. brevicaule.

genetics↗

bioRxiv2026

Multiple domains of Mata1 transcription factor contribute to binding site specificity

Among homologous transcription factors with the same function, DNA-binding specificity can diverge. Mat1 is a high mobility group (HMG) box transcription factor in budding yeast whose Saccharomyces cerevisiae and Candida albicans homologs regulate -specific genes but bind distinct cis-regulatory sequences. To identify the protein features underlying this divergence, we generated structure-guided chimeras and measured their activity using species-specific reporters. Replacing any of the four Mat1 regions reduced activation of the S. cerevisiae reporter, while all chimeras retained activity on the C. albicans reporter. Thus, all four regions of Mat - not just the HMG box domain - are important for sequence specificity.

genetics↗

bioRxiv2026

A multi-tissue RNA-seq atlas of adult medaka (Oryzias latipes) under salinity and winter-summer sampling contrasts

Medaka (Oryzias latipes) is a euryhaline and eurythermal teleost widely used in genetics and environmental biology. We generated an RNA-sequencing atlas of 11 adult tissues (brain, eye, gill, heart, intestine, kidney, liver, muscle, spleen, ovary, testis) of the strain d-rR/TOKYO, sampled under two independent environmental contrasts: salinity (freshwater versus seawater) and season (winter versus summer). The freshwater and summer groups, reared indoors and outdoors under long days, provide a third contrast between laboratory and outdoor rearing. Typically, one male and one female were sampled per condition, with ten tissues taken from each individual. Ninety libraries were quantified against the medaka RefSeq transcript set (GCF_053564925.1). The resource comprises gene-level TPM and count matrices, differential expression tables for each tissue and contrast, tissue-specificity indices, human ortholog annotations, sample metadata, and a self-contained interactive browser. Because replication is limited and each condition was sampled on its own date, the differential expression tables are intended for hypothesis generation. The dataset supports studies of gene-expression plasticity and comparisons between medaka and humans.

genetics↗