Biology subjects

Varoqui, M.

Publications and source records attributed to Varoqui, M..

3 recordsLinked to original sources

bioRxiv2024

Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome

Transposable elements (TEs), widespread genetic parasites, pose potential threats to the stability of their host genomes. Hence, the interactions observed today between TEs and their host genomes, as well as among the different TE species coexisting in the same host, likely reflect those that did not lead to the extinction of either the host or the TEs. It is not clear to what extent the expression and integration steps of the TE replication cycles are involved in this peaceful coexistence. Here, we show that four Drosophila LTR RetroTransposable Elements (LTR-RTEs), although sharing the same overall integration mechanism, preferentially integrate into distinct open chromatin domains of the host germline. Notably, the differential expressions of the gtwin and ZAM LTR-RTEs in ovarian and embryonic somatic tissues, respectively, result in differential integration timings and targeting of accessible chromatin landscapes that differ between early and late embryonic nuclei, highlighting connections between temporal and spatial LTR-RTEs niche partitionings.

genomics↗

bioRxiv2024

Intricate interactions between antiviral immunity and transposable element control in Drosophila

Transposable elements (TEs) are parasite DNA sequences that are controlled by RNA interference pathways in many organisms. In insects, antiviral immunity is also achieved by the action of small RNAs. In the present study, we analyzed the impacts of an infection with Drosophila C Virus (DCV) and found that TEs are involved in a dual response: on the one hand TE control is released upon DCV infection, and on the other hand TE transcripts help the host reduce viral replication. This discovery highlights the intricate interactions in the arms race between host, genomic parasites, and viral pathogens. Significance statementTransposable elements (TEs) are widespread components of all genomes. They were long considered as mere DNA parasites but are now acknowledged as major sources of genetic diversity and phenotypic innovations. Using Drosophila C virus, here we show that TEs are at the center of defense and counter-attack between host and virus. On the one hand, TE control is released upon viral infection, and on the other hand, TE transcripts help the host reduce viral replication. To our knowledge, this is the first time such a complex host-pathogen interaction involving TEs is shown.

evolutionary biology↗

bioRxiv2022

TrEMOLO: Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches

Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using high- or low-quality genome assemblies, TrEMOLO can detect most TE insertions and deletions and estimate their allele frequency in populations. Benchmarking with simulated data revealed that TrEMOLO outperforms other state-of-the-art computational tools. TE detection and frequency estimation by TrEMOLO were validated using simulated and experimental datasets. Therefore, TrEMOLO is a comprehensive and suitable tool to accurately study TE dynamics. TrEMOLO is available under GNU GPL3.0 at https://github.com/DrosophilaGenomeEvolution/TrEMOLO.

bioinformatics↗