Biology subjects

Fernandez-Moreno, M.

Publications and source records attributed to Fernandez-Moreno, M..

3 recordsLinked to original sources

bioRxiv2026

Pervasive co-option of prokaryotic adenine methyltransferases by eukaryotic retrotransposons

Cytosine DNA methylation is broadly associated with transposable element silencing across eukaryotes, whereas 6-methyladenine (6mA) in unicellular eukaryotes is linked to actively transcribed chromatin. How transposable elements adapt to these contrasting epigenetic environments remains largely unexplored. Here we identify widely distributed eukaryotic retrotransposons encoding prokaryotic-like DNA adenine methyltransferases (DAMs). Phylogenetic analyses indicate a single ancestral acquisition from prokaryotes followed by recurrent transfers between retrotransposon classes across diverse eukaryotes. DAM-carrying LTR elements are preferentially found in species encoding AMT1, the main eukaryotic 6mA methyltransferase, and show elevated 6mA levels relative to other LTR retrotransposons in multiple lineages, accompanied by increased transcription. We further identify retrotransposons combining adenine and cytosine methyltransferases with chromodomains, indicating the assembly of unexpectedly complex epigenetic toolkits within single retrotransposon units. These findings suggest that retrotransposons have repeatedly co-opted prokaryotic-like methyltransferases to exploit host 6mA-associated chromatin, highlighting adaptation to host epigenetic landscapes as a major driver of transposable element evolution.

genomics↗

bioRxiv2024

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes

Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two groups of taxa show contrasting trends in the molecular mechanisms of 3D chromatin organization and long-term evolutionary dynamics of cis-regulatory element (CREs) conservation. To help us identify shared versus derived features that could be responsible for the evolution of these different regulatory architectures in animals, we studied the evolution and organization of the regulatory genome of echinoderms, a lineage whose phylogenetic position and relatively slow molecular evolution has proven particularly useful for evolutionary studies. First, using PacBio and HiC data, we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the purple sea urchin Strongylocentrotus purpuratus and the bat sea star Patiria miniata. Second, we characterized their 3D chromatin architecture, identifying TAD-like domains in echinoderms that, like in flies, do not seem to be associated with CTCF motif orientation. Third, we systematically profiled CREs during sea star and sea urchin development using ATAC-seq, comparing their regulatory logic and dynamics over multiple developmental stages. Finally, we investigated sea urchin and sea star CRE evolution across multiple evolutionary distances and timescales, from closely related species to other echinoderm classes and deuterostome lineages. This showed the presence of several thousand elements conserved for hundreds of millions of years, revealing a vertebrate-like pattern of CRE evolution that probably constitutes an ancestral property of the regulatory evolution of animals.

evolutionary biology↗

bioRxiv2023

ROS-mediated TNFR Wengen activation in response to apoptosis

The activation of tumor necrosis factor receptors (TNFR) controls pleiotropic pro-inflammatory functions ranging from apoptosis to survival. The ability to trigger a particular function will depend on the upstream activation, association with regulatory complexes and downstream pathways. In Drosophila, two TNFRs have been identified, Wengen (Wgn) and Grindelwald (Grnd). Although several reports associate these receptors with JNK-dependent apoptosis, it has recently been found that Wgn activates a variety of functions. We demonstrate that Wgn is required for survival by protecting cells from apoptosis. This is mediated by the signaling molecule dTRAF1 and results in the activation of the p38 MAP kinase signaling pathway. Remarkably, Wgn is required for apoptosis-induced regeneration and is activated by the reactive oxygen species (ROS) produced following apoptosis. This ROS activation is exclusive for Wgn, but not for Grnd, and occurs in the absence of the ligand Eiger/TNF. Furthermore, based on protein sequence conservation, the extracellular Cys-rich domain of Grnd is much more divergent and phylogenetically restricted than that of Wgn, which is more similar to TNFR families from other animals, including those of human TNFRs. Taken together, our results show a novel function for a TNFR that responds to cellular damage by ensuring the cell survival required for the response to damage.

developmental biology↗