Alex de Mendoza

The paper investigates how a giant virus maintains latency in a green alga by analyzing its genomic architecture and epigenetic regulation.

This study presents a multi-omic atlas of the siphonophore Physalia utriculus, revealing the regulatory mechanisms of colonial division of labour and the molecular basis of venom activity.

This study identifies eukaryotic retrotransposons that encode prokaryotic-like DNA adenine methyltransferases and shows their adaptation to host 6mA-associated chromatin.

The paper profiles 6mA methylation in 18 eukaryotes and finds it is linked to transcription and associated with H3K4me3-enriched nucleosomes, but is lost in major multicellular lineages.

The paper identifies H3K27me3's dual role in regulating transposons and cell type-specific genes in choanoflagellates, suggesting ancestral chromatin mechanisms in development.

The paper investigates the evolutionary origins of DNA methylation, finding it was likely acquired from bacterial donors to silence transposable and viral elements across eukaryotes.

The paper investigates viral lateral gene transfer in Acanthamoeba, showing viral insertions are epigenetically silenced and subject to deterioration over time.

The paper analyzes methylomes in annelids to show ancestral epigenetic erosion during development and aging, with gene body methylation linked to transcription and TE silencing.

The paper shows that DNA methylation in Amoebidium appalachense silences endogenized giant viruses, contributing 14% of its genes and revealing a dynamic process of viral integration and purging.

The paper sequences 133 Physalia genomes and analyzes citizen-science images to reveal five distinct lineages and four species, with geographic population structure and long-distance dispersal.

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

The paper identifies pervasive non-CpG methylation at zebrafish mosaic satellite repeats, showing enrichment at TGCT positions in various tissues.

Forcing DNA methylation onto thousands of human promoters with a zinc finger-DNMT3A fusion often fails to repress them, and the mark is quickly erased at H3K4me3-marked promoters.