Alex de Mendoza

A chimeric infection program and epigenetic conflict underpin endogenous giant virus latency

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

Integrative genomics of the siphonophore Physalia utriculus reveals the regulatory logic of colonial division of labour and the molecular basis of venom activity

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.

Pervasive co-option of prokaryotic adenine methyltransferases by eukaryotic retrotransposons

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

Adenine DNA methylation associated to transcription is widespread across eukaryotes

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.

Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type specific genes in choanoflagellates

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

Cytosine Methylation is a marker of Viral Gene Transfer across the eukaryotes

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.

Epigenetic silencing and host genome evolution determine fate of viral insertions in Acanthamoeba

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

Annelid methylomes reveal ancestral developmental and ageing-associated epigenetic erosion across Bilateria

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.

Global genomics of the man-o'-war (Physalia) reveals biodiversity at the ocean surface

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.

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

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).

Pervasive non-CpG methylation at zebrafish mosaic satellite repeats

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

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

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.