Purow-Ruderman, R. | bioRxiv Science

bioRxiv2025

The HMGN Proteins Are Transcriptional Regulatory Factors in Humans

The high mobility group N (HMGN) proteins, which were discovered over 50 years ago, are a multigene family of abundant nucleosome-specific binding factors that are present in all vertebrates. Despite their intriguing nucleosome-binding activity, the potential functions of the HMGN proteins in chromatin have not yet been assessed unambiguously due to the presence of several related HMGN genes in vertebrates and the lack of HMGN null cells. Here, we investigated the genome-wide activities of the human HMGN proteins by generating and analyzing an HMGN null cell line and isogenic HMGN rescue cell lines. These experiments revealed that the HMGN proteins function in the activation of gene expression at the level of transcription initiation at over a thousand specific sites that are mostly in promoters and enhancers. We additionally observed shared as well as unique functions of HMGN1 and HMGN2, which are likely to be the most abundant and ancient HMGN proteins. These findings thus indicate that the HMGN nucleosome-binding proteins are vertebrate-specific regulatory factors that primarily function in the activation of transcription initiation. Hence, any comprehensive model of vertebrate gene regulation should incorporate the contributions of the HMGN proteins, which are integral components of chromatin in all vertebrates.

molecular biology↗

bioRxiv2022

Extreme mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mitochondrial genomes and reconstruct phylogenies for comparisons to phylogenies inferred from 100s of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and >50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by recent and ancient introgressive hybridization and selection. We also found strong purifying selection across the mitochondrial genomes, cautioning their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mitochondrial genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mitochondrial genome assembly and adds to the growing knowledge of anthozoan evolution.

evolutionary biology↗