Rebl, A. | Search bioRxiv

bioRxiv2026

An integrative cardio-informatics approach identifies positionally conserved ancestors of human lncRNA genes transcribed across vertebrate hearts

The poor conservation of lncRNA genes limits their comprehensive functional studies, as genetic engineering of relevant animal models presupposes the presence of corresponding defined orthologs. This limitation is prominently evident in cardiovascular research, where heart-related lncRNAs are rarely conserved between humans and other vertebrates, despite the highly conserved nature of cardiac function. Because lncRNAs frequently regulate neighboring protein-coding genes essential for cardomyocyte function (herein termed cardiomyocyte indispensable, CMIs), we hypothesized that they are under evolutionary pressure to retain their genomic position and transcriptional activity, irrespective of sequence similarities to prototypical human lncRNA genes. By integrating mouse cardiac knockout phenotypes with human single-cell transcriptomics data, we systematically identified heart-expressed CMIs and their neighboring. lncRNA genes. Cross-species synteny analyses revealed regions flanking 109 CMIs with conserved relative positions and transcriptional orientations across vertebrate genomes. As most of these loci reside within poorly annotated non-coding regions, we developed VertLncRNAchecker, a neural network-based web interface, that predicts lncRNA-like genes within these regions, which we termed positional ancestors. Finally, we validated in situ that these positional ancestors express mature lncRNA transcripts in the hearts of mice, pigs, and frogs, mirroring the expression of their human lncRNA counterparts. We present an accurate and retrainable computational platform for cross-species lncRNA discovery that prioritizes conserved genomic position over sequence conservation or existing genome annotations. This pipeline revealed putative ancestors of human heart-related lncRNAs hidden within the vertebrate non-coding dark genome, providing novel insights into lncRNA biology and evolution.

evolutionary biology↗

bioRxiv2024

Immunological memory in a teleost fish: common carp IgM+ B cells differentiate into memory and plasma cells

From ancient cold-blooded fishes to mammals, all vertebrates are protected by adaptive immunity, and retain immunological memory. Although immunologists can demonstrate these phenomena in all fish, the responding cells remain elusive for lack of defining markers and tools to study them. Fundamentally, we posited that it is longevity that defines a memory cell like how antibody production defines a plasma cell. We infected the common carp with Sphaerospora molnari, a cnidarian parasite which causes seasonal outbreaks to which no vaccine is available. B cells proliferated and expressed gene signatures of differentiation. Despite a half-year gap between EdU labeling and sampling, B cells retained the thymidine analogue, suggesting that these are at least six-month-old resting memory cells stemming from proliferating precursors. Additionally, we identified a lymphoid organ-resident population expressing exceptional levels of IgM as plasma cells. Thus, teleost fish produce the lymphocytes key to vaccination success and long-term disease protection, and immunological memory is universal and universally demonstrable.

immunology↗