Comparative primate transcriptomics identifies a ZNF90/OVOL2 regulatory axis shaping human neural progenitor cell dynamics

Bastidas Betancourt, C. M.; Negretti Ingravallo, I.; Goeloglu, I. B.; Begenova, D.; Puig-Segui, M. S.; Mendes Costa, A.; Reshetar, M.; Heide, S.; Ivanov, M.; Veleva, L.; Kachovski, T.; Kovachev, E.; Tonchev, A.; Heide, M.

doi:10.64898/2026.07.27.740929

bioRxiv · 10.64898/2026.07.27.740929

Comparative primate transcriptomics identifies a ZNF90/OVOL2 regulatory axis shaping human neural progenitor cell dynamics

Bastidas Betancourt, C. M.·Negretti Ingravallo, I.·Goeloglu, I. B.·Begenova, D.·Puig-Segui, M. S.·Mendes Costa, A.·Reshetar, M.·Heide, S.·Ivanov, M.·Veleva, L.·Kachovski, T.·Kovachev, E.·Tonchev, A.·Heide, M.

View original source ↗Export metadata ↓

Abstract

Understanding the behavior of human neural progenitor cells (NPCs) requires comparative characterization of their transcriptomic landscape, particularly through comparisons with closely related primate species. The rhesus macaque represents a key non-hominoid outgroup for such analyses, and several representative transcriptomic datasets are now available. Here, we compare genes enriched in human NPCs with those enriched in rhesus macaque NPCs and found that human NPC-enriched genes are associated with gene programs supporting radial glial identity and proliferative capacity, as well as functions related to sister chromatid segregation. This analysis identified two zinc-finger transcription factors for functional investigation: the ape-specific ZNF90 and the highly conserved OVOL2. By analysing their genome-wide binding, transcriptional output, and cellular effects in cerebral organoids, we uncovered a previously uncharacterized regulatory axis with divergent but partially overlapping effects that converge on apical progenitor (AP) maintenance. Together, our findings support a model in which lineage-specific / evolutionarily young transcription factor become integrated into a conserved developmental gene regulatory network, generating novel NPC dynamics during primate corticogenesis.

Explore related subjects

developmental biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Bastidas Betancourt, C. M., Negretti Ingravallo, I., Goeloglu, I. B., Begenova, D., Puig-Segui, M. S., Mendes Costa, A., Reshetar, M., Heide, S., Ivanov, M., Veleva, L., Kachovski, T., Kovachev, E., Tonchev, A., Heide, M.. 2026-07-28. Comparative primate transcriptomics identifies a ZNF90/OVOL2 regulatory axis shaping human neural progenitor cell dynamics. https://doi.org/10.64898/2026.07.27.740929

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A bicistronic Aldh1a3-P2A-TagBFP knock-in reporter mouse line for studying genitourinary tract development

Aldehyde dehydrogenase 1a3 (Aldh1a3) is an enzyme involved in retinoic acid synthesis with dynamic expression patterns during development, including in the urogenital system. Here, we generated a bicistronic Aldh1a3-P2A-TagBFP knock-in mouse using CRISPR/Cas9 genome editing, inserting TagBFP immediately upstream of the endogenous Aldh1a3 stop codon. Correct targeting was confirmed by Oxford Nanopore long-read sequencing, and heterozygous and homozygous mice were viable and fertile without overt morphological abnormalities. TagBFP fluorescence faithfully overlapped with endogenous Aldh1a3 immunoreactivity and reproduced established expression domains in the developing craniofacial region, intestine, kidney, and broader urogenital system. Extensive characterization of the urogenital system revealed dynamic, spatially restricted BFP reporter activity in Aldh1a3-expressing domains across several key structures, including the ureteric bud and collecting duct lineage, seminal vesicles, caput epididymis, and developing uterine horns. The Aldh1a3-P2A-TagBFP mouse provides a fluorescent resource for visualizing Aldh1a3 expression across development and in adult tissues, including for the characterization of Aldh1a3-expressing domains in the urogenital system. The relatively low fluorescence intensity of TagBFP should be considered when assessing low-level reporter expression.

developmental biology↗

bioRxiv2026

Translation of a small upstream open reading frame functions as a rheostat for the regulation of lin-41 by the Let-7 microRNA in Caenorhabditis elegans

MicroRNAs have been likened to the "dark matter" of eukaryotic genomes, reflecting their pervasive regulatory influence. MicroRNAs were first identified through genetic studies of developmental timing in the nematode Caenorhabditis elegans. Let-7 was the first microRNA recognized to be broadly conserved. The principal target of Let-7 in the developmental timing pathway is the TRIM-NHL RNA-binding protein LIN-41. During the L4 larval stage, Let-7 represses lin-41 translation by binding to two Let-7 complementary sites in the lin-41 3'UTR. Despite the importance of microRNA-based translational regulation, the underlying molecular mechanisms are incompletely understood. Through genetic analysis, we discovered an unrecognized feature of the mechanism by which Let-7 controls lin-41 translation. This mechanism requires a 5'-regulatory exon containing a seven-amino acid upstream open reading frame (uORF) and conserved sequence elements. Genome editing indicates that the specific uORF amino acid sequence itself is not important. Our data suggest that uORF translation and 5'UTR structure limit initiation at the downstream lin-41 start codon, enabling tight control by Let-7. Without this mechanism, the Let-7 microRNA is unable to properly regulate lin-41 to enable proper development.

developmental biology↗

bioRxiv2026

Ductal myofibroblasts reactivate contractile program to stabilize alveolar architecture during lung regeneration

The alveolar sac architecture is essential for efficient gas exchange and must be precisely maintained throughout life; however, how this delicate structure is preserved during adult regeneration remains poorly understood. Using a mouse pneumonectomy model, we found that Lgr6+ Hhip+ ductal myofibroblasts, a poorly characterized mesenchymal population, are indispensable for maintaining alveolar integrity during lung regrowth. Comprehensive characterization using single-cell transcriptomics, mouse genetics, and pharmacological assays demonstrated that these ductal myofibroblasts secrete myogenic factors, most notably CCN4, to reactivate a myogenic program that converts them into contractile PA-DMFs, thereby preserving alveolar architecture. Lineage-tracing further revealed that these ductal myofibroblasts originate from embryonic MCAM- SMA+ distal progenitors via subepithelial TGF-{beta} signaling, serving as a lifelong guardian of alveolar structural integrity. Notably, cross-species analysis identified an analogous population of LGR6+ fibromyocytes in human respiratory bronchioles. Together, these findings indicate ductal myofibroblasts as a developmentally programmed cell population that reactivate a contractile program to structurally support the regeneration of adult lungs.

developmental biology↗