Biology subjects

Borgman, K. J. E.

Publications and source records attributed to Borgman, K. J. E..

3 recordsLinked to original sources

bioRxiv2026

An optimized workflow for spatial transcriptomics across early development in Xenopus

How gene expression patterns change spatially as the embryo transitions from simple to complex structures remains a major developmental biology question. Recently developed imaging-based spatial transcriptomics (ST) enable mapping expression of multiple gene at a single-cell resolution. Although Xenopus is a key model in embryology there is no established ST pipeline, and commercially available techniques face many challenges (sample preparation, probe design, cell segmentation). Furthermore, the highly diverse cell shapes and sizes across developmental stages and between different tissues represent major hurdles to accurately defining cells. Here, we describe an optimized workflow for ST in blastula-to-tailbud-stage frog embryos using Merscope, commercial MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization) originally designed for standard mammalian tissues. With stringent quality control and tailored computational pipelines, we optimize this technology for robust, semi-quantitative profiling of spatial transcriptomic landscapes in non-mammalian embryos. Reliable tissue preservation and cell-segmentation enable high-resolution mapping of gene expression during the development of a complex multi-tissue organization. This versatile strategy applies broadly to various dynamic systems, from embryos of various model organisms to complex and heterogeneous organs in mammals. Summary statementThis Single-cell Spatial Transcriptomics pipeline and reference atlas in Xenopus - a model organism in embryology - overcome technical challenges and resolve dynamic changes in patterning during development.

developmental biology↗

bioRxiv2025

Transcriptional coregulation in cis around a contact insulation site revealed by single-molecule microscopy

Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend to show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, where transcription occurs in sporadic bursts, transcriptional coordination has been observed between proximal genes, but how the local folding of mammalian chromosomes influences gene coregulation in cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent transcription from three adjacent genes located around a strong contact insulation site at the FOS locus, during the estrogen response in human breast cancer cells. To interpret this data, we developed two new analysis approaches to dissect the sources of (co)variation in gene activities: one to separate allele-extrinsic, allele-intrinsic, and gene-autonomous components; and another one to quantify the contributions of burst co-occurrence and burst size correlations. We find that transcriptional variability is largely gene-autonomous, yet correlations between genes display distinct patterns and occur almost exclusively in cis. Correlations are stronger between proximal and less insulated genes. However, unexpectedly, substantial correlations also occur across the strong insulation site and, under certain conditions, two proximal genes on the same side can exhibit uncorrelated burst occurrences. By disentangling burst co-occurrence from burst size correlations, we reveal transcriptional patterns suggesting two distinct coregulatory mechanisms influenced by local chromosome folding.

biophysics↗

bioRxiv2020

Membrane receptor MerTK is a newly identified transcriptional regulator that associates to chromatin as nanoclusters during human DC differentiation

MerTK is a transmembrane receptor tyrosine kinase (RTK) mainly expressed in dendritic cells (DCs) and macrophages where it plays an important role in immunotolerance, but also in activating oncogenic signalling pathways. Albeit MerTK is exploited as clinical target in cancer and auto-immune disorders, the mechanisms that regulate its diverse functions are poorly understood. Here, we identified a remarkably high pool of the full receptor in the nucleus of human DCs. Nuclear translocation was ligand-dependent. Importantly, MerTK nuclear levels correlated to DC differentiation and were spatiotemporally regulated by the transmembrane receptor LRP-1. Using dual-colour super-resolution nanoscopy we discovered that nuclear MerTK forms nanoclusters, whose strength strongly depends on chromatin accessibility during DC differentiation. We finally revealed high transcription capacity of MerTK. Overall, our work indicates that nuclear MerTK acts as a transcription factor regulating DC differentiation, thus implicating for the first time a physiological function for RTK nuclear translocation in immunity.

immunology↗