Biology subjects

van der Burght, S. N.

Publications and source records attributed to van der Burght, S. N..

4 recordsLinked to original sources

bioRxiv2026

An integrated pipeline to count individual transcripts with single-cell resolution

Quantifying transcript abundance at single-cell resolution is important for understanding gene regulation in intact multicellular organisms. In Caenorhabditis elegans, RNA fluorescence in situ hybridization has been widely used to visualize transcripts, but conventional smFISH approaches can be limited by low signal-to-noise, poor performance with short transcripts, and workflows that do not readily support absolute transcript counting in identified cells. Here, we present an integrated experimental and computational pipeline for quantitative transcript analysis in whole-mount C. elegans embryos, larvae, and adults. The pipeline combines Hybridization Chain Reaction (HCR), confocal microscopy, RS-FISH spot detection, manual cell annotation in FIJI, and custom MATLAB-based spot assignment to quantify individual transcripts within defined cells. We show that this approach enables sensitive, specific, and multiplexed detection of transcripts, including short insulin-like peptide mRNAs, with single-cell resolution. Known spatial expression patterns were resolved in embryos, larvae, and adults, and probe specificity was validated using deletion mutants that remove HCR probe-binding sites. Applying this pipeline to ins-4, ins-6, and daf-28 in ASI and ASJ sensory neurons revealed cell-specific and context-dependent regulatory relationships across multiple mutant backgrounds. This workflow provides an accessible method for absolute transcript counting in anatomically intact C. elegans and should support mechanistic studies of gene regulation, cellular heterogeneity, and transcriptional network function.

molecular biology↗

bioRxiv2024

A lineage-resolved multimodal single-cell atlas reveals the genomic dynamics of early C. elegans development

Multimodal single-cell profiling provides a powerful approach for unravelling the gene regulatory mechanisms that drive development, by simultaneously capturing cell-type- specific transcriptional and chromatin states. However, its inherently destructive nature hampers the ability to trace regulatory dynamics between mother and daughter cells. Taking advantage of the invariant cell lineage of Caenorhabditis elegans, we constructed a lineage- resolved single-cell multimodal map of pre-gastrulation development, which allows the tracing of chromatin and gene expression changes across cell divisions and regulatory cascades. We characterise the early dynamics of genome regulation, revealing that zygotic genome activation occurs on an accessible chromatin landscape pre-patterned both maternally and zygotically, and we identify a redundant family of transcriptional regulators that drive a transient pre-gastrulation program. Our findings demonstrate the power of a lineage-resolved atlas for dissecting the genome regulatory events of development.

genomics↗

bioRxiv2020

Mechanism of life-long maintenance of neuron identity despite molecular fluctuations

Cell fate is maintained over long timescales, yet molecular fluctuations can lead to spontaneous loss of this differentiated state. We uncovered a mechanism that explains life-long maintenance of ASE neuron fate in C. elegans by the terminal selector transcription factor CHE-1. Fluctuations in CHE-1 level are buffered by the reservoir of CHE-1 bound at its target promoters, which ensure continued che-1 expression by preferentially binding the che-1 promoter. We validated this mechanism by showing that che-1 expression was resilient to induced transient CHE-1 depletion, while both expression of CHE-1 targets and ASE function were lost. We identified a 130 bp che-1 promoter fragment responsible for this resilience, with deletion of a homeodomain binding site in this fragment causing stochastic loss of ASE identity long after its determination. Because network architectures that support this mechanism are highly conserved in cell differentiation, it may explain stable cell fate maintenance in many systems.

developmental biology↗

bioRxiv2019

Signaling compartment at the ciliary tip is formed and maintained by intraflagellar transport and functions as sensitive salt detector

Primary cilia are ubiquitous antenna-like organelles that mediate cellular signaling and represent hotspots for human diseases termed ciliopathies. How signaling subcompartments are established within the microtubule-based organelle, and for example support Hedgehog or cGMP signal transduction pathways, remains a central question. Here we show that a C. elegans salt-sensing receptor type guanylate cyclase, GCY-22, accumulates at a high concentration within the distal region of the cilium. This receptor uses DAF-25 (Ankmy2 in mammals) to cross the transition zone (TZ) membrane diffusion barrier in the proximal-most region of the ciliary axoneme. Targeting of GCY-22 to the ciliary tip is dynamic, requiring the cargo-mobilizing intraflagellar transport (IFT) system. Disruption of transit across the TZ barrier or IFT trafficking causes GCY-22 protein mislocalization and defects in the formation, maintenance, and function of the ciliary tip compartment required for chemotaxis to low NaCl concentrations. Together, our findings reveal how a previously undescribed cilium tip cGMP signaling compartment is established and contributes to the physiological function of a primary cilium.

cell biology↗