@article {69455,
	title = {Analysis of developmental gene expression using smFISH and in silico staging of C. elegans embryos},
	journal = {bioRxiv},
	year = {2024},
	month = {2024 May 16},
	abstract = {<p>Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout Caenorhabditis elegans embryogenesis at single-molecule resolution, we developed a high-throughput single-molecule fluorescence in situ hybridization (smFISH) method that relies on computational methods to developmentally stage embryos and quantify individual mRNA molecules in single embryos. We applied our system to sdc-2, a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that sdc-2 is rapidly activated during early embryogenesis by increasing both the number of mRNAs produced per transcription site and the frequency of sites engaged in transcription. Knockdown of sdc-2 and dpy-27, a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene dpy-23 but not the autosomal gene mdh-1, suggesting that the DCC reduces the frequency of dpy-23 transcription. The temporal resolution from in silico staging of embryos showed that the deletion of a single DCC recruitment element near the dpy-23 gene causes higher dpy-23 mRNA expression after the start of dosage compensation, which could not be resolved using mRNAseq from mixed-stage embryos. In summary, we have established a computational approach to quantify temporal regulation of transcription throughout C. elegans embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.</p>
},
	doi = {10.1101/2024.05.15.594414},
	url = {https://www.biorxiv.org/content/early/2024/05/16/2024.05.15.594414},
	author = {Breimann, Laura and Bahry, Ella and Zouinkhi, Marwan and Kolyvanov, Klim and Street, Lena Annika and Preibisch, Stephan and Ercan, Sevin{\c c}}
}
