{"doi":"10.1101/2024.05.15.594414","title":"Analysis of developmental gene expression using smFISH and <i>in silico</i> staging of <i>C. elegans</i> embryos","abstract":"Abstract 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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":497677,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9607,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":750131,"name":"Ella Bahry","orcid":"0000-0002-6358-2576","position":2,"is_corresponding":false},{"id":805464,"name":"Marwan Zouinkhi","orcid":"0000-0002-9441-2908","position":3,"is_corresponding":false},{"id":806061,"name":"Klim Kolyvanov","orcid":null,"position":4,"is_corresponding":false},{"id":750128,"name":"Lena Annika Street","orcid":"0000-0002-5473-6713","position":5,"is_corresponding":false},{"id":52909,"name":"Stephan Preibisch","orcid":"0000-0002-0276-494X","position":6,"is_corresponding":false},{"id":23423,"name":"Sevinç Ercan","orcid":"0000-0001-7297-1648","position":8,"is_corresponding":false},{"id":750121,"name":"Laura Breimann","orcid":"0000-0001-7702-5749","position":0,"is_corresponding":true}],"reference_count":90,"raw_metadata":null,"created_at":"2026-07-19T02:09:34.764412Z","pmid":"38798598","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}