{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T21:26:49Z","timestamp":1768512409954,"version":"3.49.0"},"posted":{"date-parts":[[2024,5,16]]},"group-title":"Developmental Biology","reference-count":89,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,5,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Regulation of transcription during embryogenesis is key to development and differentiation. To study transcript expression throughout\n                  <jats:italic>Caenorhabditis elegans<\/jats:italic>\n                  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\n                  <jats:italic>sdc-2<\/jats:italic>\n                  , a zygotically transcribed gene essential for hermaphrodite development and dosage compensation. We found that\n                  <jats:italic>sdc-2<\/jats:italic>\n                  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\n                  <jats:italic>sdc-2<\/jats:italic>\n                  and\n                  <jats:italic>dpy-27<\/jats:italic>\n                  , a subunit of the dosage compensation complex (DCC), increased the number of active transcription sites for the X chromosomal gene\n                  <jats:italic>dpy-23<\/jats:italic>\n                  but not the autosomal gene\n                  <jats:italic>mdh-1<\/jats:italic>\n                  , suggesting that the DCC reduces the frequency of\n                  <jats:italic>dpy-23<\/jats:italic>\n                  transcription. The temporal resolution from\n                  <jats:italic>in silico<\/jats:italic>\n                  staging of embryos showed that the deletion of a single DCC recruitment element near the\n                  <jats:italic>dpy-23<\/jats:italic>\n                  gene causes higher\n                  <jats:italic>dpy-23<\/jats:italic>\n                  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\n                  <jats:italic>C. elegans<\/jats:italic>\n                  embryogenesis and demonstrated its potential to provide new insights into developmental gene regulation.\n                <\/jats:p>","DOI":"10.1101\/2024.05.15.594414","type":"posted-content","created":{"date-parts":[[2024,5,16]],"date-time":"2024-05-16T21:10:29Z","timestamp":1715893829000},"source":"Crossref","is-referenced-by-count":0,"title":["Analysis of developmental gene expression using smFISH and\n                  <i>in silico<\/i>\n                  staging of\n                  <i>C. elegans<\/i>\n                  embryos"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7702-5749","authenticated-orcid":false,"given":"Laura","family":"Breimann","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6358-2576","authenticated-orcid":false,"given":"Ella","family":"Bahry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9441-2908","authenticated-orcid":false,"given":"Marwan","family":"Zouinkhi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Klim","family":"Kolyvanov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5473-6713","authenticated-orcid":false,"given":"Lena Annika","family":"Street","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0276-494X","authenticated-orcid":false,"given":"Stephan","family":"Preibisch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7297-1648","authenticated-orcid":false,"given":"Sevin\u00e7","family":"Ercan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2024052103050894000_2024.05.15.594414v1.1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0040309"},{"key":"2024052103050894000_2024.05.15.594414v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.07.025"},{"key":"2024052103050894000_2024.05.15.594414v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2014.05.053"},{"key":"2024052103050894000_2024.05.15.594414v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.01.027"},{"key":"2024052103050894000_2024.05.15.594414v1.5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0084301"},{"key":"2024052103050894000_2024.05.15.594414v1.6","doi-asserted-by":"publisher","DOI":"10.1126\/science.1216379"},{"key":"2024052103050894000_2024.05.15.594414v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyad142"},{"key":"2024052103050894000_2024.05.15.594414v1.8","doi-asserted-by":"publisher","DOI":"10.7554\/elife.56076"},{"key":"2024052103050894000_2024.05.15.594414v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2020.07.007"},{"key":"2024052103050894000_2024.05.15.594414v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.05.025"},{"key":"2024052103050894000_2024.05.15.594414v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0836-1"},{"key":"2024052103050894000_2024.05.15.594414v1.12","doi-asserted-by":"publisher","DOI":"10.1101\/gr.139378.112"},{"key":"2024052103050894000_2024.05.15.594414v1.13","doi-asserted-by":"publisher","DOI":"10.1126\/science.1198817"},{"key":"2024052103050894000_2024.05.15.594414v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2018.04.012"},{"key":"2024052103050894000_2024.05.15.594414v1.15","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2018100809"},{"key":"2024052103050894000_2024.05.15.594414v1.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2012.05.008"},{"key":"2024052103050894000_2024.05.15.594414v1.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2011.04.021"},{"key":"2024052103050894000_2024.05.15.594414v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2019.07.001"},{"key":"2024052103050894000_2024.05.15.594414v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/nature08781"},{"key":"2024052103050894000_2024.05.15.594414v1.20","doi-asserted-by":"publisher","DOI":"10.1242\/dev.120.2.443"},{"key":"2024052103050894000_2024.05.15.594414v1.21","doi-asserted-by":"publisher","DOI":"10.1242\/dev.00302"},{"key":"2024052103050894000_2024.05.15.594414v1.22","first-page":"2823","article-title":"Soma-germline 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