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We measured how acclimation shifts the upper thermal limit and profiled chromatin accessibility and gene expression in Drosophila melanogaster embryos using single-nucleus multiome sequencing. Acclimation preserved shared primordial cell types yet rapidly shifted heat tolerance. Cool-acclimated embryos showed a homeostatic response characterized by increased accessibility at binding motifs for the transcriptional activator Zelda, along with enhanced activity of gene regulatory networks in a subset of primordial cell types, including the gut, muscle and nervous system. Cool-acclimated embryos also had higher expression of ribosomal and oxidative phosphorylation genes, suggesting a coordinated increase in translation and energy production to buffer slower biochemical kinetics in the cold. Our results indicate that maintaining developmental robustness across temperature requires homeostatic gene expression responses that may carry metabolic costs constraining upper thermal limits.<\/jats:p>","DOI":"10.1242\/dev.205729","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T08:32:47Z","timestamp":1789374767000},"source":"Crossref","is-referenced-by-count":1,"title":["Single-nucleus multiome sequencing reveals the molecular basis of thermal acclimation in\n                    <i>Drosophila melanogaster<\/i>\n                    embryos"],"prefix":"10.1242","volume":"153","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5297-3777","authenticated-orcid":false,"given":"Thomas S.","family":"O'Leary","sequence":"first","affiliation":[{"name":"University of Vermont 1 Department of Biology , , Burlington, VT 05405 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1906-1247","authenticated-orcid":false,"given":"Emily E.","family":"Mikucki","sequence":"additional","affiliation":[{"name":"University of Vermont 1 Department of Biology , , Burlington, VT 05405 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3725-4157","authenticated-orcid":false,"given":"Sumaetee","family":"Tangwancharoen","sequence":"additional","affiliation":[{"name":"University of Vermont 1 Department of Biology , , Burlington, VT 05405 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8969-9676","authenticated-orcid":false,"given":"Joseph R.","family":"Boyd","sequence":"additional","affiliation":[{"name":"University of Vermont 2 Department of Biomedical and Health Sciences , , Burlington, VT 05401 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9531-400X","authenticated-orcid":false,"given":"Sara Helms","family":"Cahan","sequence":"additional","affiliation":[{"name":"University of Vermont 1 Department of Biology , , Burlington, VT 05405 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4058-3661","authenticated-orcid":false,"given":"Seth","family":"Frietze","sequence":"additional","affiliation":[{"name":"University of Vermont 2 Department of Biomedical and Health Sciences , , Burlington, VT 05401 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4694-5897","authenticated-orcid":false,"given":"Brent L.","family":"Lockwood","sequence":"additional","affiliation":[{"name":"University of Vermont 1 Department of Biology , , Burlington, VT 05405 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"key":"2026092904470040800_DEV205729C1","doi-asserted-by":"publisher","first-page":"8739","DOI":"10.1128\/MCB.01304-07","article-title":"Drosophila Blimp-1 is a transient transcriptional repressor that controls timing of the ecdysone-induced developmental pathway","volume":"27","author":"Agawa","year":"2007","journal-title":"Mol. 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