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R. Soc. B."],"published-print":{"date-parts":[[2024,6]]},"abstract":"<jats:p>\n            Regulating transcription allows organisms to respond to their environment, both within a single generation (plasticity) and across generations (adaptation). We examined transcriptional differences in gill tissues of fishes in the\n            <jats:italic>Poecilia mexicana<\/jats:italic>\n            species complex (family Poeciliidae), which have colonized toxic springs rich in hydrogen sulfide (H\n            <jats:sub>2<\/jats:sub>\n            S) in southern Mexico. There are gene expression differences between sulfidic and non-sulfidic populations, yet regulatory mechanisms mediating this gene expression variation remain poorly studied. We combined capped-small RNA sequencing (csRNA-seq), which captures actively transcribed (i.e. nascent) transcripts, and messenger RNA sequencing (mRNA-seq) to examine how variation in transcription, enhancer activity, and associated transcription factor binding sites may facilitate adaptation to extreme environments. csRNA-seq revealed thousands of differentially initiated transcripts between sulfidic and non-sulfidic populations, many of which are involved in H\n            <jats:sub>2<\/jats:sub>\n            S detoxification and response. Analyses of transcription factor binding sites in promoter and putative enhancer csRNA-seq peaks identified a suite of transcription factors likely involved in regulating H\n            <jats:sub>2<\/jats:sub>\n            S-specific shifts in gene expression, including several key transcription factors known to respond to hypoxia. Our findings uncover a complex interplay of regulatory processes that reflect the divergence of extremophile populations of\n            <jats:italic>P. mexicana<\/jats:italic>\n            from their non-sulfidic ancestors and suggest shared responses among evolutionarily independent lineages.\n          <\/jats:p>","DOI":"10.1098\/rspb.2024.0412","type":"journal-article","created":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T23:07:33Z","timestamp":1718752053000},"update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments"],"prefix":"10.1098","volume":"291","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4905-7852","authenticated-orcid":false,"given":"Blair W.","family":"Perry","sequence":"first","affiliation":[{"name":"Washington State University","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6388-3873","authenticated-orcid":true,"given":"Kerry L.","family":"McGowan","sequence":"additional","affiliation":[{"name":"Washington State University","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lenin","family":"Arias-Rodriguez","sequence":"additional","affiliation":[{"name":"Universidad Ju\u00e1rez Aut\u00f3noma de Tabasco","place":["M\u00e9xico"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sascha H.","family":"Duttke","sequence":"additional","affiliation":[{"name":"Washington State University","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Tobler","sequence":"additional","affiliation":[{"name":"University of Missouri\u2014St Louis","place":["USA"]},{"name":"University of Missouri\u2014St Louis","place":["USA"]},{"name":"WildCare Institute, Saint Louis Zoo","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7731-605X","authenticated-orcid":true,"given":"Joanna L.","family":"Kelley","sequence":"additional","affiliation":[{"name":"University of California Santa Cruz","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2024,6,19]]},"reference":[{"key":"e_1_3_8_2_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2019.0910"},{"key":"e_1_3_8_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msv263"},{"key":"e_1_3_8_4_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmars.2018.00349"},{"key":"e_1_3_8_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4873"},{"key":"e_1_3_8_6_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf9070"},{"key":"e_1_3_8_7_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.860134"},{"key":"e_1_3_8_8_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1090005"},{"key":"e_1_3_8_9_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.165.3891.349"},{"key":"e_1_3_8_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msv076"},{"key":"e_1_3_8_11_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1175826"},{"key":"e_1_3_8_12_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0507648103"},{"key":"e_1_3_8_13_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.193607.115"},{"key":"e_1_3_8_14_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1138341"},{"key":"e_1_3_8_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep12648"},{"key":"e_1_3_8_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-020-00315-9"},{"key":"e_1_3_8_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab443"},{"key":"e_1_3_8_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41556-019-0294-5"},{"key":"e_1_3_8_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2016.07.025"},{"key":"e_1_3_8_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/mec.14497"},{"key":"e_1_3_8_21_2","doi-asserted-by":"publisher","DOI":"10.1111\/evo.12133"},{"key":"e_1_3_8_22_2","unstructured":"Greenway R Brown AP Camarillo H Delich C McGowan KL Nelson J Arias-Rodriguez L Kelley JL Tobler M. 2021 Convergent adaptation and ecological speciation result from unique genomic mechanisms in sympatric extremophile fishes. bioRxiv 2021.06.28.450104. 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