{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T20:58:24Z","timestamp":1790801904187,"version":"4.1.0"},"reference-count":103,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T00:00:00Z","timestamp":1699228800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["AGL2015-73864-JIN"],"award-info":[{"award-number":["AGL2015-73864-JIN"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["2PID2020-113781RB-I00"],"award-info":[{"award-number":["2PID2020-113781RB-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["PID2019-108888RB-I00"],"award-info":[{"award-number":["PID2019-108888RB-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["02030E004"],"award-info":[{"award-number":["02030E004"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["CEX2019-000928-S"],"award-info":[{"award-number":["CEX2019-000928-S"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003339","name":"Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","doi-asserted-by":"publisher","award":["AGL2015-73864-JIN"],"award-info":[{"award-number":["AGL2015-73864-JIN"]}],"id":[{"id":"10.13039\/501100003339","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003339","name":"Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","doi-asserted-by":"publisher","award":["2PID2020-113781RB-I00"],"award-info":[{"award-number":["2PID2020-113781RB-I00"]}],"id":[{"id":"10.13039\/501100003339","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003339","name":"Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","doi-asserted-by":"publisher","award":["PID2019-108888RB-I00"],"award-info":[{"award-number":["PID2019-108888RB-I00"]}],"id":[{"id":"10.13039\/501100003339","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003339","name":"Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","doi-asserted-by":"publisher","award":["02030E004"],"award-info":[{"award-number":["02030E004"]}],"id":[{"id":"10.13039\/501100003339","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003339","name":"Consejo Superior de Investigaciones Cient\u00edficas (CSIC)","doi-asserted-by":"publisher","award":["CEX2019-000928-S"],"award-info":[{"award-number":["CEX2019-000928-S"]}],"id":[{"id":"10.13039\/501100003339","id-type":"DOI","asserted-by":"publisher"}]},{"name":"\u2018Severo Ochoa Centre of Excellence accreditation","award":["AGL2015-73864-JIN"],"award-info":[{"award-number":["AGL2015-73864-JIN"]}]},{"name":"\u2018Severo Ochoa Centre of Excellence accreditation","award":["2PID2020-113781RB-I00"],"award-info":[{"award-number":["2PID2020-113781RB-I00"]}]},{"name":"\u2018Severo Ochoa Centre of Excellence accreditation","award":["PID2019-108888RB-I00"],"award-info":[{"award-number":["PID2019-108888RB-I00"]}]},{"name":"\u2018Severo Ochoa Centre of Excellence accreditation","award":["02030E004"],"award-info":[{"award-number":["02030E004"]}]},{"name":"\u2018Severo Ochoa Centre of Excellence accreditation","award":["CEX2019-000928-S"],"award-info":[{"award-number":["CEX2019-000928-S"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Rearing density directly impacts fish welfare, which, in turn, affects productivity in aquaculture. Previous studies have indicated that high-density rearing during sexual development in fish can induce stress, resulting in a tendency towards male-biased sex ratios in the populations. In recent years, research has defined the relevance of the interactions between the environment and epigenetics playing a key role in the final phenotype. However, the underlying epigenetic mechanisms of individuals exposed to confinement remain elucidated. By using zebrafish (Danio rerio), the DNA methylation promotor region and the gene expression patterns of six genes, namely dnmt1, cyp19a1a, dmrt1, cyp11c1, hsd17b1, and hsd11b2, involved in the DNA maintenance methylation, reproduction, and stress were assessed. Zebrafish larvae were subjected to two high-density conditions (9 and 66 fish\/L) during two periods of overlapping sex differentiation of this species (7 to 18 and 18 to 45 days post-fertilization, dpf). Results showed a significant masculinization in the populations of fish subjected to high densities from 18 to 45 dpf. In adulthood, the dnmt1 gene was differentially hypomethylated in ovaries and its expression was significantly downregulated in the testes of fish exposed to high-density. Further, the cyp19a1a gene showed downregulation of gene expression in the ovaries of fish subjected to elevated density, as previously observed in other studies. We proposed dnmt1 as a potential testicular epimarker and the expression of ovarian cyp19a1a as a potential biomarker for predicting stress originated from high densities during the early stages of development. These findings highlight the importance of rearing densities by long-lasting effects in adulthood conveying cautions for stocking protocols in fish hatcheries.<\/jats:p>","DOI":"10.3390\/ijms242116002","type":"journal-article","created":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T08:15:56Z","timestamp":1699258556000},"page":"16002","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Exploring the Effects of Rearing Densities on Epigenetic Modifications in the Zebrafish Gonads"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6653-1491","authenticated-orcid":false,"given":"Alejandro","family":"Valdivieso","sequence":"first","affiliation":[{"name":"IHPE, Universit\u00e9 de Montpellier, CNRS, IFREMER, Universit\u00e9 de Perpignan Via Domitia, 34090 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2616-1094","authenticated-orcid":false,"given":"Marta","family":"Caballero-Huertas","sequence":"additional","affiliation":[{"name":"CIRAD, UMR ISEM, 34398 Montpellier, France"},{"name":"ISEM, Universit\u00e9 de Montpellier, CIRAD, CNRS, IRD, EPHE, 34090 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4857-3126","authenticated-orcid":false,"given":"Javier","family":"Moraleda-Prados","sequence":"additional","affiliation":[{"name":"Institut de Ci\u00e8ncies del Mar, Consejo Superior de Investigaciones Cient\u00edficas (ICM-CSIC), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0903-4736","authenticated-orcid":false,"given":"Francesc","family":"Piferrer","sequence":"additional","affiliation":[{"name":"Institut de Ci\u00e8ncies del Mar, Consejo Superior de Investigaciones Cient\u00edficas (ICM-CSIC), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5538-6236","authenticated-orcid":false,"given":"Laia","family":"Ribas","sequence":"additional","affiliation":[{"name":"Institut de Ci\u00e8ncies del Mar, Consejo Superior de Investigaciones Cient\u00edficas (ICM-CSIC), 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,11,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1111\/jfb.13377","article-title":"Stress and welfare in ornamental fishes: What can be learned from aquaculture?","volume":"91","author":"Stevens","year":"2017","journal-title":"J. Fish Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1204021","DOI":"10.3389\/fnbeh.2023.1204021","article-title":"Optimizing zebrafish rearing\u2212Effects of fish density and environmental enrichment","volume":"17","author":"Sarma","year":"2023","journal-title":"Front. Behav. Neurosci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"5394","DOI":"10.2527\/jas.2014-8266","article-title":"Economic values of growth and feed efficiency for fish farming in recirculating aquaculture system with density and nitrogen output limitations: A case study with African catfish (Clarias gariepinus)","volume":"92","author":"Besson","year":"2014","journal-title":"J. Anim. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1007\/s10695-020-00905-6","article-title":"High stocking density alters growth performance, blood biochemical profiles, and hepatic antioxidative capacity in gibel carp (Carassius gibelio)","volume":"47","author":"Onxayvieng","year":"2021","journal-title":"Fish Physiol. Biochem."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1210\/jcem-6-2-117","article-title":"The general adaptation syndrome and the diseases of adaptation1","volume":"6","author":"Selye","year":"1946","journal-title":"J. Clin. Endocrinol. Metab."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/S1095-6433(98)10027-2","article-title":"Immunological suppression in gilthead sea bream Sparus aurata of the North-West Mediterranean at low temperatures","volume":"120","author":"Tort","year":"1998","journal-title":"Comp. Biochem. Physiol. Part A Mol. Integr. Physiol."},{"key":"ref_7","first-page":"1","article-title":"Stress, burnout and coping in health professionals: A literature review","volume":"1","author":"Costa","year":"2017","journal-title":"J. Psychol. Brain Stud."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"737152","DOI":"10.1016\/j.aquaculture.2021.737152","article-title":"Effect of different stocking densities on fish growth performance: A me-ta-analysis","volume":"544","author":"Li","year":"2021","journal-title":"Aquaculture"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"245","DOI":"10.20506\/rst.33.1.2285","article-title":"Pain and stress responses in farmed fish","volume":"33","author":"Braithwaite","year":"2014","journal-title":"Rev. Sci. Tech."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1387\/ijdb.200072jf","article-title":"Stress and sex determination in fish: From brain to gonads","volume":"65","author":"Fernandino","year":"2021","journal-title":"Int. J. Dev. Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1210\/edrv-17-1-64","article-title":"Immune-neuro-endocrine interactions: Facts and hypotheses","volume":"17","author":"Besedovsky","year":"1996","journal-title":"Endocr. Rev."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.cbpb.2003.11.007","article-title":"The brain\u2013pituitary\u2013gonad axis in male teleosts, with special emphasis on flatfish (Pleuronectiformes)","volume":"137","author":"Weltzien","year":"2004","journal-title":"Comp. Biochem. Physiol. Part A Mol. Integr. Physiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e12590","DOI":"10.1111\/jne.12590","article-title":"Emerging insights into hypothalamic-pituitary-gonadal axis regulation and interaction with stress signalling","volume":"30","author":"Kauffman","year":"2018","journal-title":"J. Neuroendocr."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1159\/000223077","article-title":"Environmental Effects on Fish Sex Determination and Differentiation","volume":"3","author":"Baroiller","year":"2009","journal-title":"Sex. Dev."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Ospina-\u00c1lvarez, N., and Piferrer, F. (2008). Temperature-Dependent Sex Determination in Fish Revisited: Prevalence, a Single Sex Ratio Response Pattern, and Possible Effects of Climate Change. PLoS ONE, 3.","DOI":"10.1371\/journal.pone.0002837"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1093\/jhered\/esab006","article-title":"Sex Ratios in a Warming World: Thermal Effects on Sex-Biased Survival, Sex Determination, and Sex Reversal","volume":"112","author":"Edmands","year":"2021","journal-title":"J. Hered."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"4223","DOI":"10.1007\/s00018-020-03532-9","article-title":"Activation of stress response axis as a key process in environment-induced sex plasticity in fish","volume":"77","author":"Hattori","year":"2020","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1163\/156853984X00542","article-title":"The effects of bidirectional selection for social dominance on agonistic behavior and sex ratios in the paradise fish (Macropodus opercularis)","volume":"90","author":"Francis","year":"1984","journal-title":"Behaviour"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1093\/beheco\/5.4.375","article-title":"Density-dependent protogynous sex change in territorial-haremic fishes: Models and evidence","volume":"5","author":"Lutnesky","year":"1994","journal-title":"Behav. Ecol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"4369","DOI":"10.1038\/srep04369","article-title":"Testing the Low-density Hypothesis for Reversed Sex Change in Polygynous Fish: Experiments in Labroides dimidiatus","volume":"4","author":"Kuwamura","year":"2014","journal-title":"Sci. Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1111\/j.1439-0426.1997.tb00112.x","article-title":"Influence of stocking density of European eel (Anguilla anguilla, L.) elvers on sex differentiation and zootechnical performances","volume":"13","author":"Roncarati","year":"1997","journal-title":"J. Appl. Ichthyol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1023\/A:1007575600789","article-title":"Evidence for environmental sex determination in the American eel, Anguilla rostrata","volume":"55","author":"Krueger","year":"1999","journal-title":"Environ. Biol. Fishes"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"286","DOI":"10.2307\/4134550","article-title":"Stocking density at early developmental stages affects growth and sex ratio in the European eel (Anguilla anguilla)","volume":"211","author":"Huertas","year":"2006","journal-title":"Biol. Bull."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0044-8486(02)00539-2","article-title":"Effects of rearing density, size grading and parental factors on sex ratios of the sea bass (Dicentrarchus labrax L.) in intensive aquaculture","volume":"221","author":"Saillant","year":"2003","journal-title":"Aquaculture"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"13620","DOI":"10.1038\/s41598-021-93116-9","article-title":"Parental selection for growth and early-life low stocking density increase the female-to-male ratio in European sea bass","volume":"11","author":"Geffroy","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Hazlerigg, C.R.E., Lorenzen, K., Thorbek, P., Wheeler, J.R., and Tyler, C.R. (2012). Density-Dependent Processes in the Life History of Fishes: Evidence from Laboratory Populations of Zebrafish Danio rerio. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0037550"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"E941","DOI":"10.1073\/pnas.1609411114","article-title":"Heat-induced masculinization in domesticated zebrafish is family-specific and yields a set of different gonadal transcriptomes","volume":"114","author":"Ribas","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s10126-006-5139-0","article-title":"Learning from small fry: The zebrafish as a genetic model organism for aquaculture fish spe-cies","volume":"8","author":"Dahm","year":"2006","journal-title":"Mar. Biotechnol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1111\/raq.12041","article-title":"The zebrafish (Danio rerio) as a model organism, with emphasis on applications for finfish aquaculture research","volume":"6","author":"Ribas","year":"2014","journal-title":"Rev. Aquac."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/bs.fp.2020.10.003","article-title":"The use of the zebrafish as a model in fish aquaculture research","volume":"38","author":"Piferrer","year":"2020","journal-title":"Fish Physiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1080\/10641260802324644","article-title":"Fish Gonadogenesis. Part II: Molecular Biology and Genomics of Sex Differentiation","volume":"16","author":"Piferrer","year":"2008","journal-title":"Rev. Fish. Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.mce.2009.04.014","article-title":"Long and winding roads: Testis differentiation in zebrafish","volume":"312","author":"Orban","year":"2009","journal-title":"Mol. Cell. Endocrinol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Chen, W., and Ge, W. (2012). Ontogenic Expression Profiles of Gonadotropins (fshb and lhb) and Growth Hormone (gh) During Sexual Differentiation and Puberty Onset in Female Zebrafish1. Biol. Reprod., 86.","DOI":"10.1095\/biolreprod.111.094730"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1002\/mrd.22172","article-title":"Gonad differentiation and puberty onset in the zebrafish: Evidence for the dependence of puberty onset on body growth but not age in females","volume":"80","author":"Chen","year":"2013","journal-title":"Mol. Reprod. Dev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.aquaculture.2012.09.022","article-title":"The effects of feeding frequency on growth and reproduction in zebrafish (Danio rerio)","volume":"368","author":"Lawrence","year":"2012","journal-title":"Aquaculture"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Liew, W.C., Bartfai, R., Lim, Z., Sreenivasan, R., Siegfried, K.R., and Orban, L. (2012). Polygenic Sex Determination System in Zebrafish. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0034397"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1534\/genetics.114.169284","article-title":"Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains","volume":"198","author":"Wilson","year":"2014","journal-title":"Genetics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1111\/1755-0998.13725","article-title":"Development of epigenetic biomarkers for the identification of sex and thermal stress in fish using DNA methylation analysis and machine learning procedures","volume":"23","author":"Valdivieso","year":"2022","journal-title":"Mol. Ecol. Resour."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/S1095-6433(03)00178-8","article-title":"An aromatase inhibitor or high water temperature induce oocyte apoptosis and depletion of P450 aromatase activity in the gonads of genetic female zebrafish during sex-reversal","volume":"137","author":"Uchida","year":"2004","journal-title":"Comp. Biochem. Physiol. Part A Mol. Integr. Physiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1159\/000336297","article-title":"Elevated Temperature Applied during Gonadal Transformation Leads to Male Bias in Zebrafish (Danio rerio)","volume":"6","author":"Abozaid","year":"2012","journal-title":"Sex. Dev."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3118","DOI":"10.1021\/es0522579","article-title":"Hypoxia affects sex differentiation and development, leading to a male-dominated population in zebrafish (Danio rerio)","volume":"40","author":"Shang","year":"2006","journal-title":"Environ. Sci. Technol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1007\/s10641-007-9195-8","article-title":"Rapid growth and out-crossing promote female development in zebrafish (Danio rerio)","volume":"81","author":"Lawrence","year":"2008","journal-title":"Environ. Biol. Fishes"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"37926","DOI":"10.1074\/jbc.M112.386284","article-title":"Activation of NF-\u03baB protein prevents the transition from juvenile ovary to testis and promotes ovarian development in zebrafish","volume":"287","author":"Pradhan","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"103848","DOI":"10.1016\/j.dci.2020.103848","article-title":"Epigenetic differences in the innate response after immune stimulation during zebrafish sex differentiation","volume":"114","author":"Valdivieso","year":"2021","journal-title":"Dev. Comp. Immunol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1242\/jeb.167437","article-title":"Appropriate rearing density in domesticated zebrafish to avoid masculinization: Links with the stress response","volume":"220","author":"Ribas","year":"2017","journal-title":"J. Exp. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4079","DOI":"10.1242\/jeb.167437","article-title":"Response to \u201cThe importance of controlling genetic variation-remarks on \u2018Appropriate rearing density in domesticated zebrafish to avoid masculinization: Links with the stress response\u2019\u201d","volume":"220","author":"Ribas","year":"2017","journal-title":"J. Exp. Biol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Navarro-Mart\u00edn, L., Vi\u00f1as, J., Ribas, L., D\u00edaz, N., Guti\u00e9rrez, A., Di Croce, L., and Piferrer, F. (2011). DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass. PLOS Genet., 7.","DOI":"10.1371\/journal.pgen.1002447"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s13072-018-0205-1","article-title":"Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species","volume":"11","author":"Anastasiadi","year":"2018","journal-title":"Epigenetics Chromatin"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1080\/15592294.2018.1529504","article-title":"Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination","volume":"13","author":"Anastasiadi","year":"2018","journal-title":"Epigenetics"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Sun, L.-X., Wang, Y.-Y., Zhao, Y., Wang, H., Li, N., and Ji, X.S. (2016). Global DNA Methylation Changes in Nile Tilapia Gonads during High Temperature-Induced Masculinization. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0158483"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.jtherbio.2017.06.006","article-title":"Epigenetic control of cyp19a1a expression is critical for high temperature induced Nile tilapia masculinization","volume":"69","author":"Wang","year":"2017","journal-title":"J. Therm. Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.cbpb.2017.04.007","article-title":"Identification and expression of piwil2 in turbot Scophthalmus maximus, with implications of the involvement in embryonic and gonadal development","volume":"208","author":"Wang","year":"2017","journal-title":"Comp. Biochem. Physiol. Part B Biochem. Mol. Biol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1101\/gr.162172.113","article-title":"Epigenetic modification and inheritance in sexual reversal of fish","volume":"24","author":"Shao","year":"2014","journal-title":"Genome Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1111\/jfb.12277","article-title":"CpG methylation of dmrt1 and cyp19a promoters in relation to their sexual dimorphic expression in the Japanese flounder Paralichthys olivaceus","volume":"84","author":"Wen","year":"2014","journal-title":"J. Fish Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"113549","DOI":"10.1016\/j.envres.2022.113549","article-title":"Environmentally-induced sex reversal in fish with chromosomal vs. polygenic sex determination","volume":"213","author":"Valdivieso","year":"2022","journal-title":"Environ. Res."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"109601","DOI":"10.1016\/j.envres.2020.109601","article-title":"Exposure of zebrafish to elevated temperature induces sex ratio shifts and alterations in the testicular epigenome of unexposed offspring","volume":"186","author":"Valdivieso","year":"2020","journal-title":"Environ. Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1038\/s41594-021-00603-8","article-title":"Dnmt1 has de novo activity targeted to transposable elements","volume":"28","author":"Haggerty","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.ygcen.2009.03.002","article-title":"Ovarian aromatase and estrogens: A pivotal role for gonadal sex differentiation and sex change in fish","volume":"165","author":"Guiguen","year":"2010","journal-title":"Gen. Comp. Endocrinol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1111\/j.1742-4658.2011.08030.x","article-title":"Dmrt1 genes at the crossroads: A widespread and central class of sexual development factors in fish","volume":"278","author":"Herpin","year":"2011","journal-title":"FEBS J."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"bqaa048","DOI":"10.1210\/endocr\/bqaa048","article-title":"Zebrafish cyp11c1 Knockout Reveals the Roles of 11-ketotestosterone and Cortisol in Sexual Development and Reproduction","volume":"161","author":"Zhang","year":"2020","journal-title":"Endocrinology"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.physbeh.2010.09.004","article-title":"Physiological and health consequences of social status in zebrafish (Danio rerio)","volume":"101","author":"Filby","year":"2010","journal-title":"Physiol. Behav."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Theodoridi, A., Dinarello, A., Badenetti, L., Pavlidis, M., Valle, L.D., and Tsalafouta, A. (2021). Knockout of the hsd11b2 Gene Extends the Cortisol Stress Response in Both Zebrafish Larvae and Adults. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222212525"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1095\/biolreprod.116.144964","article-title":"Expression analysis of growth differentiation factor 9 (Gdf9\/gdf9), anti-m\u00fcllerian hormone (Amh\/amh) and aromatase (Cyp19a1a\/cyp19a1a) during gonadal differentiation of the zebrafish, Danio rerio","volume":"96","author":"Chen","year":"2017","journal-title":"Biol. Reprod."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/bs.ctdb.2019.02.004","article-title":"Genetic regulation of sex determination and maintenance in zebrafish (Danio rerio)","volume":"134","author":"Kossack","year":"2019","journal-title":"Curr. Top. Dev. Biol."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Ye, D., Tu, Y.-X., Wang, H., He, M., Wang, Y., Chen, Z., Chen, Z.-X., and Sun, Y. (2022). A landscape of differentiated biological processes involved in the initiation of sex differentiation in zebrafish. Water Biol. Secur., 1.","DOI":"10.1101\/2022.04.14.488425"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"567","DOI":"10.3934\/molsci.2016.4.567","article-title":"Regulation of zebrafish gonadal sex differentiation","volume":"3","author":"Pradhan","year":"2016","journal-title":"AIMS Mol. Sci."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13072-017-0168-7","article-title":"Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads","volume":"10","author":"Ribas","year":"2017","journal-title":"Epigenetics Chromatin"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"4078","DOI":"10.1242\/jeb.164293","article-title":"The importance of controlling genetic variation\u2014Remarks on \u2018Appropriate rearing density in domesticated zebrafish to avoid masculinization: Links with the stress response\u2019","volume":"220","author":"Delomas","year":"2017","journal-title":"J. Exp. Biol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/0044-8486(94)90064-7","article-title":"Effects of stocking density on growth rate of halibut (Hippoglossus hippoglossus L.) reared in large circular tanks for three years","volume":"123","year":"1994","journal-title":"Aquaculture"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1046\/j.1365-2109.2002.00700.x","article-title":"Effects of stocking density and feeding levels on growth and feed efficiency of Nile tilapia (Oreochromis niloticus L.) fry","volume":"33","year":"2002","journal-title":"Aquac. Res."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Piferrer, F., and Wang, H.P. (2023). Epigenetics in Aquaculture, John Wiley & Sons, Inc.","DOI":"10.1002\/9781119821946"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"738918","DOI":"10.1016\/j.aquaculture.2022.738918","article-title":"Development of epigenetic biomarkers with diagnostic and prognostic value to assess the lasting effects of early temperature changes in farmed fish","volume":"563","author":"Valdivieso","year":"2023","journal-title":"Aquaculture"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1016\/j.tibs.2014.05.002","article-title":"New concepts in DNA methylation","volume":"39","author":"Jeltsch","year":"2014","journal-title":"Trends Biochem. Sci."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.gene.2012.03.041","article-title":"Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development","volume":"500","author":"Campos","year":"2012","journal-title":"Gene"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.fct.2017.08.041","article-title":"Atrazine exposure decreases the activity of DNMTs, global DNA methylation levels, and dnmt expression","volume":"109","author":"Sanchez","year":"2017","journal-title":"Food Chem. Toxicol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.aquatox.2014.07.017","article-title":"Global and cyp19a1a gene specific DNA methylation in gonads of adult rare minnow Gobiocypris rarus under bisphenol A exposure","volume":"156","author":"Liu","year":"2014","journal-title":"Aquat. Toxicol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1080\/15592294.2016.1182272","article-title":"Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio)","volume":"11","author":"Laing","year":"2016","journal-title":"Epigenetics"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"143055","DOI":"10.1016\/j.scitotenv.2020.143055","article-title":"BPA\u2019s transgenerational disturbance to transcription of ovarian steroidogenic genes in rare minnow via DNA and histone methylation","volume":"762","author":"Zhu","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.cbpb.2014.08.006","article-title":"Differential expression analysis of genes involved in high-temperature induced sex differentiation in Nile tilapia","volume":"177","author":"Li","year":"2014","journal-title":"Comp. Biochem. Physiol. Part B Biochem. Mol. Biol."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Lee, S.L.J., Horsfield, J.A., Black, M.A., Rutherford, K., Fisher, A., and Gemmell, N.J. (2017). Histological and transcriptomic effects of 17\u03b1-methyltestosterone on zebrafish gonad development. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3915-z"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1093\/bfgp\/elt041","article-title":"Zebrafish sex: A complicated affair","volume":"13","author":"Liew","year":"2014","journal-title":"Briefings Funct. Genom."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/B978-0-12-381320-6.00020-5","article-title":"The Role of Fanconi Anemia\/BRCA Genes in Zebrafish Sex Determination","volume":"Volume 105","author":"Postlethwait","year":"2011","journal-title":"Methods in Cell Biology"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1186\/s12931-020-01495-w","article-title":"Oxidative stress mediates the apoptosis and epigenetic modification of the Bcl-2 promoter via DNMT1 in a cigarette smoke-induced emphysema model","volume":"21","author":"Zeng","year":"2020","journal-title":"Respir. Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"35903","DOI":"10.1038\/srep35903","article-title":"Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia","volume":"6","author":"Wan","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.gene.2016.05.042","article-title":"Sex differences in DNA methylation and expression in zebrafish brain: A test of an extended \u2018male sex drive\u2019 hypothesis","volume":"590","author":"Chatterjee","year":"2016","journal-title":"Gene"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.fsi.2019.12.013","article-title":"Immune genes, IL1\u03b2 and Casp9, show sexual dimorphic methylation patterns in zebrafish gonads","volume":"97","author":"Joly","year":"2020","journal-title":"Fish Shellfish. Immunol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"857","DOI":"10.3389\/fgene.2019.00857","article-title":"The model of the con-served epigenetic regulation of sex","volume":"10","author":"Piferrer","year":"2019","journal-title":"Front. Genet."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1002\/jez.b.22848","article-title":"Ovarian transcriptomic signatures of zebrafish females resistant to different environmental perturbations","volume":"332","author":"Valdivieso","year":"2019","journal-title":"J. Exp. Zool. B Mol. Dev. Evol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1242\/jeb.066027","article-title":"Constraints-based stoichiometric analysis of hypoxic stress on steroidogenesis in fathead minnows, Pimephales promelas","volume":"215","author":"Hala","year":"2012","journal-title":"J. Exp. Biol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1126\/science.1063852","article-title":"The Role of DNA Methylation in Mammalian Epigenetics","volume":"293","author":"Jones","year":"2001","journal-title":"Science"},{"key":"ref_91","first-page":"1010","article-title":"CpG islands and the regulation of transcription","volume":"25","author":"Deaton","year":"2011","journal-title":"Minerva Anestesiol."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Brenet, F., Moh, M., Funk, P., Feierstein, E., Viale, A.J., Socci, N.D., and Scandura, J.M. (2011). DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0014524"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Blattler, A., Yao, L., Witt, H., Guo, Y., Nicolet, C.M., Berman, B.P., and Farnham, P.J. (2014). Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol., 15.","DOI":"10.1186\/s13059-014-0469-0"},{"key":"ref_94","unstructured":"Krueger, F. (2023, October 08). Trim galore. A wrapper Tool around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ files. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/."},{"key":"ref_95","unstructured":"Andrews, S. (2010). FastQC, Babraham Bioinformatics. A Quality Control Tool for High throughput Sequence Data."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: Summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Haider, S., Waggott, D., Lalonde, E., Fung, C., Liu, F.-F., and Boutros, P.C. (2016). A bedr way of genomic interval processing. Source Code Biol. Med., 11.","DOI":"10.1186\/s13029-016-0059-5"},{"key":"ref_98","unstructured":"R Development Core Team (2018). R: A Language and Environment for Statistical Computing, R Found. Stat. Comput."},{"key":"ref_99","first-page":"1","article-title":"Package \u2018ggplot2\u2019. Create elegant data visualisations using the grammar of graphics","volume":"2","author":"Wickham","year":"2016","journal-title":"Version"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1080\/01621459.1934.10502686","article-title":"The analysis of multiple classifications with unequal numbers in the different classes","volume":"29","author":"Yates","year":"1934","journal-title":"J. Am. Stat. Assoc."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1111\/j.1745-7270.2007.00283.x","article-title":"Validation of zebrafish (Danio rerio) reference genes for quan-titative real-time RT-PCR normalization","volume":"39","author":"Tang","year":"2007","journal-title":"Acta Biochim. Biophys. Sin."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1038\/nprot.2008.73","article-title":"Analyzing real-time PCR data by the comparative CT method","volume":"3","author":"Schmittgen","year":"2008","journal-title":"Nat. Protoc."},{"key":"ref_103","first-page":"e24","article-title":"Package \u2018corrplot\u2019","volume":"56","author":"Wei","year":"2017","journal-title":"Statistician"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/21\/16002\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:18:11Z","timestamp":1760131091000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/21\/16002"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,6]]},"references-count":103,"journal-issue":{"issue":"21","published-online":{"date-parts":[[2023,11]]}},"alternative-id":["ijms242116002"],"URL":"https:\/\/doi.org\/10.3390\/ijms242116002","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,6]]}}}