{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T14:12:28Z","timestamp":1777990348603,"version":"3.51.4"},"reference-count":70,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T00:00:00Z","timestamp":1777939200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Provincial Key Research and Development Program of Anhui","award":["202423l10050003"],"award-info":[{"award-number":["202423l10050003"]}]},{"name":"key research and development plan of Guangxi","award":["AB241484006"],"award-info":[{"award-number":["AB241484006"]}]},{"name":"key Research and Development Program of the Ningxia Hui Autonomous Region","award":["2026BBF02005"],"award-info":[{"award-number":["2026BBF02005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>In this study, we systematically analyzed the dynamic changes in chromatin accessibility and the transcriptional responses in the spleen of largemouth bass (Micropterus salmoides) following infection with iridovirus (LMBV) using the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and transcriptome sequencing (RNA-seq). Based on post-infection survival status, largemouth bass were classified into a resistant group (SR) and a susceptible group (SS). A total of 11,317 differentially accessible regions were identified between the two groups, among which the chromatin accessibility of core promoter regions was entirely increased in the SR group, suggesting that chromatin remodeling in these regions may directly participate in the transcriptional regulation of immune-related genes. Functional enrichment analysis revealed that genes associated with differentially accessible regions were significantly enriched in immune-related pathways such as autophagy, apoptosis, Toll-like receptor signaling, and NOD-like receptor signaling. Motif analysis further identified that transcription factors significantly enriched in the SR group included CTCF and heterodimers composed of multiple members of the ETS and FOX transcription factor families. Through integrative analysis, seven transcription factors (CTCF, Spi1, ETV2::FOXI1, FOXJ2::ELF1, FOXO1::ELK1, SPIC, and FOXO1::ELF1) were found to be significantly enriched in core promoter regions. To further screen for differentially expressed genes directly regulated by chromatin accessibility changes, an overlapping analysis was performed between 629 predicted target genes and 2656 differentially expressed genes (DEGs), resulting in the identification of 71 candidate genes. Among these, three immune-related genes (irf4a, btk, and nfil3-2) belonging to the ETS and FOX families were identified. This study reveals the dynamic chromatin accessibility landscape of largemouth bass in response to LMBV infection and demonstrates that increased chromatin accessibility in core promoter regions is closely associated with the resistant phenotype. Heterodimers of ETS and FOX family transcription factors may participate in antiviral immune responses by regulating the expression of key immune genes such as irf4a, btk, and nfil3-2, providing potential epigenetic molecular markers for disease resistance breeding in fish.<\/jats:p>","DOI":"10.3390\/ijms27094124","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T13:23:37Z","timestamp":1777987417000},"page":"4124","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Integrative ATAC-Seq and RNA-Seq Analysis of Spleen Tissues from Largemouth Bass (Micropterus salmoides) Infected with Iridovirus (LMBV)"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-3465-2061","authenticated-orcid":false,"given":"Hui","family":"Sun","sequence":"first","affiliation":[{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jixiang","family":"Hua","sequence":"additional","affiliation":[{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2406-1775","authenticated-orcid":false,"given":"Yifan","family":"Tao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siqi","family":"Lu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-0224-4511","authenticated-orcid":false,"given":"Wen","family":"Wang","sequence":"additional","affiliation":[{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"},{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yalun","family":"Dong","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linbing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jixiang","family":"He","sequence":"additional","affiliation":[{"name":"Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"He","sequence":"additional","affiliation":[{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4718-6618","authenticated-orcid":false,"given":"Jun","family":"Qiang","sequence":"additional","affiliation":[{"name":"Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China"},{"name":"Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"734901","DOI":"10.1016\/j.aquaculture.2019.734901","article-title":"Aquaculture industry development, annual price analysis and out-of-season spawning in largemouth bass Micropterus 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