Integrative ATAC-Seq and RNA-Seq Analysis Reveals Key Transcription Factors Mediating Low Salinity Adaptation in Penaeid Shrimp
文献类型：期刊论文
| 作者 | Zhang, Chuntao2,3; Yuan, Jianbo1,2,4; Li, Roujing2,3; Yang, Zhanyuan2,4; Luo, Man2,3; Zhong, Xiaoyun2,3; Hu, Jie2,3; Si, Shuqing2,3; Zhang, Xiaojun1,2,4; Li, Fuhua1,2,4 |
| 刊名 | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
 |
| 出版日期 | 2025-05-11 |
| 卷号 | 26期号:10页码:17 |
| 关键词 | penaeid shrimp RNA-seq ATAC-seq transcription factor low salinity |
| ISSN号 | 1661-6596 |
| DOI | 10.3390/ijms26104605 |
| 通讯作者 | Yuan, Jianbo(yuanjb@qdio.ac.cn) |
| 英文摘要 | Salinity serves as an important environmental factor in ecosystems, driving the evolution of adaptive strategies in euryhaline species. The Pacific white shrimp, Litopenaeus vannamei, is a representative euryhaline species. However, the molecular mechanisms, particularly the roles of cis-regulatory elements, remain elusive in penaeid shrimp. This study tackles this gap by subjecting L. vannamei to a gradual reduction in salinity from 30 parts per thousand to 3 parts per thousand, and then applying ATAC-seq and RNA-seq techniques to dissect the cis-regulation mechanisms underlying low salinity adaptation. A key finding reveals a positive correlation between chromatin accessibility and gene expression, with 36.8% of differentially expressed genes directly associated with changes in chromatin accessibility. The cis-regulation of many osmoregulation-related pathways, such as betaine synthesis and PI3K-Akt signaling pathways, appeared to be a crucial strategy for salinity adaptation in shrimp. By analyzing differentially accessible regions under low salinity stress, we uncovered two known and seven novel candidate transcription factors (TFs) that may play pivotal roles in salinity adaptation. We further conducted a comprehensive analysis of these TFs, including their functions, expression profiles, consensus TFBS motifs, and the functional enrichment and expression profiles of their targeted genes. This study elucidates a complex cis-regulatory network that enables exceptional salinity tolerance in L. vannamei, which provides a foundation for the refinement of genetic breeding programs and desalination aquaculture for penaeid shrimp. |
| WOS关键词 | WHITE SHRIMP ; GENE-EXPRESSION ; PATHWAYS ; STRESS ; INDUCTION ; VANNAMEI ; SURVIVAL ; GROWTH ; TOOL |
| 资助项目 | Natural Science Foundation of Shandong Province ; Natural Science Foundation of China[42176105] ; Science & Technology Innovation Project of Laoshan Laboratory[LSKJ202203001] ; National Key Research & Development Program of China[2022YFD2400203] ; National Key Research & Development Program of China[system-48 (CARS-48)] ; Taishan Scholars Program ; [ZR2024YQ030] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Chemistry |
| 语种 | 英语 |
| WOS记录号 | WOS:001496494200001 |
| 出版者 | MDPI |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/202106]  |
| 专题 | 海洋研究所_实验海洋生物学重点实验室 |
| 通讯作者 | Yuan, Jianbo |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266500, Peoples R China 2.Chinese Acad Sci, Inst Oceanol, Key Lab Breeding Biotechnol & Sustainable Aquacult, Qingdao 266500, Peoples R China 3.Univ Chinese Acad Sci, Beijing 101400, Peoples R China 4.Qingdao Marine Sci & Technol Ctr, Lab Marine Biol & Biotechnol, Qingdao 266071, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Chuntao,Yuan, Jianbo,Li, Roujing,et al. Integrative ATAC-Seq and RNA-Seq Analysis Reveals Key Transcription Factors Mediating Low Salinity Adaptation in Penaeid Shrimp[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2025,26(10):17. |
| APA | Zhang, Chuntao.,Yuan, Jianbo.,Li, Roujing.,Yang, Zhanyuan.,Luo, Man.,...&Li, Fuhua.(2025).Integrative ATAC-Seq and RNA-Seq Analysis Reveals Key Transcription Factors Mediating Low Salinity Adaptation in Penaeid Shrimp.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,26(10),17. |
| MLA | Zhang, Chuntao,et al."Integrative ATAC-Seq and RNA-Seq Analysis Reveals Key Transcription Factors Mediating Low Salinity Adaptation in Penaeid Shrimp".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 26.10(2025):17. |
入库方式： OAI收割
来源：海洋研究所
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