Dynamic Chromatin Accessibility and Transcriptional Regulation in the Eyes of Red Tilapia (Oreochromis sp.) in Response to Wintering Stress

IF 2.6 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Ying Bai, Gan Yang, Tongde Liu, Fuyan Chen, Junhong Xia
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引用次数: 0

Abstract

During wintering, red tilapia may develop variable black spots on their bodies, significantly reducing their market value. Understanding the mechanisms driving this phenomenon is essential for molecular improvements in body color. In this study, we investigated chromatin accessibility landscapes in the eyes of red tilapia with two distinct phenotypes (normal pure red and black spot) under wintering stress using ATAC-seq and RNA-seq analyses. We observed that approximately 32.7% of chromatin accessibility peaks were located in promoter regions, followed by intergenic regions (32.4%) and intronic regions (26.7%). One thousand two hundred twenty-nine differentially accessible regions (DARs) and 1448 differentially expressed genes (DEGs) were identified between the RS and DS groups. Notably, DEGs associated with melanin synthesis, including tyrp1, tyr, tyrp1b, pmela, slc24a5, and mlph, were significantly upregulated in the DS group, which aligns with the observed 1.85-fold increase in melanin content, compared to the RS group. 92 DEGs were associated with significant changes in chromatin accessibility between groups (R2 = 0.8059; p < 0.0001), indicating potential regulatory relationships. Interestingly, 23.92% of the DARs were located on the chromosome 3. Specifically, a 2.5-fold difference in average peak height on LG3: 11,215,273–11,217,225 were observed between DS and RS tilapia. In the region, transcription factors including HSF1 and HSF2 were identified as key regulators of chromatin structure and gene expression under wintering stress. Our findings reveal that dynamic chromatin accessibility in the eyes of red tilapia facilitates adaptation to wintering stress by regulating visual signaling, melanin production, and downstream pigmentation.

红罗非鱼(Oreochromis sp.)眼睛对冬季胁迫的动态染色质可及性和转录调控
在越冬期间,红罗非鱼的身上可能会出现各种各样的黑点,大大降低了它们的市场价值。理解驱动这种现象的机制对于身体颜色的分子改善至关重要。在这项研究中,我们利用ATAC-seq和RNA-seq分析了冬季胁迫下两种不同表型(正常纯红和黑斑)的红罗非鱼眼睛的染色质可及性景观。我们观察到大约32.7%的染色质可及性峰位于启动子区域,其次是基因间区域(32.4%)和内含子区域(26.7%)。在RS组和DS组之间共鉴定出1229个差异可达区(DARs)和1448个差异表达基因(DEGs)。值得注意的是,与黑色素合成相关的DEGs,包括tyrp1、tyrr、tyrp1b、pmela、slc24a5和mlph,在DS组中显著上调,与RS组相比,黑色素含量增加了1.85倍。92个deg与组间染色质可及性的显著变化相关(R2 = 0.8059;P < 0.0001),表明潜在的监管关系。有趣的是,23.92%的dar位于3号染色体上。具体而言,DS罗非鱼和RS罗非鱼在LG3上的平均峰高(11,215,273-11,217,225)相差2.5倍。在该区域,包括HSF1和HSF2在内的转录因子被确定为冬季胁迫下染色质结构和基因表达的关键调节因子。我们的研究结果表明,红罗非鱼眼睛中的动态染色质可及性通过调节视觉信号、黑色素产生和下游色素沉着来促进对冬季胁迫的适应。
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来源期刊
Marine Biotechnology
Marine Biotechnology 工程技术-海洋与淡水生物学
CiteScore
4.80
自引率
3.30%
发文量
95
审稿时长
2 months
期刊介绍: Marine Biotechnology welcomes high-quality research papers presenting novel data on the biotechnology of aquatic organisms. The journal publishes high quality papers in the areas of molecular biology, genomics, proteomics, cell biology, and biochemistry, and particularly encourages submissions of papers related to genome biology such as linkage mapping, large-scale gene discoveries, QTL analysis, physical mapping, and comparative and functional genome analysis. Papers on technological development and marine natural products should demonstrate innovation and novel applications.
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