Shi Jiale, Qi Zhangru, Yin Miaomiao, Zeng Qifan, Hu Jingjie, Bao Zhenmin, Ye Zhi
MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Sanya, 266003, 572024, China.
Hainan Seed Industry Laboratory, Sanya, Hainan, 572025, China.
Epigenetics Chromatin. 2025 Aug 4;18(1):50. doi: 10.1186/s13072-025-00615-4.
The Pacific white shrimp (Litopenaeus vannamei) is the most widely farmed shrimp species globally, yet the epigenetic regulation underlying its embryonic development remains largely unexplored. Histone modifications are known to orchestrate gene expression during early development in model organisms, but their role in crustaceans is poorly understood.
In this study, we present the first comprehensive histone modification landscape during L. vannamei embryogenesis using CUT&Tag (Cleavage Under Targets and Tagmentation). We profiled high-resolution landscapes of four histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3) across seven developmental stages from blastula to nauplius, revealing dynamic chromatin state transitions associated with developmental progression. Integration with transcriptomic data uncovered a strong temporal correlation between chromatin states and gene expression, particularly during zygotic genome activation (ZGA). Furthermore, our analysis uncovered key developmental genes associated with critical biological processes such as molting, body segmentation, and neurogenesis, providing novel insights into the epigenetic regulation of these events. Functional annotation of cis-regulatory elements based on histone marks identified candidate enhancers and regulatory loci linked to these key genes.
Our study provides the first epigenomic framework of shrimp embryogenesis, uncovering chromatin-based regulatory mechanisms during early development. The identification of stage-specific enhancers and active chromatin regions offers valuable resources for functional genomics in crustaceans and sheds light on conserved and divergent aspects of ZGA regulation beyond model systems.
凡纳滨对虾（Litopenaeus vannamei）是全球养殖最广泛的虾类品种，但其胚胎发育过程中的表观遗传调控仍 largely unexplored。已知组蛋白修饰在模式生物的早期发育过程中协调基因表达，但其在甲壳类动物中的作用了解甚少。
在本研究中，我们使用CUT&Tag（靶向切割与标签化）技术呈现了凡纳滨对虾胚胎发生过程中首个全面的组蛋白修饰图谱。我们分析了从囊胚到无节幼体的七个发育阶段中四种组蛋白标记（H3K4me1、H3K4me3、H3K27ac、H3K27me3）的高分辨率图谱，揭示了与发育进程相关的动态染色质状态转变。与转录组数据整合发现染色质状态与基因表达之间存在强烈的时间相关性，特别是在合子基因组激活（ZGA）期间。此外，我们的分析揭示了与蜕皮、身体分段和神经发生等关键生物学过程相关的关键发育基因，为这些事件的表观遗传调控提供了新的见解。基于组蛋白标记对顺式调控元件进行功能注释，确定了与这些关键基因相关的候选增强子和调控位点。
我们的研究提供了首个虾胚胎发生的表观基因组框架，揭示了早期发育过程中基于染色质的调控机制。阶段特异性增强子和活性染色质区域的鉴定为甲壳类动物的功能基因组学提供了宝贵资源，并揭示了模型系统之外ZGA调控的保守和差异方面。
