Dynamic epigenomic landscape and gene regulatory networks during embryonic development in Pacific white shrimp (Litopenaeus vannamei) as revealed by histone modification profiling using CUT&Tag

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.