Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis

Abstract Background Follicular development is a prerequisite for vertebrate reproduction, and it is precisely regulated by complex genomic conformations and regulatory elements. However, the dynamic changes in the interaction between the three-dimensional genome and regulatory elements of granulosa cells (GCs) during avian follicular development are still unclear. Here, we integrated RNA sequencing, ATAC sequencing, CUT&Tag, and Hi-C of GCs in 7 stages of Pekin ducks (Anas platyrhynchos domestica) to construct a high-resolution three-dimensional cis-regulatory map of follicular development, revealing the chromatin dynamics basis of avian folliculogenesis. Results Our integrative analysis reveals that H3K27ac dynamics, rather than chromatin accessibility alone, are strongly associated with the stage-specific transcriptional increase of follicle selection and maturation. We identified enhancers and super-enhancers (SEs) that are significantly correlated with the expression of key follicular genes. Regarding 3D genome organization, we observed that topologically associating domains (TADs) remained largely stable, serving as a structural scaffold. However, stage-specific boundary changes coincided with the transcriptional alterations of key regulator genes. Furthermore, we inferred putative gene regulatory networks (GRNs) comprising 46 core transcription factors (TFs) predicted to be closely linked to follicular development. Finally, comparative analysis highlighted both the conservation and species-specificity of these regulatory elements between birds and mammals. Conclusions Our study provides an integrative, multi-omics resource that offers novel insights into the epigenomic landscape of duck follicular development. The resulting dataset and regulatory map establish a valuable foundation for further mechanistic studies of folliculogenesis and for understanding regulatory divergence across species. Graphical Abstract