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Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis
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Zhen Li1, Yunxiao Sun1, Dandan Sun1, Ning Yang1, Zhongtao Yin1, *, Zhuocheng Hou1, *
Journal of Animal Science and Biotechnology | 2026, 17(4) : 1992 - 2010
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Journal of Animal Science and Biotechnology | 2026, 17(4): 1992-2010
• ANIMAL REPRODUCTION •
Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis
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Zhen Li1, Yunxiao Sun1, Dandan Sun1, Ning Yang1, Zhongtao Yin1, *, Zhuocheng Hou1, *
Affiliations
  • 1Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
Published: 2026-08-15 doi: 10.1186/s40104-026-01393-z
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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.

Bird  /  Cis-regulatory map  /  Folliculogenesis  /  Regulatory network  /  Three-dimensional
Zhen Li, Yunxiao Sun, Dandan Sun, Ning Yang, Zhongtao Yin, Zhuocheng Hou. Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis[J]. Journal of Animal Science and Biotechnology, 2026 , 17 (4) : 1992 -2010 . DOI: 10.1186/s40104-026-01393-z
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Funding
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  • National Key R&D Program of China(2024YFF1000900; 2023YFD1300300; 2022YFF1000100)
  • National Natural Science Foundation of China(32302730)
  • China Agriculture Research System of MOF and MARA CARS-42
  • Chinese Universities Scientific Fund(2024TC170)
  • Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(G20220628007)
Appendix
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Year 2026 volume 17 Issue 4
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Article Info
doi: 10.1186/s40104-026-01393-z
  • Receive Date：2025-11-11
  • Online Date：2026-08-13
  • Published：2026-08-15
Article Data
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History
  • Received：2025-11-11
  • Accepted：2026-03-09
Funding
National Key R&D Program of China(2024YFF1000900; 2023YFD1300300; 2022YFF1000100)
National Natural Science Foundation of China(32302730)
China Agriculture Research System of MOF and MARA CARS-42
Chinese Universities Scientific Fund(2024TC170)
Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(G20220628007)
Affiliations
    1Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China

Corresponding:

* Zhongtao Yin
Zhuocheng Hou
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Citations
表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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