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

Zhen Li, Yunxiao Sun, Dandan Sun, Ning Yang, Zhongtao Yin, Zhuocheng Hou

Abstract read

In one paragraph

Article in Journal of animal science and biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

Zhen LiFrontiers 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.

Yunxiao SunFrontiers 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.

Dandan SunFrontiers 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.

Ning YangFrontiers 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.

Zhongtao YinFrontiers 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. yinzhongtao@cau.edu.cn.

Zhuocheng HouFrontiers 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. zchou@cau.edu.cn.

Funding

China Agriculture Research System of MOF and MARA CARS-42National Key Research and Development Program of China 2023YFD1300300National Key Research and Development Program of China 2024YFF1000900National Natural Science Foundation of China 32302730the Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding G20220628007the Chinese Universities Scientific Fund 2024TC170

6 · The paper itself

Abstract

backgroundFollicular 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.

resultsOur 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.

conclusionsOur 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.

Indexed as

BirdCis-regulatory mapFolliculogenesisRegulatory networkThree-dimensional

Identifiers

PMID42063177

DOI10.1186/s40104-026-01393-z

PMCPMC13134274

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.