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Long-distance chromatin interaction of IGF1 during embryonic and postnatal development in the liver of Sus scrofa

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Abstract

The dynamics of chromatin have been the focus of studies aimed at characterizing gene regulation. Among various chromosome conformation capture methods, 4C-seq is a powerful technique to identify genome-wide interactions with a single locus of interest. Insulin-like growth factor 1 (IGF1) is a member of the somatotropin axis that plays a significant role in cell proliferation and growth. Determining the IGF1-involved genome-wide chromatin interaction profile at different growth stages not only is important for understanding IGF1 transcriptional regulation but also provides a representation of genome-wide chromatin transformation during development. Using the IGF1 promoter as a “bait”, we identified genome-wide interactomes of embryonic (E70) and postnatal (P1 and P70) pig liver cells by 4C-seq. The IGF1 promoter interactomes varied significantly among the three developmental stages. The most active chromatin interaction was observed in the P1 stage, while the highest interaction variability was observed in the P70 stage. The identified 4C sites were enriched around transcription start sites, CpG sites and functional pig QTLs. In addition, the genes located in the interacting regions and the involved pathways were also analysed. Overall, our work reveals a distinct long-distance regulatory pattern in pig liver during development for the first time, and the identified interacting sites and genes may serve as candidate targets in further transcriptional mechanism studies and effective molecular markers for functional traits.

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Data availability

All data generated or analysed during this study are available from the corresponding author on reasonable request.

Abbreviations

4C:

circularized chromosome conformation capture

DIGs:

differentially interacting genes

DISs:

differentially interacting sites

TSSs:

transcription start sites

QTLs:

quantitative trait loci

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Funding

This work was supported by the Natural Science Foundation of China (31902123), the Postdoctoral Science Foundation of China (2016 M601837) and the National Natural Science Foundation of China (31672421).

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Authors and Affiliations

  1. College of Animal Science and Technology, Jinling Institute of Technology, Nanjing, 211169, People’s Republic of China

    Jinbi Zhang

  2. College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095, People’s Republic of China

    Jinbi Zhang, Wang Yao, Zengxiang Pan & Honglin Liu

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  1. Jinbi Zhang
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  2. Wang Yao
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  3. Zengxiang Pan
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  4. Honglin Liu
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Contributions

JZ, ZP and HL designed the study. JZ and WY performed the experiments, and ZP analysed the data. JZ wrote the paper. HL and ZP revised the paper critically for important content. ZP had primary responsibility for the final content. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Zengxiang Pan.

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Competing interests

The authors declare that they have no competing interests.

Ethics approval and consent to participate

All procedures performed in studies involving animals were conducted according to the Guidelines for the Care and Use of Animals of Nanjing Agricultural University, 1999. The study was approved by the Ethics Committee of Nanjing Agricultural University, Nanjing, China.

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Not applicable.

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Zhang, J., Yao, W., Pan, Z. et al. Long-distance chromatin interaction of IGF1 during embryonic and postnatal development in the liver of Sus scrofa. Funct Integr Genomics 21, 59–72 (2021). https://doi.org/10.1007/s10142-020-00761-w

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  • DOI: https://doi.org/10.1007/s10142-020-00761-w

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