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Biology2025; 14(6); 678; doi: 10.3390/biology14060678

DNA Methylation of Igf2r Promoter CpG Island 2 Governs Cis-Acting Inheritance and Gene Dosage in Equine Hybrids.

Abstract: Genomic imprinting is critical for mammalian development, but its regulation varies across species. The insulin-like growth factor 2 receptor (IGF2R), which is a maternally expressed imprinted gene critical for cell proliferation and differentiation, as well as embryonic and placental development, is classically regulated by differentially methylated regions (DMRs) and lncRNA- in mice. However, studies on this in equus are scarce, especially in terms of mechanistic studies. In the present study, heart, liver, spleen, lung, kidney, brain, and muscle samples were obtained from horses, donkeys, and hybrids, and gene expression and imprinting state were tested to investigate the imprinting regulation of in these animals. Bisulfite sequencing combined with an allele-specific expression analysis revealed a tissue-specific loss of imprinting in the mule liver and hybrid brain tissues. Strikingly, we found that the maternal-specific expression of equine did not rely on the canonical DMRs or lncRNA-. Surprisingly, DNA methylation of a specific region called CpG island 2 (CpGI2) in the promoter showed -acting inheritance, meaning that the DNA methylation patterns of the parental alleles are retained in hybrid tissues. Notably, the DNA methylation of CpGI2 correlated negatively with expression in the spleen (R = 0.8797, = 6.46 × 10), lung (R = 0.8569, = 1.57 × 10), and kidney (R = 0.8650, = 3.85 × 10). Our findings suggest that imprinting may work differently in other species. This study provides a framework for understanding imprinting diversity in hybrids and shows that equine hybrids can be used to study how epigenetic inheritance works.
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Publication Date: 2025-06-11 PubMed ID: 40563929PubMed Central: PMC12189881DOI: 10.3390/biology14060678Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study investigates the regulation of the imprinted gene IGF2R in horses, donkeys, and their hybrids (mules), focusing on DNA methylation patterns and gene expression.
  • The researchers discovered a unique regulatory mechanism involving a specific CpG island in the IGF2R promoter that governs gene expression and imprinting in equine hybrids, differing from classical models seen in other mammals.

Background

  • Genomic Imprinting: A genetic phenomenon where genes are expressed in a parent-of-origin-specific manner, crucial for normal development in mammals.
  • IGF2R Gene: This maternally expressed imprinted gene plays a key role in cell proliferation, differentiation, and development of embryos and placenta.
  • Known Regulation in Mice: Traditionally controlled by differentially methylated regions (DMRs) and long non-coding RNAs (lncRNA), which regulate gene expression specifically from one parental allele.
  • Research Gap: Mechanistic studies on IGF2R imprinting regulation in equids (horses, donkeys) are limited, especially regarding epigenetic mechanisms in hybrids.

Research Methods

  • Sample Collection: Tissues including heart, liver, spleen, lung, kidney, brain, and muscle from horses, donkeys, and their hybrids (mules) were collected.
  • Gene Expression Analysis: Expression levels of IGF2R were measured to determine imprinting status and if expression was parent-specific or biallelic.
  • Bisulfite Sequencing: Used to analyze DNA methylation patterns in specific gene regions, providing insight into epigenetic regulation.
  • Allele-Specific Expression: Techniques identifying whether gene expression occurs from the maternal or paternal allele in hybrids.

Key Findings

  • Tissue-Specific Loss of Imprinting: In mules, the liver and brain tissues showed loss of the typical parent-specific expression of IGF2R, indicating tissue-specific variation in imprinting.
  • Non-Canonical Regulation: Unlike mice, equine IGF2R maternal expression did not depend on the well-known DMRs or lncRNA-based mechanisms.
  • Role of CpG Island 2 (CpGI2): A specific region in the IGF2R promoter called CpGI2 was identified as crucial for imprinting.
  • Cis-Acting Inheritance: DNA methylation patterns of CpGI2 were preserved from the parental alleles into hybrid tissues, meaning parental epigenetic marks are maintained in offspring.
  • Correlation with Gene Expression: DNA methylation levels at CpGI2 inversely correlated with IGF2R expression, particularly in spleen (R = 0.8797), lung (R = 0.8569), and kidney (R = 0.8650), indicating methylation suppresses gene expression.

Implications

  • Species-Specific Imprinting: The regulation of IGF2R imprinting in horses and hybrids differs significantly from classical models in mice, highlighting evolutionary diversity in imprinting mechanisms.
  • Epigenetic Inheritance in Hybrids: The study reveals that epigenetic marks like DNA methylation can be inherited in a parent-specific manner (cis-acting) even across species crosses, as seen in equine hybrids.
  • Model for Imprinting Studies: Equine hybrids (mules) serve as a valuable model system for studying epigenetic inheritance and the diversity of imprinting mechanisms in mammals.
  • Broader Understanding: Findings encourage further exploration of DNA methylation beyond canonical DMRs and lncRNAs, expanding understanding of imprinting regulation.

Conclusion

  • This research provides new insights into how genomic imprinting can be regulated through DNA methylation at non-canonical regions like CpGI2 in the IGF2R promoter in equids.
  • The retention of parental methylation patterns in hybrids emphasizes the importance of epigenetic mechanisms in governing gene dosage and inheritance across species.
  • The discovery underscores the evolutionary variability of imprinting and sets a foundation for future studies on epigenetic inheritance using hybrid animal models.

Cite This Article

APA
Wang X, Shen Y, Ren H, Yi M, Bou G. (2025). DNA Methylation of Igf2r Promoter CpG Island 2 Governs Cis-Acting Inheritance and Gene Dosage in Equine Hybrids. Biology (Basel), 14(6), 678. https://doi.org/10.3390/biology14060678

Publication

Biology
ISSN: 2079-7737
NlmUniqueID: 101587988
Country: Switzerland
Language: English
Volume: 14
Issue: 6
PII: 678

Researcher Affiliations

Wang, Xisheng
  • Lin He's Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining 272067, China.
Shen, Yingchao
  • Anchee (Shandong) Animal Nutrition Research Academy Co., Ltd., Jinan 250104, China.
Ren, Hong
  • Vocational and Technical College, Inner Mongolia Agricultural University, Hohhot 010018, China.
Yi, Minna
  • Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.
Bou, Gerelchimeg
  • Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China.
  • College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China.

Grant Funding

  • 202402010752 / The medical health science and technology project of Shandong Province
  • 6001/601004001 / Jining Medical University scientific research start-up funds for young doctor

Conflict of Interest Statement

Yingchao Shen was employed by the company Anchee (Shandong) Animal Nutrition Research Academy Co., Ltd., Jinan, Shandong. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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