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Integrative Methylome and Transcriptome Analysis Reveals Epigenetic Regulation of Pigmentation in Oujiang Color
Wenqi Zhao1, Xiaowen Chen1, Ayesha Arif1
1Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by the Ministry of Agriculture and Rural Affairs, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
International Journal of Molecular Sciences
|October 29, 2025
Summary
Epigenetic analysis of Oujiang color common carp reveals DNA methylation patterns influencing pigmentation. Promoter methylation inversely correlates with gene expression, identifying key regulators of color diversity in carp.
Area of Science:
- * Genomics and Epigenetics
- * Aquaculture and Fish Biology
- * Molecular Biology
Background:
- * Oujiang color common carp exhibit diverse pigmentation, but the underlying epigenetic mechanisms remain largely unknown.
- * Understanding the genetic and epigenetic basis of color variation is crucial for selective breeding and aquaculture.
Purpose of the Study:
- * To investigate the genome-wide DNA methylation and transcriptome profiles of different Oujiang color common carp varieties.
- * To identify epigenetic regulators associated with pigmentation differences, particularly in black-spotted carp.
- * To explore the interplay between DNA methylation, gene expression, and metabolic pathways in determining carp coloration.
Main Methods:
- * Integration of whole-genome DNA methylation (MBD-seq) and RNA sequencing (RNA-seq) data from dorsal skin samples.
- * Comparative analysis of methylation levels and gene expression between black-spotted and non-black-spotted carp varieties.
- * Quantitative real-time PCR (RT-qPCR) validation of key gene expression patterns.
Main Results:
- * Black-spotted carp exhibited higher global DNA methylation (approx. 6%) compared to non-black-spotted varieties.
- * Differential DNA methylation was predominantly found in introns and intergenic regions.
- * A significant inverse correlation between promoter methylation and gene expression was observed, with 96 pigmentation-related genes identified, including epigenetically silenced regulators like ASIP and frmA.
- * Pathway analysis highlighted the involvement of melanogenesis, tyrosine, lipid, and fatty acid metabolism in color determination.
Conclusions:
- * Promoter DNA methylation plays a critical role in regulating gene expression and influencing color diversity in Oujiang color common carp.
- * Epigenetic silencing of key genes like ASIP and frmA contributes to the black-spotted phenotype.
- * The findings provide insights into the epigenetic control of coloration and its link to metabolic regulation in fish.
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