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Updated: Jul 25, 2025
Targeted DNA Methylation Analysis by Next-generation Sequencing
Published on: February 24, 2015
m6A mRNA Methylation Analysis Provides Novel Insights into Pigmentation in Sheep Skin
Yuanyuan Zhao1, Jinzhu Meng1,2, Xingchao Song1
1Guizhou Provincial Key Laboratory for Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, Guizhou, P. R. China.
Abstract:
N6-methyladenosine (m6A) is the most universal post-transcriptional modification of mRNA which may play important roles in verious species. However, the potential roles of m6A in the pigmentation of skin are not completely understood. To explore the role of m6A modification in pigmentation of sheep skin, we used MeRIP-seq and RNA-seq to profile the skin transcriptome in black and white coat color (n=3). Our results showed that an average of 7701 m6A peaks were obtained for all samples and the average length was 305.89 bp. The GGACUU sequence was the most enrichment motif and shared in black skin and white skin. The m6A peaks were mainly enriched in the CDS, 3'UTR and 5'UTR, especially in CDS region near the stop codon of the transcript. 235 significantly differential peaks were found in black skin vs. white skin. The KEGG signaling pathways of downregulated and upregulated m6A peaks were mainly enriched in AGE-RAGE signaling pathway in diabetic complications, Viral carcinogenesis, Transcriptional misregulation in cancer, ABC transporters, Basal transcription factors and Thyroid hormone synthesis (P value <0.05). For RNA-seq, 71 differently expressed genes (DEGs) were scanned in black skin vs. white skin. DEGs were significantly enriched in tyrosine metabolism, melanogenesis, neuroactive ligand-receptor interaction pathway (P value <0.05). Combined m6A-seq and RNA-seq analysis showed that the hyper-up genes and hypo-up genes were both enriched in ErbB signaling pathway (P value <0.05). In conclusion, it provide a basis for further research into the functions of m6A methylation modifications in pigmentation.
Insights
N6-methyladenosine (m6A) RNA modification plays a role in sheep skin pigmentation. This study identified differential m6A peaks and gene expression patterns, providing a basis for further research into m6A functions in coat color.
Area of Science:
- Epigenetics
- Molecular Biology
- Genomics
Background:
- N6-methyladenosine (m6A) is a prevalent mRNA modification with diverse biological roles.
- The specific involvement of m6A in skin pigmentation remains incompletely understood.
- Investigating m6A in sheep skin offers insights into the genetic and epigenetic regulation of coat color.
Purpose of the Study:
- To explore the role of m6A modification in sheep skin pigmentation.
- To profile the skin transcriptome and m6A landscape in sheep with different coat colors.
- To identify differentially modified m6A sites and their associated genes in black versus white sheep skin.
Main Methods:
- MeRIP-seq and RNA-seq were employed to analyze skin transcriptomes from black and white sheep (n=3).
- m6A peak analysis identified common motifs (GGACUU) and enrichment in CDS, 3'UTR, and 5'UTR regions.
- Differential m6A peaks and gene expression (DEGs) were analyzed, alongside KEGG pathway enrichment.
Main Results:
- An average of 7701 m6A peaks were detected, with 235 significantly differential peaks between black and white skin.
- DEGs were enriched in pathways including tyrosine metabolism, melanogenesis, and neuroactive ligand-receptor interaction.
- Combined analysis revealed enrichment in the ErbB signaling pathway for both upregulated and downregulated genes.
Conclusions:
- This study provides a foundational understanding of m6A methylation's role in sheep skin pigmentation.
- Differential m6A modifications and gene expression patterns are associated with coat color variation.
- Further research into m6A functions can elucidate epigenetic mechanisms regulating pigmentation.
