Differential m6A methylation landscapes in breast and leg muscles of Zhijin white geese: Epigenetic insights into muscle development

Abstract

Muscle growth is a crucial economic trait in poultry, influenced by a combination of environmental, nutritional, and genetic factors. N⁶-methyladenosine (m6A) modification, the most abundant form of RNA modification, has been identified in various poultry tissues. However, the m6A modification profiles during goose muscle development remain poorly understood. In this study, we characterized m6A modification profiles in breast (n = 5) and leg (n = 5) muscles of Zhijin white geese using MeRIP-seq and RNA-seq. Samples were collected from healthy 6-month-old male geese of similar body weight after euthanasia. Compared to breast muscles, leg muscles exhibited significant differences in muscle fiber morphology (cross-sectional area, diameter, and density), intramuscular fat content, and overall m6A levels (P < 0.001). Leg muscles exhibited upregulation of m6A regulators (including ALKBH5, METTL14, METTL16, and ZC3H13) (P < 0.05) and showed predominant m6A peaks in coding sequences (CDS) and 3′UTRs, with conserved RRACH motifs. Compared with breast muscles, 78 differentially methylated genes (DMGs) were identified by MeRIP-seq, including 43 hyper-methylated and 35 hypo-methylated genes in leg muscles. Integrated analysis with RNA-seq revealed 11 overlapping DMGs, comprising 7 hypo-methylated and 4 hyper-methylated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DMGs were significantly enriched in neuroactive ligand–receptor interaction, glycosaminoglycan biosynthesis, and regulation of actin cytoskeleton. Furthermore, we identified LGI1, CDK18, and LPAR2 from the significantly enriched pathways as potential candidate genes influencing muscle development. This study provides a theoretical foundation for further investigation into the regulatory role of m6A modification in goose muscle development.