Transcriptome-wide study revealed m6A regulation of embryonic muscle development in Dingan goose (Anser cygnoides orientalis)

• Published in: BMC genomics Vol. 22; no. 1; p. 270
• Main Authors: Xu, Tieshan, Xu, Zijie, Lu, Lizhi, Zeng, Tao, Gu, Lihong, Huang, Yongzhen, Zhang, Shunjin, Yang, Peng, Wen, Yifan, Lin, Dajie, Xing, Manping, Huang, Lili, Liu, Guojun, Chao, Zhe, Sun, Weiping
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 14-04-2021; BioMed Central; BMC
• Subjects: Animals; Anser cygnoides orientalis; Aquatic birds; Breast muscle; Breast muscle tissues; Developmental stages; Differentially methylated genes; Embryogenesis; Embryonic Development; Embryonic growth stage; Epigenetics; Forkhead protein; Geese - genetics; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genes; Genetic aspects; Genetic regulation; Genomes; Genomics; Localization; m6A-sequencing; Mammals; Methylation; MicroRNA; miRNA; miRNAs-sequencing; Muscle Development - genetics; Muscles; Musculoskeletal system; Myogenesis; N6-methyladenosine; Physiological aspects; Proteins; Ribonucleic acid; RNA; Roles; Signal transduction; Signaling; Skeletal muscle; TOR protein; Transcription; Transcriptome; Transcriptomes; Wnt protein; Zoological research; China; m6A-sequencing; Differentially methylated genes; miRNAs-sequencing; Breast muscle tissues; Anser cygnoides orientalis
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-021-07556-8

The number of myofiber is determined during the embryonic stage and does not increase during the postnatal period for birds, including goose. Thus, muscle production of adult goose is pre-determined during embryogenesis. Previous studies show N
-methyladenosine (m6A) is an important regulator for skeletal muscle development of birds and miRNAs play as a co-regulator for the skeletal muscle development in birds. Herein, we sequenced m6A and miRNA transcriptomes to investigate the profiles of m6A and their potential mechanism of regulating breast muscle development in Dingan Goose.
We selected embryonic 21th day (E21) and embryonic 30th day (E30) to investigate the roles of transcriptome-wide m6A modification combining with mRNAs and miRNAs in goose breast muscle development. In this study, m6A peaks were mainly enriched in coding sequence (CDS) and start codon and397 genes were identified as differentially methylated genes (DMGs). GO and KEGG analysis showed that DMGs were highly related to cellular and metabolic process and that most DMGs were enriched in muscle-related pathways including Wnt signaling pathway, mTOR signaling and FoxO signaling pathway. Interestingly, a negative correlation between m6A methylation level and mRNA abundance was found through the analysis of m6A-RNA and RNA-seq data. Besides, we found 26 muscle-related genes in 397 DMGs. We also detected 228 differentially expressed miRNAs (DEMs), and further found 329 genes shared by the target genes of DEMs and DMGs (m6A-miRNA-genes), suggesting a tightly relationship between DEMs and DMGs. Among the m6A-miRNA-genes, we found 10 genes are related to breast muscle development. We further picked out an m6A-miRNA-gene, PDK3, from the 10 genes to visualize it and the result showed differentially methylated peaks on the mRNA transcript consistent with our m6A-seq results.
GO and KEGG of DMGs between E21 and E30 showed most DMGs were muscle-related. In total, 228 DEMs were found, and the majority of DMGs were overlapped with the targets of DEGs. The differentially methylated peaks along with an m6A-miRNA-gene, PDK3, showed the similar results with m6A-seq results. Taken together, the results presented here provide a reference for further investigation of embryonic skeletal muscle development mechanism in goose.