Global Landscape of m6A Methylation of Differently Expressed Genes in Muscle Tissue of Liaoyu White Cattle and Simmental Cattle

Shen

et al. 2023

Foods

In mammals, skeletal muscle development is a complex biological process regulated by many factors. N6-methyladenosine (m6A) RNA modification plays an important role in many biological processes. However, the regulation of m6A on skeletal muscle growth and development in adult goats remains unclear. In this study, Duan goats (DA) and Nubia goats (NBY), both female and 12 months old, were selected as the research objects, and m6A-Seq and RNA-Seq were mainly used to detect the difference of m6A modification and gene expression during the development of the longissimus dorsi (LD) muscle in the two breeds. The results showed that compared with DA, the meat production performance of NBY was better than that of DA, and the modification level of m6A was higher than that of DA in LD. The m6A-Seq of LD indicated m6A peaks were mainly enriched in the coding sequence (CDS) and stop codon. A total of 161 differentially methylated genes (DMGs) and 1294 differentially expressed genes (DEGs) were identified in two breeds. GO and KEGG analysis showed that DMGs were closely related to cellular metabolism, and most of DMGs were enriched in pathways related to energy metabolism, muscle growth and development, mainly MAPK signaling pathway, Wnt signaling pathway and CGMP-PKG signaling pathway. The DEGs were significantly enriched in actin binding, calcium ion binding, angiogenesis, and other biological processes, and most of them were enriched in PI3K-Akt and CGMP-PKG signaling pathways. Combined analysis of m6A-Seq and RNA-Seq data revealed a negative correlation between differentially methylated m6A levels and mRNA abundance, and mRNA expression of the gene with m6A peak near 3′UTR will decrease. In addition, 11 DMGs regulating cell differentiation, muscle growth and development were identified. This study displayed the m6A profiles and distribution patterns in the goat transcriptome, determined the potential role of m6A modification in muscle growth and provided a new reference for the further study of goat skeletal muscle development.

Section: Introductionmentioning

confidence: 99%

Transcriptome-Wide Study Revealed That N6-Methyladenosine Participates in Regulation Meat Production in Goats

Shen

et al. 2023

Foods

“…( 13 ) explored the involvement of m6A mRNA modifications in mediating muscle regulation. Dang et al ( 14 ) identified the key genes involved in cattle muscle growth and m6A modification development by bioinformatics analysis. The results showed that the differentially expressed genes modified by m6A are mainly involved in skeletal muscle contraction, steroid biosynthesis, redox process, the PPAR pathway, and fatty acid metabolism.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-wide study revealed m6A and miRNA regulation of embryonic breast muscle development in Wenchang chickens

Jiang

Chen³

et al. 2022

Front. Vet. Sci.

N6-Methyladenosine (m6A) modification has been shown to play important role in skeletal muscle development. Wenchang chickens are commonly used as a high-quality animal model in researching meat quality. However, there have been no previous reports regarding the profile of m6A and its function in the embryonic breast muscle development of Wenchang chickens. In this paper, we identified different developmental stages of breast muscle in Wenchang chickens and performed m6A sequencing and miRNA sequencing in the breast muscle of embryos. Embryo breast muscles were weighed and stained with hematoxylin–eosin after hatching. We found that myofibers grew fast on the 10th day after hatching (E10) and seldom proliferated beyond the 19th day after hatching (E19). A total of 6,774 differentially methylated genes (DMGs) were identified between E10 and E19. For RNA-seq data, we found 5,586 differentially expressed genes (DEGs). After overlapping DEGs and DMGs, we recorded 651 shared genes (DEMGs). Subsequently, we performed miRNA-seq analysis and obtained 495 differentially expressed miRNAs (DEMs). Then, we overlapped DEMGs and the target genes of DEMs and obtained 72 overlapped genes (called miRNA-m6A-genes in this study). GO and KEGG results showed DEMGs enriched in many muscle development-related pathways. Furthermore, we chose WNT7B, a key regulator of skeletal muscle development, to perform IGV visualization analysis and found that the m6A levels on the WNT7B gene between E10 and E19 were significantly different. In conclusion, we found that miRNAs, in conjunction with m6A modification, played a key role in the embryonic breast muscle development of Wenchang chickens. The results of this paper offer a theoretical basis for the study of m6A function in muscle development and fat deposition of Wenchang chickens.

“…N6-methyladenosine (m 6 A) modification of RNA refers to A methylation modification of the adenine (A) 6-position nitrogen atom catalyzed by methyltransferase, which was first discovered in the 1970s. [1][2][3] It is similar to DNA or histone methylation in that m 6 A modification has an impact on RNA metabolism, function, and localization. 1,4,5 More than 150 post-transcriptional modifications are known to modify RNA at its four nucleotides (A, G, C, and U).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome‐wide high‐throughput m⁶A sequencing of differential m⁶A methylation patterns in the decidual tissues from RSA patients

et al. 2023

Recurrent spontaneous abortion (RSA) is characterized by two or more consecutive pregnancy losses in the first trimester of pregnancy, experienced by 5% of women during their reproductive age. As a complex pathological process, the etiology of RSA remains poorly understood. Recent studies have established that gene expression changes dramatically in human endometrial stromal cells (ESCs) during decidualization. N6‐methyladenosine (m6A) modification is the most prevalent epigenetic modification of mRNA in eukaryotic cells and it is closely related to the occurrence and development of many pathophysiological phenomena. In this study, we first confirmed that high levels of m6A mRNA methylation in decidual tissues are associated with RSA. Then, we used m6A‐modified RNA immunoprecipitation sequence (m6A‐seq) and RNA sequence (RNA‐seq) to identify the differentially expressed m6A methylation in decidual tissues from RSA patients and identified the key genes involved in abnormal decidualization by bioinformatics analysis. Using m6A‐seq, we identified a total of 2169 genes with differentially expressed m6A methylation, of which 735 m6A hypermethylated genes and 1434 m6A hypomethylated genes were identified. Further joint analysis of m6A‐seq and RNA‐seq revealed that 133 genes were m6A modified with mRNA expression. GO and KEGG analyses indicated that these unique genes were mainly enriched in environmental information processing pathways, including the cytokine–cytokine receptor interaction and PI3K‐Akt signaling pathway. In summary, this study uncovered the transcriptome‐wide m6A modification pattern in decidual tissue of RSA, which provides a theoretical basis for further research into m6A modification and new therapeutic strategies for RSA.