N6-Methyladenosine Methylome Profiling of Muscle and Adipose Tissues Reveals Methylase–mRNA Metabolic Regulatory Networks in Fat Deposition of Rex Rabbits

Abstract

N6-methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and plays an important role in cancer, immunity, reproduction, development, and fat deposition. Intramuscular fat is the main factor used to measure the meat quality of an animal. The deposition of intramuscular fat and perirenal fat increases with age. However, there is no data on m6A modification of Rex rabbits and its potential biological roles in adipose deposition and muscle growth. Here, we performed two high-throughput sequencing methods, m6A-modified RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq), to identify key genes with m6A modification on fat deposition in the muscle and adipose tissues of Rex rabbits. Then, qRT-PCR was used to identify the differently methylated genes related to fat deposition. Our findings showed that there were 12,876 and 10,973 m6A peaks in the rabbit muscle and adipose tissue transcriptomes, respectively. Stop codons, 3′-untranslated regions, and coding regions were found to be mainly enriched for m6A peaks. In addition, we found 5 differential methylases and 12 key genes of methylation modification related to fat deposition between muscle and adipose tissues samples. The expression levels of six random key genes were significantly higher in the fat than that in the muscle of Rex rabbits at different stages (p < 0.01). Finally, five differential methylases were found to regulate adipogenesis by affecting the expression of screened genes in different ways. These findings provided a theoretical basis for our future research on the function of m6A modification during the growth of fat deposits.

RNA N6-methyladenosine profiling reveals differentially methylated genes associated with intramuscular fat metabolism during breast muscle development in chicken

“…Many m 6 A methylation sites were present in the breast muscle at all 3 developmental stages, with these m 6 A peaks primarily enriched in the CDS and 3′ UTR. This modification pattern is similar to that observed in rex rabbits, yaks, and pigs ( Jiang et al, 2019 ; Zhang et al, 2021 ; Guo et al, 2022 ; Luo et al, 2022 ). However, species- and tissue-specific m 6 A methylation patterns were identified in poultry studies.…”

Regulatory role of N6-methyladenosine in intramuscular fat deposition in chicken

“…In this study, we identified numerous m 6 A methylation modification sites in both breast and leg tissues of Jingyuan chickens. These m 6 A peaks were primarily concentrated in the 3′UTR, CDS, and Stop codon regions, which aligns with findings from studies on Lexus rabbit and yak ( Luo et al, 2022 ; Ma et al, 2022 ). However, this pattern differed from the findings of Xu et al (2021) in their study on Ding'an goose, where m 6 A was primarily enriched in the CDS and start codon sequence, implying that the pattern of m 6 A modification could be species and tissue specific.…”