Abstract
Liaoyu white cattle (LYWC) is a local breed in Liaoning Province, China. It has the advantages of grow quickly, high slaughter ratew, high meat quality and strong anti-stress ability. N6 methyladenosine (m6A) is a methylation modification of N6 position of RNA adenine, which is an important modification mechanism affecting physiological phenomena. In this study, we used the longissimus dorsi muscle of LYWC and SIMC for m6A-seq and RNA-seq high-throughput sequencing, and identified the key genes involved in muscle growth and m6A modification development by bioinformatics analysis. There were 31532 m6A peaks in the whole genome of LYWC and 47217 m6A peaks in the whole genome of SIMC. Compared with Simmental cattle group, LYWC group had 17,351 differentially expressed genes: 10,697 genes were up-regulated, 6,654 genes were down regulated, 620 differentially expressed genes were significant, while 16,731 differentially expressed genes were not significant. Among the 620 significantly differentially expressed genes, 295 genes were up-regulated and 325 genes were down regulated. In order to explore the relationship between m6A and mRNA expression in the muscles of LYWC and SIMC, the combined analysis of MeRIP-seq and RNA-seq revealed that 316 genes were m6A modified with mRNA expression. To identify differentially methylated genes related to muscle growth, four related genes were selected for quantitative verification in LYWC and SIMC. GO enrichment and KEGG analysis showed that the differentially expressed genes modified by m6A are mainly involved in skeletal muscle contraction, steroid biosynthesis process, redox process, PPAR pathway and fatty acid metabolism, and galactose metabolism. These results provide a theoretical basis for further research on the role of m6A in muscle growth and development.
Highlights
To date, more than 150 types of posttranscriptional modifications have been identified in the RNA of all living organisms (Boccaletto et al, 2018)
The modification of m6A is involved in many physiological processes, such as: Mediates mRNA output and synthesis, affects cell maturation, lipogenesis, maintains embryonic development stability, affects cell circadian rhythm, regulates stem cell differentiation, maintains Tregs stability, participates in inflammatory response, apoptosis, muscle production, cell Physiological and biochemical processes such as division
New methods based on m6A immunoprecipitation or modified selective RNA chemistry methods to isolate modified RNA fragments coupled with high-throughput sequencing, namely, m6A, Growth and Development, Modification m6A-seq and MeRIP-seq, have identified thousands of hundred-nucleotide fragments containing modifications in the transcriptomes of mammalian cells (Dominissini et al, 2012; Meyer et al, 2012)
Summary
More than 150 types of posttranscriptional modifications have been identified in the RNA of all living organisms (Boccaletto et al, 2018). Biological functions of m6A modification are mediated m6A, Growth and Development, Modification by special binding proteins, including methyltransferases, demethylases, and effectors (Zhang et al, 2019) It is involved in various biological processes, such as lipid production and energy metabolism (Zhao et al, 2014; Wang et al, 2015a). M6A readers protein contains two kinds: one is a stable and direct protein containing YT521-B homology (YTH) domain, and the other is the common RNA binding domain (RBD) (Shi et al, 2019) Both the YTH domain family 1–3 (YTHDF1-3) and the YTH domain containing 1–2 (YTHDC1-2) in humans are stable and directly exercise the reading function of m6A.YTHDF1 and YTHDF3 translation initiation factors promote the translation of target transcripts in cells, and YTHDC2 mediates mRNA stability and translation and regulates cell development (Hsu et al, 2017).
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