Single Nucleotide Polymorphisms of Porcine lncMGPF Regulate Meat Production Traits by Affecting RNA Stability

Abstract

lncMGPF is a novel positive regulator of myogenic differentiation, muscle growth and regeneration in mouse, pig, and human. But whether natural mutations within lncMGPF gene regulate animal meat production traits is unclear. In this study, ten single nucleotide polymorphisms (SNPs) of pig lncMGPF (plncMGPF) gene were identified among commercial pig breeds and Chinese local pig breeds. These SNPs are highly linked and constructed into multiple haplotypes, and haplotype ATTCATGTTC (H1) mainly exists in commercial pig breeds while haplotype GCCTGCACCT (H3) is more frequent in Chinese local pig breeds. Association analysis indicated that all SNPs are significantly associated with the backfat thickness and loin muscle area (P < 0.05), respectively, and homologous H1 individuals have higher loin muscle area and lower backfat thickness than H3 pigs. Bioinformatics and functional analysis showed that haplotype H1 has a longer half-life and more stable RNA secondary structure than haplotype H3. plncMGPF haplotype H1 has stronger effects on pig primary myogenic progenitor cells differentiation and muscle growth than haplotype H3. Further experiments showed that two SNPs (rs81403974 and rs325492834) function together to confer plncMGPF stability and function. Our observation suggested that the SNPs in lncMGPF can change the RNA stabilities and lncMGPF function, thereby affecting the porcine meat production traits.

Circular Intronic RNA circTTN Inhibits Host Gene Transcription and Myogenesis by Recruiting PURB Proteins to form Heterotypic Complexes

“…Chen et al [ 39 ] pointed out that circMYBPC1 can directly bind MyHC protein, promote the differentiation of myoblasts, and possibly promote skeletal muscle regeneration. One study showed that LncMGPF promoted the expression of HuR in C2C12 cytoplasm, enhancing the stability of MyoD and MyoG mRNA, and thus promoting myogenesis [ 40 , 41 ]. In this study, we found that PURB and the TTN promoter have a binding motif through the use of the UCSC genome browser and PROMO database, and we found that circTTN overexpression promoted the binding of PURB and the TTN promoter and inhibited the generation of the TTN gene.…”

The Functional Role of Long Non-Coding RNA in Myogenesis and Skeletal Muscle Atrophy

“…Additionally, lncMGPF promoted human antigen R (HuR)-mediated mRNA stabilization of both MyoD and myogenin ( Figure 1 , left panel) [ 83 ]. Interestingly, 10 single nucleotide polymorphisms (SNPs) in pig lncMGPF have been identified in commercial and Chinese local pig breeds [ 84 ]. These SNPs are linked to lncMGPF stability and skeletal muscle growth.…”

Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs

“…In addition, SNPs located in lncRNAs can affect the expression level of ln-cRNAs by modifying their secondary structures. For example, SNPs in the lncMGPF gene can affect the secondary structures and stability of RNA, thereby regulating the growth and development of muscle (Lv et al, 2021). However, only very few functional SNPs in lncRNAs have been identified until now.…”

“…Since then, relevant databases containing porcine lncRNAs, such as ALDB (Li et al., 2015), LncRNAnet (Liang et al., 2018), NONCODEV5 (Fang et al., 2018) and lncRNASNP v3 (Yang et al., 2022), have been established successively. Moreover, many functional lncRNAs affecting muscle growth and development have been identified, such as H19 (Li et al., 2020), Neat1 (Wang et al., 2020), MEG3 (Cheng et al., 2020) and plncMGPF (Lv et al., 2021).…”