N⁶-methyladenosine (m⁶A) is the most common modification in eukaryotic RNAs. Accumulating evidence shows m⁶A methylation plays vital roles in various biological processes, including muscle and fat differentiation. However, there is a lack of research on lncRNAs’ m⁶A modification in regulating pig muscle-fiber-type conversion. In this study, we identified novel and differentially expressed lncRNAs in oxidative and glycolytic skeletal muscles through RNA-seq, and further reported the m⁶A-methylation patterns of lncRNAs via MeRIP-seq. We found that most lncRNAs have one m⁶A peak, and the m⁶A peaks were preferentially enriched in the last exon of the lncRNAs. Interestingly, we found that lncRNAs’ m⁶A levels were positively correlated with their expression homeostasis and levels. Furthermore, we performed conjoint analysis of MeRIP-seq and RNA-seq data and obtained 305 differentially expressed and differentially m⁶A-modified lncRNAs (dme-lncRNAs). Through QTL enrichment analysis of dme-lncRNAs and PPI analysis for their cis-genes, we finally identified seven key m⁶A-modified lncRNAs that may play a potential role in muscle-fiber-type conversion. Notably, inhibition of one of the key lncRNAs, MSTRG.14200.1, delayed satellite cell differentiation and stimulated fast-to-slow muscle-fiber conversion. Our study comprehensively analyzed m⁶A modifications on lncRNAs in oxidative and glycolytic skeletal muscles and provided new targets for the study of pig muscle-fiber-type conversion.

The composition of muscle fibers, characterized by distinct contractile and metabolic properties, significantly influences meat quality and glucose homeostasis. However, the mechanisms by which three-dimensional (3D) genome topology integrates with epigenetic states to regulate muscle fiber specification and transformation remain poorly understood. Here, we present an integrative analysis of the transcriptome, epigenome, and 3D genome architecture in the slow-twitch glycolytic extensor digitorum longus (EDL) and fast-twitch oxidative soleus (SOL) muscles of the pig (Sus scrofa). Global remodeling of enhancer-promoter (E-P) interactions emerged as a central driver of transcriptional reprogramming associated with muscle contraction and glucose metabolism. We identified tissue-specific super-enhancers (SEs) that regulate muscle fiber-type specification through cooperation of chromatin looping and transcription factors such as KLF5. Notably, the SE-driven activation of STARD7 facilitated the transformation of glycolytic fibers into oxidative fibers by mitigating reactive oxygen species levels and suppressing ERK MAPK signaling. This study elucidates the principles of 3D genome organization in the epigenetic regulation of muscle fiber specification and transformation, providing a foundation for novel therapeutic strategies targeting metabolic disorders and enhancing meat quality.

Proper placental development is crucial for the conceptus to grow and survive, because the placenta is responsible for transporting nutrients and oxygen from the pregnant female to the developing fetus. However, the processes of placental morphogenesis and fold formation remain to be fully elucidated. In this study, we used whole-genome bisulfite sequencing and RNA sequencing to produce a global map of DNA methylation and gene expression changes in placentas from Tibetan pig fetuses 21, 28, and 35 days post-coitus. Substantial changes in morphology and histological structures at the uterine–placental interface were revealed via hematoxylin–eosin staining. Transcriptome analysis identified 3959 differentially expressed genes (DEGs) and revealed the key transcriptional properties in three stages. The DNA methylation level in the gene promoter was negatively correlated with gene expression. We identified a set of differentially methylated regions associated with placental developmental genes and transcription factors. The decrease in DNA methylation level in the promoter was associated with the transcriptional activation of 699 DEGs that were functionally enriched in cell adhesion and migration, extracellular matrix remodeling, and angiogenesis. Our analysis provides a valuable resource for understanding the mechanisms of DNA methylation in placental development. The methylation status of different genomic regions plays a key role in establishing transcriptional patterns from placental morphogenesis to fold formation.

Birth weight is a complex multifactorial trait relevant to health states and disease risks in later life. The placenta is essential for proper fetal growth and facilitates gas, nutrient, and waste exchange between the mother and developing fetus. How changes in placental DNA methylation affect fetal birth weight remains to be fully elucidated. In this study, we used whole-genome bisulfite sequencing and RNA sequencing to reveal a global map of DNA methylation and gene expression changes between the placentas of highest birth weight and lowest birth weight piglets in the same litters. The transcriptome analysis identified 1682 differential expressed genes and revealed key transcriptional properties in distinct placentas. We also identified key transcription factors that may drive the differences in DNA methylome patterns between placentas. The decrease in DNA methylation level in the promoter was associated with the transcriptional activation of genes associated with angiogenesis, extracellular matrix remodeling, and transmembrane transport. Our results revealed the regulatory role of DNA methylation in gene transcription activity leading to the differences in placental morphological structures and birth weights of piglets. These results could provide novel clues to clarify the underlying regulatory mechanisms of placental development and fetal growth.

Skeletal muscle is the largest heterogeneous organ in the body, and multiple factors in intrinsic genetic and epigenetic regulation influence its growth. The N⁶-methyladenosine ed(m⁶A) modification is a conserved and most prevalent RNA modification, whose function is dependent on m⁶A writers, erasers, and m⁶A readers, such as the YTH protein family. YTHDC1 is the only member of the YTH protein family member that exists in the cell nucleus, which plays an important role in mRNA alternative polyadenylation and alternative splicing processes. However, the function of YTHDC1 in regulating myoblast proliferation, differentiation, and in vivo skeletal muscle development remains unclear. Therefore, in this study, we studied the function of YTHDC1 in C2C12 cell line and mouse. Our results showed that YTHDC1 significantly promoted myogenic differentiation while inhibiting myoblast proliferation in C2C12 cells, and the results of our in vivo experiment showed that interfering with YTHDC1 led to a significant enhancement of muscle growth in mice. Furthermore, the transcriptome sequencing analysis revealed that YTHDC1 might modulate skeletal muscle development by regulating alternative splicing of genes, including Akap13, Smarca2, Tnnt3, and Neb. Our study shed light on understanding the function and molecular mechanisms of YTHDC1 in regulating skeletal muscle development, highlighting the critical contribution of m⁶A-mediated RNA splicing in muscle growth. These results indicated that YTHDC1 could be a potential breeding target gene to enhance meat quality in livestock.