Genome-wide characterization of lncRNAs and mRNAs in muscles with differential intramuscular fat contents

Abstract

Meat quality is one of the most important traits in pig production. Long non-coding RNAs (lncRNAs) have been involved in diverse biological processes such as muscle development through regulating gene expression. However, studies on lncRNAs lag behind and a comparatively small number of lncRNAs have been identified in pigs. Also, the effects of lncRNAs on meat quality remain to be characterized. Here, we analyzed lncRNAs in longissimus thoracis (LT) and semitendinosus (ST) muscles, being different in meat quality, with RNA-sequencing technology. A total of 500 differentially expressed lncRNAs (DELs) and 2,094 protein-coding genes (DEGs) were identified. Through KEGG analysis on DELs, we first made clear that fat deposition might be the main reason resulting in the differential phenotype of LT and ST, for which cGMP–PKG and VEGF signaling pathways were the most important ones. In total, forty-one key DELs and 50 DEGs involved in the differential fat deposition were then characterized. One of the key genes, cAMP-response element binding protein 1, was selected to confirm its role in porcine adipogenesis with molecular biology methods and found that it promotes the differentiation of porcine preadipocytes, consistent with its higher expression level and intramuscular fat contents in LT than that in ST muscle. Furthermore, through integrated analysis of DELs and DEGs, transcription factors important for differential fat deposition were characterized among which BCL6 has the most target DEGs while MEF2A was targeted by the most DELs. The results provide candidate genes crucial for meat quality, which will contribute to improving meat quality with molecular-breeding strategies.

A Parasite Odyssey: An RNA virus concealed inToxoplasma gondii

“…Due to a paucity of data within the family Narnaviridae , and the divergent nature of Ao, we re-queried Serratus for Ao-like RdRp palmprints. We retrieved and assembled 166 matching runs from 46 BioProjects with 32 species-like operational taxonomic units (sOTUs) (186 distinct virus-run observations, Supplementary Table S3) (Chen et al, 2022; Zhou et al, 2021; Gil and Hird, 2022; Gao et al, 2021; He et al, 2021; Chen et al, 2021b; Rhie et al, 2021; Bittner et al, 2022; Chen et al, 2021a; Xie et al, 2021; Cui et al, 2022; Wen et al, 2022; Zhou et al, 2022b; Sun et al, 2022; Wu et al, 2021). We recovered relevant Narnavirus RdRp contigs for all 32/32 (100%) sOTU, of which 22/32 (75%) contained a sufficiently long RdRp sequence ( ≈ 390 amino acids, motif F-E (Venkataraman et al, 2018) and thumb) for robust phylogenetic reconstruction.…”

Effects of HOXC8 on the Proliferation and Differentiation of Porcine Preadipocytes

“…We performed RNA-seq to identify fat-associated genes using muscles from different depots and pig breeds that differed in fat contents previously [ 21 , 27 ]. Through rechecking these data, we found that the expression of HOXC8 was associated with the fat contents of muscle.…”

“…The RNA-seq data were processed as described previously [ 21 ]. Briefly, the raw reads were cleaned using SOAPnuke software (v2.1.0) [ 22 ] with default parameters.…”

“…The differentially expressed genes (DEGs) were identified with DESeq2 (v1.22.2) [ 23 ] and the threshold was set as absolute Log2 fold change (FC) ≥ 1, p < 0.05 (unless otherwise indicated). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to analyze the function of DEGs as described previously [ 21 ]. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) ( , accessed on 1 June 2022) was used to reveal the interaction between DEGs with default parameters, and the results were visualized with Cytoscape.…”