A New lncRNA, lnc-LLMA, Regulates Lipid Metabolism in Pig Hepatocytes

LncRNA ENSGALG00000021686 regulates fat metabolism in chicken hepatocytes via miR-146b/AGPAT2 pathway

The liver contributes to lipid metabolism as the hub of fat synthesis. Long non-coding RNAs (lncRNAs) are considered the regulators of cellular processes. Since LncRNA ENSGALG00000021686 (lncRNA 21 686) has been described as a regulator of lipid metabolism, the present study aimed to clarify the role of lncRNA 21 686 in chicken hepatocytes' lipid metabolism. Thirty-two chickens were divided into four groups and were treated with diets containing different amounts of fat, and the hepatic expression of lncRNA 21 686 and miR-146b along with the levels of proteins involved in the regulation of fat metabolism, lipid indices and oxidative stress were measured. Moreover, primary chicken hepatocytes were transfected with lncRNA 21 686 small interfering RNA or microRNA (miRNA, miR)-146b mimics to measure the consequences of suppressing lncRNA or inducing miRNA expression on the levels of proteins involved in fat metabolism and stress markers. The results showed that the high-fat diet modulated the expression of lncRNA 21 686 and miR-146b (p-value < 0.001). Moreover, there was a significant increase in 1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (AGPAT2) gene expression and protein levels and modulated fat-related markers. Furthermore, the results showed that lncRNA 21 686 suppression reduced the expression of AGPAT2 and its downstream proteins (p-value < 0.05). Overexpression of miR-146b regulated fat metabolism indicator expression. Transfection experiments revealed that lncRNA 21 686 suppression increased miR-146b expression. The findings suggested a novel mechanism containing lncRNA 21 686/miR-146b/AGPAT2 in the regulation of fat metabolism in chicken hepatocytes.

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Structural variants (SVs), such as deletions (DELs) and insertions (INSs), contribute substantially to pig genetic diversity and phenotypic variation. Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes, we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes. Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation. Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. We identify that the genotypes of two DELs (296-bp DEL, chr7: 52,172,101-52,172,397; 278-bp DEL, chr18: 23,840,143-23,840,421) located in muscle-specific enhancers are associated with the expression of target genes related to meat quality (FSD2) and muscle fiber hypertrophy (LMOD2 and WASL) in pigs. Our results highlight the role of SVs in domestic porcine evolution, and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

The landscape of super-enhancer regulates remote target gene transcription through loop domains in adipose tissue of pig

Background

A super-enhancer (SE) is a huge cluster of multiple enhancers that control the key genes for cell identity and function. The rise of advanced chromatin immunoprecipitation sequencing (ChIP-seq) technology such as Cleavage Under Targets and Tagmentation (CUT&Tag) allows more SEs to be discovered. However, SE studies in Luchuan and Duroc pigs are very rare in animal husbandry.

Results

We used the CUT&Tag technique to identify 145 and 378 SEs from the adipose tissues of Luchuan and Duroc pigs, respectively. There were significant differences in the peak coverage ratio of SE peaks in the gene promoter region between the two breeds. Not only that, peak signals at the start and end point of the SE peak profile showed obvious spikes. The proximal target genes of SE were highly expressed compared with the background genes and the typical enhancer target genes. Subsequently, in conjoint analysis with high-throughput chromosome conformation capture sequencing (Hi-C seq) data, we predicted the remote regulatory genes of SE and found that their expression level was related to the distance of SE extended to the loop's anchor, but not the length of loops. According to our prediction model, SEs can maintain promoter accessibility of partial remote target genes through loop domains. Finally, a batch of SEs closely related to fat metabolism traits were obtained by performing a coalition analysis of quantitative trait loci and SE data.

Conclusions

This work enabled us to obtain hundreds of SEs from Luchuan and Duroc pigs. Our model provides a new method for predicting the SE remote target genes based on loop domains, and to further explore the potential role of super-enhancer in the regulation of fat metabolism.

Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs

BACKGROUND

As the largest substantive organ of animals, the liver plays an essential role in the physiological processes of digestive metabolism and immune defense. However, the cellular composition of the pig liver remains poorly understood. This investigation used single-nucleus RNA sequencing technology to identify cell types from liver tissues of pigs, providing a theoretical basis for further investigating liver cell types in pigs.

RESULTS

The analysis revealed 13 cells clusters which were further identified 7 cell types including endothelial cells, T cells, hepatocytes, Kupffer cells, stellate cells, B cells, and cholangiocytes. The dominant cell types were endothelial cells, T cells and hepatocytes in the liver tissue of Dahe pigs and Dahe black pigs, which accounts for about 85.76% and 82.74%, respectively. The number of endothelial cells was higher in the liver tissue of Dahe pigs compared to Dahe black pigs, while the opposite tendency was observed for T cells. Moreover, functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic endothelial cells were significantly enriched in the protein processing in endoplasmic reticulum, MAPK signaling pathway, and FoxO signaling pathway. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic T cells were significantly enriched in the thyroid hormone signaling pathway, B cell receptor signaling pathway, and focal adhesion. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic hepatocytes were significantly enriched in the metabolic pathways.

CONCLUSIONS

In summary, this study provides a comprehensive cell atlas of porcine hepatic tissue. The number, gene expression level and functional characteristics of each cell type in pig liver tissue varied between breeds.

Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs

Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds.

Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig

Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.