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Genome-wide identification and comparison of mRNAs, lncRNAs, and circRNAs in porcine intramuscular, subcutaneous, retroperitoneal, and mesenteric adipose tissues

ABSTRACT: Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), which were proved to play a crucial role in regulating cell differentiation and tissue development. However, the expression profiles of different RNAs, such as mRNA, lncRNAs, and circRNAs in different adipose tissues, are still largely unclear. To shed light on this issue, we performed the systematic analysis of mRNAs, lncRNAs, and circRNAs obtained from intramuscular adipose tissues (IAT), subcutaneous adipose tissues (SAT), visceral adipose tissues (RPAT), and mesenteric adipose tissues (MAT) tissues of Chinese Erhualian pigs using high-throughput sequencing. A total of 1,695, 1,878, 494, 1,300, 902, and 355 differentially expressed (DE) mRNAs, 318, 399, 192, 251, 249, and 347 DE lncRNAs, 1,367, 1,007, 999, 1,153, 1,256, and 837 DE circRNAs were identified in IAT versus SAT, IAT versus RPAT, SAT versus RPAT, MAT versus IAT, MAT versus SAT, and MAT versus RPAT, respectively. Gene ontology (GO) enrichment analyses showed these DE genes were mainly involved in lipid metabolic and immune response. Next the co-expression network construction of mRNAs-lncRNAs revealed several key lncRNAs such as MSTRG.604204 and MSTRG.604206 might associated with lipid metabolic. Tissue specific analysis indicated that circRNA exhibited the highest tissue specificity than lncRNA and mRNA, and the IAT had the most tissue specific lncRNA, mRNA, and circRNA compared with other tissues. Taken together, this study gives us a novel clue to the role of mRNAs, lncRNAs and circRNAs in fat metabolism, thus improving our understanding of the regulation mechanism of different gene expression profiles in adipose deposition

ORGANISM(S): Sus scrofa

PROVIDER: GSE110478 | GEO | 2019/02/09

REPOSITORIES: GEO

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Project description:Purpose: Whole-transcriptome sequencing technology and bioinformatics analysis were applied to systematically analyze the differentially expressed mRNAs, lncRNAs, circRNAs and miRNAs in adipose stem cells (ASCs) from diabetic, old and young patients. Methods: MRNAs, lncRNAs and cirRNAs profiles of adipose stem cells were generated by RNA sequencing, in triplicate, using Illumina HiSeq X Ten . MiRNAs profiles of adipose stem cells were generated by RNA sequencing, in triplicate, using BGISEQ-500. The sequence reads that passed quality filters were analyzed at the transcript isoform level by using sequence analysis programs, including HISAT, Stringtie, CIRI, find_circ and DESeq. qRT–PCR validation was performed using Takara, Vazyme and Clontech kits. Results: The data showed that 1377 mRNAs, 5353 circRNAs, 932 lncRNAs and 85 miRNAs were significantly differently expressed in adipose stem cells from old patients compared with young patients, with a fold change ≥2 or ≤ -2 and q value <0.001. The data showed that 1878 mRNAs, 22988 circRNAs, 2638 lncRNAs and 122 miRNAs were significantly differently expressed (DE) in adipose stem cells from old patients compared with diabetic patients, with a fold change ≥2 or ≤ -2 and q value <0.001. The results of qRT-PCR confirmed 25 mRNAs, 9 lncRNAs, 8 circRNAs and 13 miRNAs which were consistent with the RNA-seq data. GO and KEGG analyses demonstrated DE mRNAs were significantly enriched in aging and cell senescence terms separately. Conclusion: Our group simultaneously examined the changing expression of miRNAs, mRNAs, lncRNAs and circRNAs in ASCs associated with diabetes and aging. GO and KEGG pathway analyses were conducted to annotate the possible function of the differentially expressed mRNAs. PPI networks were established in order to find critical protein genes highly involved in our disease models. The ceRNA networks including lncRNA-miRNA-mRNA and cirRNA-miRNA-mRNA interactions were successfully constructed based on the bioinformatic analyses and PCR results. Thus, this study may contribute to our understanding of the underlying mechanisms of ASCs instability and provide novel targets to reverse the dysfunction of ASCs isolated from diabetic and old patients.

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Genome-wide identification and comparison of mRNAs, lncRNAs, and circRNAs in porcine intramuscular, subcutaneous, retroperitoneal, and mesenteric adipose tissues

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