Dataset Information

Intrinsic features in microRNA transcriptomes link porcine visceral rather than subcutaneous adipose tissues to metabolic risk.

ABSTRACT: MicroRNAs (miRNAs) are non-coding small RNA ?22 nucleotides in length that can regulate the expression of a wide range of coding genes at the post-transcriptional level. Visceral adipose tissues (VATs) and subcutaneous adipose tissues (SATs), the two main fat compartments in mammals, are anatomically, physiologically, metabolically, and clinically distinct. Various studies of adipose tissues have focused mainly on DNA methylation, and mRNA and protein expression, nonetheless little research sheds directly light on the miRNA transcriptome differences between these two distinct adipose tissue types. Here, we present a comprehensive investigation of miRNA transcriptomes across six variant porcine adipose tissues by small RNA-sequencing. We identified 219 known porcine miRNAs, 97 novel miRNA*s, and 124 miRNAs that are conserved to other mammals. A set of universally abundant miRNAs (i.e., miR-148a-3p, miR-143-3p, miR-27b-3p, miR-let-7a-1-5p, and miR-let-7f-5p) across the distinct adipose tissues was found. This set of miRNAs may play important housekeeping roles that are involved in adipogenesis. Clustering analysis indicated significant variations in miRNA expression between the VATs and SATs, and highlighted the role of the greater omentum in responding to potential metabolic risk because of the observed enrichment in this tissue of the immune- and inflammation-related miRNAs, such as the members of miR-17-92 cluster and miR-181 family. Differential expression of the miRNAs between the VATs and SATs, and miRNA target prediction analysis revealed that the VATs-specific enriched miRNAs were associated mainly with immune and inflammation responses. In summary, the differences of miRNA expression between the VATs and SATs revealed some of their intrinsic differences and indicated that the VATs might be closely associated with increased risk of metabolic disorders.

SUBMITTER: Ma J

PROVIDER: S-EPMC3819305 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Intrinsic features in microRNA transcriptomes link porcine visceral rather than subcutaneous adipose tissues to metabolic risk.

Ma Jideng J Jiang Zhi Z He Shen S Liu Yingkai Y Chen Lei L Long Keren K Jin Long L Jiang An'an A Zhu Li L Wang Jinyong J Li Mingzhou M Li Xuewei X

PloS one 20131106 11

MicroRNAs (miRNAs) are non-coding small RNA ∼22 nucleotides in length that can regulate the expression of a wide range of coding genes at the post-transcriptional level. Visceral adipose tissues (VATs) and subcutaneous adipose tissues (SATs), the two main fat compartments in mammals, are anatomically, physiologically, metabolically, and clinically distinct. Various studies of adipose tissues have focused mainly on DNA methylation, and mRNA and protein expression, nonetheless little research shed ...[more]

PMID: 24223210

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Project description:BackgroundFat accumulation in visceral adipose tissue (VAT) confers increased risk for metabolic disorders of obesity, whereas accumulation of subcutaneous adipose tissue (SAT) is associated with lower risk and may be protective. Previous studies have shed light on the gene expression profile differences between SAT and VAT; however, the chromatin accessibility landscape differences and how the cis-regulatory elements govern gene expression changes between SAT and VAT are unknown.MethodsPig were used to characterize the differences in chromatin accessibility between the two adipose depots-derived stromal vascular fractions (SVFs) using DNase-sequencing (DNase-seq). Using integrated data from DNase-seq, H3K27ac ChIP-sequencing (ChIP-seq), and RNA-sequencing (RNA-seq), we investigated how the regulatory locus complexity regulated gene expression changes between SAT and VAT and the possible impact that these changes may have on the different biological functions of these two adipose depots.ResultsSVFs form SAT and VAT (S-SVF and V-SVF) have differential chromatin accessibility landscapes. The differential DNase I hypersensitive site (DHS)-associated genes, which indicate dynamic chromatin accessibility, were mainly involved in metabolic processes and inflammatory responses. Additionally, the Krüppel-like factor family of transcription factors were enriched in the differential DHSs. Furthermore, the chromatin accessibility data were highly associated with differential gene expression as indicated using H3K27ac ChIP-seq and RNA-seq data, supporting the validity of the differential gene expression determined using DNase-seq. Moreover, by combining epigenetic and transcriptomic data, we identified two candidate genes, NR1D1 and CRYM, could be crucial to regulate distinct metabolic and inflammatory characteristics between SAT and VAT. Together, these results uncovered differences in the transcription regulatory network and enriched the mechanistic understanding of the different biological functions between SAT and VAT.

Project description:BackgroundAdipose tissue plays important roles in health and disease. Given the unique association of visceral adipose tissue with obesity-related metabolic diseases, the distribution of lipids between the major fat depots located in subcutaneous and visceral regions may shed new light on adipose tissue-specific roles in systemic metabolic perturbations.ObjectiveWe sought to characterize the lipid networks and unveil differences in the metabolic infrastructure of the 2 adipose tissues that may have functional and nutritional implications.MethodsPaired visceral and subcutaneous adipose tissue samples were obtained from 17 overweight patients undergoing elective abdominal surgery. Ultra-performance LC-MS was used to measure 18,640 adipose-derived features; 520 were putatively identified. A stem cell model for adipogenesis was used to study the functional implications of the differences found.ResultsOur analyses resulted in detailed lipid metabolic maps of the 2 major adipose tissues. They point to a higher accumulation of phosphatidylcholines, triacylglycerols, and diacylglycerols, although lower ceramide concentrations, in subcutaneous tissue. The degree of unsaturation was lower in visceral adipose tissue (VAT) phospholipids, indicating lower unsaturated fatty acid incorporation into adipose tissue. The differential abundance of phosphatidylcholines we found can be attributed at least partially to higher expression of phosphatidylethanolamine methyl transferase (PEMT). PEMT-deficient embryonic stem cells showed a dramatic decrease in adipogenesis, and the resulting adipocytes exhibited lower accumulation of lipid droplets, in line with the lower concentrations of glycerolipids in VAT. Ceramides may inhibit the expression of PEMT by increased insulin resistance, thus potentially suggesting a functional pathway that integrates ceramide, PEMT, and glycerolipid biosynthetic pathways.ConclusionsOur work unveils differential infrastructure of the lipid networks in visceral and subcutaneous adipose tissues and suggests an integrative pathway, with a discriminative flux between adipose tissues.

Dataset Information

Intrinsic features in microRNA transcriptomes link porcine visceral rather than subcutaneous adipose tissues to metabolic risk.

Publications

Intrinsic features in microRNA transcriptomes link porcine visceral rather than subcutaneous adipose tissues to metabolic risk.

Similar Datasets

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