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Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Sus scrofa

PROVIDER: GSE193609 | GEO | 2022/06/07

REPOSITORIES: GEO

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Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig [miRNA-seq]

Project description:Purpose: In this study, RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes. Method:The clean reads were mapped to the pig reference genome (scrofa. Sscrofa11.1) with perfect matches using Bowtie software. Annotated tRNA, rRNA, snoRNA, and snRNA sequences were filtered out, and conserved miRNAs were identified by the BLAST method against miRBase. The miRDeep2 software was used to predict new miRNAs based on the characteristics of the miRNA precursor hairpin structure. Differential expression analysis of two groups was performed using the DESeq2 R package. Differentially expressed miRNAs (DE-miRNAs) were screened with criterion of fold change > 1.5 and FDR < 0.05 using DESeq2. Target genes of DE-miRNAs were predicted by miRanda and targetscan. Results: We found 30 genes that mainly regulate the differentiation of subcutaneous adipocytes and 22 genes that mainly regulate the differentiation of subcutaneous intramuscular adipocytes. A total of 17 important candidate differential miRNAs were found, of which 4 miRNAs are believed to play a regulatory role in both types of cells, and 10 and 3 act on lipid deposition in subcutaneous and intramuscular adipocytes, respectively.

2022-06-07 | GSE193608 | GEO

Project description:Purpose: In this study, RNA-Seq was performed on intramuscular adipocytes and subcutaneous adipocytes at 0, 2, 4, and 8 days of differentiation to find genes and miRNAs that regulate the differentiation of two types of adipocytes. Methods: High-throughput sequencing was performed with NovaSeq 6000, and 150 paired-end reads were generated.Clean reads were filtered using HISAT2. The StringTie was used to assemble the transcript and calculate fragments per kilobase million mapped reads (FPKM) value. Results: We found 30 genes that mainly regulate the differentiation of subcutaneous adipocytes and 22 genes that mainly regulate the differentiation of subcutaneous intramuscular adipocytes. A total of 17 important candidate differential miRNAs were found, of which 4 miRNAs are believed to play a regulatory role in both types of cells, and 10 and 3 act on lipid deposition in subcutaneous and intramuscular adipocytes, respectively.

2022-06-07 | GSE193607 | GEO

Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig

Project description:Comparative Transcriptomic Profiles of Adipocyte in Differentiation Process Provide Insights into Different Mechanisms of Adipogenesis between Subcutaneous and Intramuscular Fat Tissues in Pig

| PRJNA796932 | ENA

| PRJNA796934 | ENA

| PRJNA796933 | ENA

MiR-218-5p Affects Subcutaneous Adipogenesis by Targeting ACSL1, a Novel Candidate for Pig Fat Deposition.

Project description:As a centre enzyme in fatty acid activation, acyl-CoA synthetase long-chain family member 1 (ACSL1) plays an important role in body lipid homeostasis. However, the functions of ACSL1 in the subcutaneous adipogenesis of pigs are largely unknown. In the present study, we found that the expression of ACSL1 significantly increased during the process of porcine preadipocyte differentiation. Moreover, silencing of ACSL1 in preadipocytes decreased levels of triglyceride and adipogenic-related markers, including FABP4, APOE, and FASN (p < 0.01), and simultaneously increased levels of lipolytic-related markers, such as ATGL and HSL (p < 0.05). Conversely, overexpression of ACSL1 in preadipocytes increased levels of triglyceride and FABP4, APOE, and FASN (p < 0.01), and reduced levels of ATGL and HSL (p < 0.05). Luciferase reporter assays revealed that ACSL1 is a target of miR-218-5p, which can reduce the mRNA and protein levels of ACSL1 by directly binding the 3' untranslated region of ACSL1. Furthermore, miR-218-5p has an inhibition role in porcine preadipocyte differentiation by suppressing ACSL1 expression. Taken together, these data provide insights into the mechanism of the miR-218-5p/ACSL1 axis in regulating subcutaneous fat deposition of pigs.

| S-EPMC8871969 | biostudies-literature

MicroRNAome comparison between intramuscular and subcutaneous vascular stem cell adipogenesis.

Project description:BackgroundAs an important factor affecting meat quality, intramuscular fat (IMF) content is a topic of worldwide concern. Emerging evidences indicate that microRNAs play important roles in adipocyte differentiation. However, miRNAome has neither been studied during porcine intramuscular preadipocyte differentiation, nor compared with subcutaneous preadipocytes. The objectives of this study were to identify porcine miRNAs involved in adipogenesis in primary preadipocytes, and to determine whether intramuscular and subcutaneous adipocytes differ in the expression and regulation of miRNAs.ResultsmiRNAomes in primary intramuscular and subcutaneous adipocytes during differentiation were first sequenced using the Solexa deep sequencing method. The sequences and relative expression levels of 224 known (98.2% in miRbase 18.0) and 280 potential porcine miRNAs were identified. Fifty-four of them changed in similar pattern between intramuscular vascular stem cells (IVSC) and subcutaneous vascular stem cells (SVSC) differentiation, such as miR-210, miR-10b and miR-99a. Expression levels of 10 miRNAs were reversely up-or down-regulated between IVSC and SVSC differentiation, 19 were up-or down-regulated only during IVSC differentiation and 55 only during SVSC differentiation. Additionally, 30 miRNAs showed fat-depot specific expression pattern (24 in cells of intramuscular origin and 6 in cells of subcutaneous origin). These adipogenesis-related miRNAs mainly functioned by targeting similar pathways in adipogenesis, obesity and syndrome.ConclusionComparison of miRNAomes in IVSC and SVSC during differentiation revealed that many different miRNAs are involved in adipogenesis, and they regulate SVSC and IVSC differentiation through similar pathways. These miRNAs may serve as biomarkers or targets for enhancing IMF content, and uncovering their function in IMF development will be of great value in the near future.

| S-EPMC3447870 | biostudies-literature

Genomic Insights into Molecular Regulation Mechanisms of Intramuscular Fat Deposition in Chicken.

Project description:Intramuscular fat (IMF) plays an important role in the tenderness, water-holding capacity, and flavor of chicken meat, which directly affect meat quality. In recent years, regulatory mechanisms underlying IMF deposition and the development of effective molecular markers have been hot topics in poultry genetic breeding. Therefore, this review focuses on the current understanding of regulatory mechanisms underlying IMF deposition in chickens, which were identified by multiple genomic approaches, including genome-wide association studies, whole transcriptome sequencing, proteome sequencing, single-cell RNA sequencing (scRNA-seq), high-throughput chromosome conformation capture (HiC), DNA methylation sequencing, and m6A methylation sequencing. This review comprehensively and systematically describes genetic and epigenetic factors associated with IMF deposition, which provides a fundamental resource for biomarkers of IMF deposition and provides promising applications for genetic improvement of meat quality in chicken.

| S-EPMC10742768 | biostudies-literature

Muscle-specific downregulation of GR levels inhibits adipogenesis in porcine intramuscular adipocyte tissue.

Project description:Intramuscular adipose is conducive to good pork quality, whereas subcutaneous adipose is considered as waste in pig production. So uncovering the regulation differences between these two adiposes is helpful to tissue-specific control of fat deposition. In this study, we found the sensitivity to glucocorticoids (GCs) was lower in intramuscular adipocytes (IMA) compared with subcutaneous adipocytes (SA). Comparison of glucocorticoid receptor (GR) revealed that IMA had lower GR level which contributed to its reduced GCs sensitivity. Higher methylation levels of GR promotor 1-C and 1-H were detected in IMA compared with SA. GR expression decrease was also found in adipocytes when treated with muscle conditioned medium (MCM) in vitro, which resulted in significant inhibition of adipocytes proliferation and differentiation. Since abundant myostatin (MSTN) was detected in MCM by ELISA assay, we further investigated the effect of this myokine on adipocytes. MSTN treatment suppressed adipocytes GR expression, cell proliferation and differentiation, which mimicked the effects of MCM. The methylation levels of GR promotor 1-C and 1-H were also elevated after MSTN treatment. Our study reveals the role of GR in muscle fiber inhibition on intramuscular adipocytes, and identifies myostatin as a muscle-derived modulator for adipose GR level.

| S-EPMC5428816 | biostudies-literature

Theaflavin-Enriched Fraction Stimulates Adipogenesis in Human Subcutaneous Fat Cells.

Project description:Skin provides the first defense line against the environment while preserving physiological homeostasis. Subcutaneous tissues including fat depots that are important for maintaining skin structure and alleviating senescence are altered during aging. This study investigated whether theaflavin (TF) in green tea (GT) has skin rejuvenation effects. Specifically, we examined whether high ratio of TF contents can induce the subcutaneous adipogenesis supporting skin structure by modulating lipid metabolism. The co-fermented GT (CoF-GT) fraction containing a high level of TF was obtained by co-fermentation with garland chrysanthemum (Chrysanthemum coronarium) and the conventionally fermented GT (F-GT) fraction was also obtained. The effects of the CoF- or F-GT fractions on adipogenesis were assessed using primary human subcutaneous fat cells (hSCF). Adipogenesis was evaluated based on lipid droplet (LD) formation, as visualized by Oil Red O staining; by analyzing of adipogenesis-related factors by real-time quantitative polyperase chain reaction (RT-qPCR); and by measuring the concentration of adiponectin released into the culture medium by enzyme-linked immunosorbent assay. TF-enriched CoF-GT fraction did not adversely affect hSCF cell viability but induced their adipogenic differentiation, as evidenced by LD formation, upregulation of adipogenesis-related genes, and adiponectin secretion. TF and TF-enriched CoF-GT fraction promoted differentiation of hSCFs and can therefore be used as an ingredient in rejuvenating agents.

| S-EPMC6515531 | biostudies-literature

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