Unknown,Transcriptomics,Genomics,Proteomics

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Comparative transcriptome analysis of various adipose depots in Hanwoo

ABSTRACT: *Background: Adipocytes mainly function as energy storage and endocrine cells. The amount and distribution of fat are important factor that influence the meat quality in the beef industry. Fat depot can be found around internal organ (ometal), beneath the skin (subcutaneous), and between muscles (intramuscular). Different adipose depot showed the biological and genetic difference depending on their location. This inter-depot variation might be influenced by the inherent genetic programing for development of adipose depots. In this study, we used RNA-seq data to investigate the difference in transcriptome of various adipose depots in Hanwoo. *Results: Using RNA-seq, we identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively (FDR<0.01) and found 853, 48, and 979 DEGs specific to subcutaneous, intramuscular and omental fat respectively. DEGs in intramuscular fat were highly enriched the metabolism related pathways compared to other fat depots. DEGs specific to the omental fat is significantly enriched in PPAR signaling pathway and cell-junction related pathway. In subcutaneous fat, cytokine-cytokine receptor interaction with chemokines (CXC and CC subfamily) was the most significantly enriched the pathways. Interestingly, melanogenesis pathway was associated with the subcutaneous depot. Even though the adipose tissues shared the same pathways for adipocyte differentiation, the regulation of genes were different based on the depot. *Conclusions: We comparatively analyzed the transcripome profile from different adipose tissues using NGS and identified DEGs between adipose depot and specific to depot in Hanwoo animals. The functional annotation analysis of DEGs found that transcriptome profile difference in various adipose tissue of intramuscular, subcutaneous, and ometal fat. whole mRNA sequencing profiles of nine Korean native cattle (nine profiles of omental fat tissue, nine profiles of intramuscular fat tissue, nine profiles of subcutaneous fat tissue and eight profiles of muscle tissue)

ORGANISM(S): Bos taurus

SUBMITTER: HYEONGMIN KIM

PROVIDER: E-GEOD-39618 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Adipose tissue is found throughout the human body. The diversity of physiological specialization of fat depots is reflected in the depot-specific alterations seen in lipodystrophies and links between specific patterns of fat distribution and susceptibility to diseases, including Type II Diabetes. We compared gene expression patterns in seven anatomically diverse fat depots and in adipocytes and stromal-vascular cells isolated from each sample. Adipocytes from different depots displayed distinct gene expression profiles. Characteristic patterns of expression of HOX genes distinguished adipocyte samples by site of origin. These depot-specific patterns were recapitulated when adipocyte precursors from each site were differentiated ex vivo, suggesting that these genes may have roles in specifying the depot-specific differentiation of adipocytes. Adipocyte expression of 300 genes with roles in energy metabolism showed both depot-dependent and inter-individual variation. Genes involved in glycogen metabolism and de novo fatty acid synthesis were generally most highly expressed in breast and abdominal subcutaneous adipocytes, suggesting a role for these depots in buffering glucose levels. Indeed, the role of adipocytes in primary metabolism of carbohydrate-rich foods may be considerably more important than has been appreciated. Genes involved in lipid uptake and hormone-stimulated lipolysis were on average most highly expressed in pericolonic, omental, and breast adipocytes; their expression covaried with each other and with that of the adipogenic transcription factor PPARG2. Two isoforms of PPARG, PPARG1 and PPARG2, were expressed in distinct patterns, each paralleling a discrete set of putative targets, suggesting that their differential regulation might influence important depot-specific and inter-individual differences in adipocytes. Dozens of genes encoding secreted proteins and receptors were highly expressed in adipocytes compared to adipose stromal-vascular cells and/or other tissues; many of these genes were not previously associated with adipocyte functions and are candidates for novel roles in sensing and signaling energy status to regulate global energy homeostasis.