Comparative Transcriptome Analysis of Adipose Tissues Reveals that ECM-Receptor Interaction Is Involved in the Depot-Specific Adipogenesis in Cattle

Abstract

Adipocytes mainly function as energy storage and endocrine cells. Adipose tissues showed the biological and genetic difference based on their depots. The difference of adipocytes between depots might be influenced by the inherent genetic programing for adipogenesis. We used RNA-seq technique to investigate the transcriptomes in 3 adipose tissues of omental (O), subcutaneous (S) and intramuscular (I) fats in cattle. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the bovine genome using Tophat2. Differentially expressed genes (DEG) between adipose tissues were detected by EdgeR. We identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively and also found 5657 DEGs in the comparison between the intramuscular and the combined omental and subcutaneous fats (C) (FDR<0.01). Depot specifically up- and down- regulated DEGs were 853 in S, 48 in I, and 979 in O. The numbers of DEGs and functional annotation studies suggested that I had the different genetic profile compared to other two adipose tissues. In I, DEGs involved in the developmental process (eg. EGR2, FAS, and KLF7) were up-regulated and those in the immune system process were down-regulated. Many DEGs from the adipose tissues were enriched in the various GO terms of developmental process and KEGG pathway analysis showed that the ECM-receptor interaction was one of commonly enriched pathways in all of the 3 adipose tissues and also functioned as a sub-pathway of other enriched pathways. However, genes involved in the ECM-receptor interaction were differentially regulated depending on the depots. Collagens, main ECM constituents, were significantly up-regulated in S and integrins, transmembrane receptors, were up-regulated in I. Different laminins were up-regulated in the different depots. This comparative transcriptome analysis of three adipose tissues suggested that the interactions between ECM components and transmembrane receptors of fat cells depend on the depot specific adipogenesis.

Bioinformatics method identifies potential biomarkers of dilated cardiomyopathy in a human induced pluripotent stem cell-derived cardiomyocyte model

“…The findings of the present study indicated that the DEG ITGB6 in DCM was significantly enriched in the ECM-receptor interaction pathway. Notably, ECM-receptor interaction is also involved in DCM pathway (35). Thus, it can be inferred that ECM-receptor interaction may be an important pathway for DCM, which may be altered by the integrin gene ITGB6.…”

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data

“…ECM‐receptor interaction is reportedly related to adipose tissue (Lee et al . 2013). These results indicate that these variants may be the reason for enhanced fat deposition in these Chinese indigenous pigs.…”

Effect of different early weaning regimens for calves on adipogenic gene expression in Hanwoo loin at the fattening stage

“…Most of our samples obtained reads in excess of 30 Mbp. Many studies have already shown that reads of around 30 Mbp were adequate in detecting 90% of annotated genes in cattle, and chicken (Lee et al, 2013;Li et al, 2011;Wang et al, 2011). These references suggest that our data had sufficient coverage, even though the tissue used for this study was different from that of previous studies.…”

“…EdgeR provided Cox-Reid profile methods to estimate the dispersion for the pairwise comparisons between control and T1, control and T2, control and T3, T1 and T2, T1 and T3, and T2 and T3 dietary treatment groups. The remaining Cox-Reid common volume dispersion methods were followed as published in our earlier study (Lee et al, 2013). In this study, important DEGs for each pairwise comparison were selected at FDR of 0.01.…”

“…Amplification was carried out for 1 cycle at 95°C for 10 min followed by 40 cycles at 95°C for 30 s, then held at specific annealing temperatures (Table S2) for 30 s, held at 72°C for 30 s, and subjected to 1 cycle of 72°C for 10 min. Glyceraldehyde-3-phosphate dehydrogenase and β-actin primer sequences were taken from our previous study (Lee et al, 2013). These genes were used as internal controls for normalization to make the results more reliable.…”