Transcriptome Analysis And Identification Of Long Noncoding Rna In Adipose Tisuues Of Qinchuan Beef Cattle

Adipogenesis of cattle is regulated by various functional genes or regulatory elements. To explore the regulate network on adipogenesis may help us to better understand the molecular mechanism of adipogenesis and is also benefit for the beef cattle breeding. Here in our research, by using high throughput sequencing methods, we analyzed the transcriptome of different adipose of cattle, including subcutaneous fat tissue from female cattle at the age of 20 month（SAT） and 6 month（WSAT）, respectively, and the visceral fat tissue from the female cattle at age of 20 month（VAT）. Based on the RNA-seq analysis, a large number of differentially expressed genes and long noncoding RNAs（lnc RNA） were identified and the expression levels were valided by q RT-PCR assay. We analyzed the classification, chromosome distribution, and other sequence information of lnc RNA, meaningful information was obtained. At last, we conducted a dual luciferase reporter assay to analyze the interaction of Lnc₆25 and bta-mi R-125 b. The mainly results as follows:1. By using RNA-seq, a large number of clean reads with high qualiy were obtained, 60% of them can be mapped on the reference genome which means that our RNA-seq is highthroughput and may reflect the transcriptome features of cattle adipose tissues.2. Compared SAT vs VAT, 5864 differentially expressed genes were identified, including 2979 genes up-regulated in VAT while 2885 were down-regulated. Function enrichmen analysis revealed that DE-expressed genes were invoved in various biological processes including lipid metabolism and immune response.3. Compared WSAT vs SAT, 6226 genes were identified differentially expressed in which 3379 were up-regulated in WSAT. Higher expression levels of these genes may cause higher activities in energy metabolism and cell differentiation.4. By comparing with the reference genome, large number of SNVs and INDELs were identified, we further analyzed the mutations in IGFALS gene and NCAPG gene, association analysis indicated the IGFALS may affect body height of cattle, while NCAPG gene might asscociated with carcass weight.5. By predicting the coding potiential of transcrips, we identified 10817, 8340 and 7183 lnc RNAs expressed in SAT, VAT, and WSAT, respectively.6. Most lnc RNAs in cattle adipose tissues are linc RNAs, then is intronic lnc RNA, antisensense lnc RNAs have the fewest numbers. Lnc RNAs is equally expressed in the chromosome. Compared with protein genes, the lnc RNAs are shorter in length, expressed at lower levels and has lower sequence conservation.7. A total of 14824 lnc RNAs were found differential expressed between VAT and SAT, by analyzing their neighbor genes, the differential expressed lnc RNAs may cause differential protein synthesis activities of these two tissues.8. A total of 11467 lnc RNAs were found differential expressed between SAT and WSAT and functional enrichment analysis revealed that these lnc RNAs may participated in lipid metabolism and signal transduction.9. At last we used dual luciferase reporter assay to analyze the interaction of Lnc₆25 and bta-mi R-125 b, bta-mi R-125 b mimics does affect the luciferase activity of mutant recombinant plasmid but significant reduce the luciferase activity of wild type recombinant plasmid which suggested that Lnc₆25 is the target gene of bta-mi R-125 b.Taken together, this research provides valuable information to better understand the transcriptome of cattle adipose tissue.