Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea.
Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Republic of Korea.
Gene. 2019 Jun 30;703:71-82. doi: 10.1016/j.gene.2019.04.014. Epub 2019 Apr 5.
Long non coding RNAs (lncRNA) have been previously found to be involved in important cellular activities like epigenetics, implantation, cell growth etc. in pigs. However, comprehensive analysis of lncRNA in back fat tissues at different developmental stages in pigs is still lacking. In this study we conducted transcriptome analysis in the back fat tissue of a F1 crossbred Korean Native Pig (KNP) × Yorkshire Pig to identify lncRNA. We investigated their role in 16 pigs at two different growth stages; stage 1 (10 weeks, n = 8) and stage 2 (26 weeks, n = 8). After quality assessment of sequencing reads, we got a total of 1,641,165 assembled transcripts out of eight paired end read from each stage. Among them, 6808 lncRNA transcripts were identified by filtering on the basis of multiple parameters like read length ≥ 200 nucleotides, exon numbers ≥2, FPKM ≥0.5, coding potential score < 0 etc. PFAM and RFAM were used to filter out all possible protein coding genes and housekeeping RNAs respectively. A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed (DE) between the two stages (|log2FC| > 2, q < 0.05). We also identified 306 genes located around 100 kb upstream and 234 genes downstream around these DE lncRNA transcripts. The expression of top eleven DE lncRNAs (COL4A6, LY7S, MYH2, OXCT1, SMPDL3A, TMEM182, TTC36, RFOOOO4, RFOOO15, RFOOO45, CADM2) had been validating by qRT-PCR. Pathway and GO terms analysis showed that, positive regulation of biosynthetic process, Wnt signaling pathway, cellular protein modification process, and positive regulation of nitrogen compound were differentially enriched. Our results suggested that, KEGG pathways such as protein digestion and absorption, Arrhythmogenic right ventricular cardiomyopathy (ARVC) to be significantly enriched in both DE lncRNAs as well as DE mRNAs and involved in back fat tissues development. It also suggests that, identified lncRNAs are involved in regulation of important adipose tissues development pathways.
长链非编码 RNA（lncRNA）已被发现参与猪的重要细胞活动，如表观遗传学、着床、细胞生长等。然而，在猪的不同发育阶段的背脂组织中，对 lncRNA 的综合分析仍然缺乏。在这项研究中，我们对 F1 杂交韩国本地猪（KNP）×约克夏猪的背脂组织进行了转录组分析，以鉴定 lncRNA。我们研究了它们在两个不同生长阶段的 16 头猪中的作用；阶段 1（10 周，n=8）和阶段 2（26 周，n=8）。在对测序读取进行质量评估后，我们从每个阶段的 8 对末端读取中总共获得了 1641165 个组装转录本。其中，通过基于多个参数（如读长≥200 个核苷酸、外显子数量≥2、FPKM≥0.5、编码潜能评分<0 等）过滤，鉴定出 6808 个 lncRNA 转录本。PFAM 和 RFAM 分别用于过滤掉所有可能的蛋白质编码基因和管家 RNA。在两个阶段之间，共发现 103 个 lncRNA 和 1057 个 mRNA 差异表达（|log2FC|>2，q<0.05）。我们还鉴定了这些差异表达 lncRNA 转录本上下游约 100kb 的 306 个基因和 234 个基因。前 11 个差异表达 lncRNA（COL4A6、LY7S、MYH2、OXCT1、SMPDL3A、TMEM182、TTC36、RFOOOO4、RFOOO15、RFOOO45、CADM2）的表达通过 qRT-PCR 进行了验证。通路和 GO 术语分析表明，生物合成过程的正调控、Wnt 信号通路、细胞蛋白修饰过程和含氮化合物的正调控是有差异的富集。我们的结果表明，KEGG 途径，如蛋白质消化吸收、心律失常性右心室心肌病（ARVC），在差异表达的 lncRNA 和 mRNAs 中都显著富集，并参与背脂组织的发育。这也表明，鉴定出的 lncRNA 参与了重要脂肪组织发育途径的调控。
