Tao Xuelian, Chen Jianning, Jiang Yanzhi, Wei Yingying, Chen Yan, Xu Huaming, Zhu Li, Tang Guoqing, Li Mingzhou, Jiang Anan, Shuai Surong, Bai Lin, Liu Haifeng, Ma Jideng, Jin Long, Wen Anxiang, Wang Qin, Zhu Guangxiang, Xie Meng, Wu Jiayun, He Tao, Huang Chunyu, Gao Xiang, Li Xuewei
Department of Zoology, College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an City, 625014, Sichuan Province, China.
Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
BMC Genomics. 2017 Apr 28;18(1):336. doi: 10.1186/s12864-017-3719-1.
N -methyladenosine (mA) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible mA methylation on mRNA have been revealed by mapping of mA methylomes in several species. mA modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on mA porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth.
In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever mA porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps.
Our findings show that there were 5,872 and 2,826 mA peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3'-untranslated regions, and coding regions were found to be mainly enriched for mA peaks. Gene ontology analysis revealed that common mA peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between mA mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the mA methylation extent and the transcript level, suggesting a regulatory role for mA in gene expression.
This comprehensive map provides a solid basis for the determination of potential functional roles for RNA mA modification in adipose deposition and muscle growth.
N-甲基腺苷（mA）是高等真核生物信使核糖核酸中最普遍的内部修饰形式，并且通过对多个物种的mA甲基化组进行定位，已经揭示了mRNA上可逆mA甲基化的潜在调控功能。活跃基因调控中的mA修饰以组织特异性方式或响应细胞或物种生存环境变化，表现为甲基化谱的改变。然而，迄今为止，尚无关于猪转录组范围的mA图谱及其在脂肪沉积和肌肉生长中的潜在生物学作用的数据。
在本研究中，我们使用甲基化RNA免疫沉淀结合下一代测序（MeRIP-Seq）技术，获得了首张猪转录组范围的mA图谱。利用来自三个不同猪品种（野猪、长白猪和荣昌猪）的肌肉和脂肪组织转录组来生成这些图谱。
我们的研究结果表明，在猪肌肉和脂肪组织转录组中分别有5872个和2826个mA峰。发现终止密码子、3'非翻译区和编码区主要富集了mA峰。基因本体分析显示，核基因中的常见mA峰与转录因子相关，这表明mA mRNA甲基化与核基因组转录之间存在关联。一些基因表现出组织和品种差异甲基化，并具有新的生物学功能。我们还发现了mA甲基化程度与转录水平之间的关系，表明mA在基因表达中具有调控作用。
这一全面的图谱为确定RNA mA修饰在脂肪沉积和肌肉生长中的潜在功能作用提供了坚实基础。
