Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs
Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs
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编码基因和非编码RNA的转录组分析揭示了中国五指山猪黑背白腹毛表型背后的复杂调控网络
DOI：
10.3390/genes10030201
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发表时间：
2019-03
期刊：
影响因子：
3.5
通讯作者：
Fang Meiying
中科院分区：
文献类型：
--
作者：
Xu Qiao;Liu Ximing;Chao Zhe;Wang Kejun;Wang Jue;Tang Qiguo;Luo Yabiao;Zheng Jie;Tan Shuyi;Fang Meiying
毛色是区分中国地方猪种的重要特征之一。五指山猪的背部是黑色的，腹部是白色的。然而，这种表型的分子遗传基础尚不清楚。在这项研究中，我们使用高通量RNA测序技术比较了五指山猪个体皮肤样本中编码RNA和非编码RNA的表达谱。表达谱分析显示，194种lncRNAs（长链非编码rna）、189种mrna（信使rna）和162种miRNAs （microRNAs）在白皮肤和黑皮肤中表达水平显著不同（|log2 fold change| > 1， p值< 0.05）。与黑皮肤的RNA水平相比，白皮肤的185个lncrna、181个mrna和23个mirna的表达水平较高，9个lncrna、8个mrna和139个mirna的表达水平较低。功能分析表明，这些差异表达的转录物参与了黑色素生物合成、色素沉着和酪氨酸代谢等生物过程。参与黑色素形成的几个关键基因，包括MLANA、PMEL、TYR、TYRP1、DTC、TRPM1和CAMK2A，在两种皮肤组织中的表达水平有显著差异。潜在的lncrna - mirna -基因相互作用也被检查。15个lncrna、11个mirna和7个基因共组成23对lncrna - mirna -基因对，提示五指山猪毛色性状由复杂的编码和非编码基因调控网络决定。我们的研究为理解lncRNA、miRNA和基因如何相互作用调控黑背/白腹猪的毛色提供了基础。我们还构建了lncrna - mirna -基因相互作用网络，以阐明皮肤生理和黑色素形成的复杂分子机制。这一结果扩展了我们对不同家畜被毛颜色多样性的认识，并为研究中国土生猪被毛颜色控制的新机制提供了基础。
Coat color is one of the most important characteristics for distinguishing Chinese indigenous pig breeds. In Wuzhishan pigs, the animals have black on the back and white on the abdomen. However, the molecular genetic basis of this phenotype is unclear. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. The expression profiling revealed that 194 lncRNAs (long non-coding RNAs), 189 mRNAs (messenger RNAs), and 162 miRNAs (microRNAs) had significantly different levels of expression (|log2 fold change| > 1, p-value < 0.05) in white and black skin. Compared to RNA levels in black skin, white skin had higher levels of expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs and lower levels of expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthesis, pigmentation and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1 and CAMK2A, had significantly different levels of expression in the two skin tissues. Potential lncRNA–miRNA–gene interactions were also examined. A total of 15 lncRNAs, 11 miRNAs and 7 genes formed 23 lncRNA–miRNA–gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. Our study provides a foundation for understanding how lncRNA, miRNA and genes interact to regulate coat color in black-back/white-belly pigs. We also constructed lncRNA–miRNA–gene interaction networks to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis. The results extend our knowledge about the diversity of coat color among different domestic animals and provide a foundation for studying novel mechanisms that control coat color in Chinese indigenous pigs.
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影响因子：
3.6
作者：
Andl T;Botchkareva NV
通讯作者：
Botchkareva NV
影响因子：
14.9
作者：
Wang L;Park HJ;Dasari S;Wang S;Kocher JP;Li W
通讯作者：
Li W
影响因子：
--
作者：
Yu, Shigang;Wang, Gang;Sun, Wenxing
通讯作者：
Sun, Wenxing
影响因子：
5.4
作者：
Kornienko AE;Guenzl PM;Barlow DP;Pauler FM
通讯作者：
Pauler FM
DOI：
--
发表时间：
2013
期刊：
--
影响因子：
--
作者：
L. Fontanesi;V. Russo
通讯作者：
L. Fontanesi;V. Russo