College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Dazhou Institute of Agricultural Sciences, Dazhou, 635000, Sichuan, China.
BMC Genomics. 2018 Jun 27;19(1):498. doi: 10.1186/s12864-018-4891-7.
The liver is mainly hematopoietic in the embryo, and converts into a major metabolic organ in the adult. Therefore, it is intensively remodeled after birth to adapt and perform adult functions. Long non-coding RNAs (lncRNAs) are involved in organ development and cell differentiation, likely they have potential roles in regulating postnatal liver development. Herein, in order to understand the roles of lncRNAs in postnatal liver maturation, we analyzed the lncRNAs and mRNAs expression profiles in immature and mature livers from one-day-old and adult (40 weeks of age) breeder roosters by Ribo-Zero RNA-Sequencing.
Around 21,939 protein-coding genes and 2220 predicted lncRNAs were expressed in livers of breeder roosters. Compared to protein-coding genes, the identified chicken lncRNAs shared fewer exons, shorter transcript length, and significantly lower expression levels. Notably, in comparison between the livers of newborn and adult breeder roosters, a total of 1570 mRNAs and 214 lncRNAs were differentially expressed with the criteria of logfold change > 1 or < - 1 and P values < 0.05, which were validated by qPCR using randomly selected five mRNAs and five lncRNAs. Further GO and KEGG analyses have revealed that the differentially expressed mRNAs were involved in the hepatic metabolic and immune functional changes, as well as some biological processes and pathways including cell proliferation, apoptotic and cell cycle that are implicated in the development of liver. We also investigated the cis- and trans- regulatory effects of differentially expressed lncRNAs on its target genes. GO and KEGG analyses indicated that these lncRNAs had their neighbor protein coding genes and trans-regulated genes associated with adapting of adult hepatic functions, as well as some pathways involved in liver development, such as cell cycle pathway, Notch signaling pathway, Hedgehog signaling pathway, and Wnt signaling pathway.
This study provides a catalog of mRNAs and lncRNAs related to postnatal liver maturation of chicken, and will contribute to a fuller understanding of biological processes or signaling pathways involved in significant functional transition during postnatal liver development that differentially expressed genes and lncRNAs could take part in.
肝脏在胚胎期主要具有造血功能，在成年期则转变为主要的代谢器官。因此，它在出生后会进行密集的重塑，以适应并发挥成人的功能。长链非编码 RNA（lncRNA）参与器官发育和细胞分化，可能在调节出生后肝脏发育方面具有潜在作用。在此，为了了解 lncRNA 在出生后肝脏成熟过程中的作用，我们通过核糖体零 RNA 测序分析了 1 日龄和成年（40 周龄）种公鸡不成熟和成熟肝脏中的 lncRNA 和 mRNA 表达谱。
在种公鸡的肝脏中，大约有 21939 个蛋白编码基因和 2220 个预测的 lncRNA 表达。与蛋白编码基因相比，鉴定出的鸡 lncRNA 具有更少的外显子、更短的转录长度和显著更低的表达水平。值得注意的是，与新生种公鸡肝脏相比，在成年种公鸡肝脏中，共有 1570 个 mRNAs 和 214 个 lncRNA 差异表达，标准为 logfold change >1 或 <-1，P 值 <0.05，通过随机选择的 5 个 mRNAs 和 5 个 lncRNA 的 qPCR 验证。进一步的 GO 和 KEGG 分析表明，差异表达的 mRNAs 参与了肝脏代谢和免疫功能的变化，以及一些生物学过程和途径，包括细胞增殖、凋亡和细胞周期，这些途径与肝脏发育有关。我们还研究了差异表达的 lncRNA 对其靶基因的顺式和反式调节作用。GO 和 KEGG 分析表明，这些 lncRNA 与其相邻的蛋白编码基因和反式调控基因与成年肝脏功能的适应有关，以及一些与肝脏发育相关的途径，如细胞周期途径、Notch 信号通路、Hedgehog 信号通路和 Wnt 信号通路。
本研究提供了与鸡出生后肝脏成熟相关的 mRNAs 和 lncRNAs 目录，将有助于更全面地了解参与出生后肝脏发育过程中重要功能转变的生物学过程或信号通路，差异表达的基因和 lncRNA 可能参与其中。
