Integrated miRNA-mRNA transcriptomic analysis reveals antler growth regulatory network [miRNA-seq]

As the only regenerative organ of mammals, antler could grow rapidly without carcinogenesis. To understand the molecular mechanisms of the growth of sika deer antler, we used de novo RNA-seq analyses to determine the di?erential expression of unigenes and miRNAs from antler at 15, 60, 90, and 110-day. A total of 55004 unigenes, 208 known miRNAs and 38 novel miRNAs were identified. 10182 unigenes and 35 miRNAs were differentially expressed between 60-day and 15-day antler, 13258 unigenes and 53 miRNAs were differentially expressed between 90-day and 60-day antler, and 10740 unigenes and 27 miRNAs were differentially expressed between 110-day and 90-day antler. GO and KEGG analyses showed that DE unigenes and miRNA were mainly related to chondrogenesis, osteogenesis and inhibition of oncogenesis, that were closely associate with antler growth. We also constructed mRNA-mRNA and miRNA-mRNA interaction networks related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler. The results showed that mRNA (COL2A1, SOX9, WWP2, FGFR1, SPARC, LOX etc.) and miRNAs (miR-145, miR-199a-3p, miR-140, miR-199a-5p etc.) may play important roles in chondrogenesis and osteogenesis of antler, and mRNA (TP53, Tpm3 and ATP1A1 etc.) and miRNAs (miR-106a, miR-145, miR-1260b and miR-2898 etc.) may have key roles in inhibiting the carcinogenesis of antlers. In this study, we identified miRNAs and unigenes related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler. This will provide a reference for in-depth analysis of the molecular mechanism of antler growth without carcinogenesis, and also provide valuable information for cartilage- and bone-related disease treatment, cancer treatment. Overall design: The miRNA expression profiles of antler at 15, 60, 90, and 110-day in sika deer were generated by Illumina HiSeq2500 sequencing

鹿茸（antler）作为哺乳动物唯一的可再生器官，能够快速生长且不发生癌变。为解析梅花鹿鹿茸生长的分子机制，本研究采用从头转录组测序（de novo RNA-seq）技术，检测了15、60、90和110日龄鹿茸的单基因（unigene）与微小RNA（miRNA）的差异表达情况。共鉴定得到55004个单基因、208个已知微小RNA以及38个新型微小RNA。在60日龄与15日龄鹿茸样本中，共有10182个单基因和35个微小RNA存在差异表达；90日龄与60日龄样本间则有13258个单基因和53个微小RNA差异表达；110日龄与90日龄样本间差异表达的单基因和微小RNA分别为10740个和27个。基因本体（Gene Ontology，GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）富集分析显示，差异表达单基因与微小RNA主要富集于软骨形成、骨形成以及癌变抑制相关通路，这些过程与鹿茸生长密切相关。本研究还构建了与鹿茸软骨形成、骨形成及癌变抑制相关的mRNA-mRNA与miRNA-mRNA互作网络。研究结果显示，mRNA（COL2A1、SOX9、WWP2、FGFR1、SPARC、LOX等）与微小RNA（miR-145、miR-199a-3p、miR-140、miR-199a-5p等）可能在鹿茸软骨形成与骨形成过程中发挥重要作用；而mRNA（TP53、Tpm3、ATP1A1等）与微小RNA（miR-106a、miR-145、miR-1260b、miR-2898等）则可能在鹿茸癌变抑制过程中起到关键调控作用。本研究鉴定得到了与鹿茸软骨形成、骨形成及癌变抑制相关的微小RNA与单基因，可为深入解析鹿茸无癌变生长的分子机制提供参考，同时也为软骨与骨相关疾病治疗以及癌症治疗提供了有价值的理论依据。实验整体设计：采用Illumina HiSeq2500测序技术，获取梅花鹿15、60、90和110日龄鹿茸的微小RNA表达谱。