Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development

Abstract

Deer antler is the only completely regenerable organ in mammals. During the rapid growth period, the antler proliferates even faster than cancerous tissue growth. However, the proliferation and development of antler have been in a stable and controllable growth cycle. In this study, we analyzed the time series expression data of nine samples from mesenchyme layer in three male sika deer in the early period of the antler with a saddle-like appearance (30 days), the rapid growth period of the antler with two branches (60 days), and the final period of the antler with three branches (90 days). Whole Transcriptome sequencing results show that in the 30 d versus 60 d group, 1,464 genes, 85 long noncoding RNAs (lncRNAs), and 61 miRNAs were identified as differentially expressed; 1,748 genes, 138 lncRNAs, and 78 miRNAs were identified as differentially expressed in 30d versus 90d group; and 816 differentially expressed genes (DEGs), 49 differentially expressed lncRNAs (DE lncRNAs), and 24 differentially expressed miRNA (DE miRNAs) were identified in 60d versus 90d group. A total of 182 miRNA-mRNA interaction pairs and 89 miRNA-lncRNA interaction pairs were screened from DEGs, DE miRNAs, and DE lncRNAs to construct the ceRNA regulatory network (ceRNET). In summary, we identified candidate mRNAs, miRNAs and lncRNAs that regulate the development of antler tip. It may lay the foundation for further investigating the molecular mechanism of antler rapid growth and development.

Integrative Analyses of Antler Cartilage Transcriptome and Proteome of Gansu Red Deer (Cervus elaphus kansuensis) at Different Growth Stages

“…In this study, transcriptomic and proteomic analyses were performed on the antler cartilage tissue of Gansu red deer grown at 30 d, 60 d, and 90 d, and DEGs and DEPs were screened at different growth stages. For RNA-seq, clean reads as a percentage of total raw reads, Q30 values, and GC content are often used to assess the quality of transcriptome sequencing [ 4 ]. The Q30 values were 94.50%, 95.31%, and 94.15% at 30 d, 60 d, and 90 d antler cartilage tissues, respectively.…”

“…Histologically, deer antler is made up of several tissues such as velvet-like skin, cartilage, bone, nerves, and blood vessels [ 3 ]. Deer antleris the only mammalian organs that iscapable of annual regeneration and rapid growth [ 4 ]. Therefore, it is a premier model organ for cancer and regeneration research.…”

Bioactive Molecular Discovery Using Deer Antlers as a Model of Mammalian Regeneration

“…Most candidate genes, as also found with ISH, are recognized as participating in cell proliferation, angiogenesis, chondrogenesis and osteogenesis. − Key identified pathways to-date include PI3K-akt, MAPK, Wnt and Hippo signaling which are highly upregulated in the reserve mesenchymal layer. Wnt signaling has also been found to be necessary in the precartilage layer indicating its roles in the maturation of chondrocytes and osteoblasts. , Transcriptomics conducted on the tip at different stages of growth suggests that differential gene expression could be negatively correlated with the growing stage; i.e., less up-regulated genes were found during rapid growing stage (60 days) compared to the initial growth (15 days) and the ossification stages (90 days). − The SOX9 gene is one of the exceptions due to its highest expression level being found during rapid antler grow; it is regarded as a master regulator involved in chondrogenesis and osteogenesis. ,,, …”

“…Similar to other approaches, research has mainly focused on antler tip tissues from both red and sika deer. Comparison between antler tips from initial and fast growing stages identifies several microRNAs involved in regulating antler chondrogenesis and osteogenesis, for example, miR-140 is highly increasing during the rapid growth stage, with the SOX9 gene as a functional target. , Numerous candidate microRNAs, such as miR-19a and 19b, have been discovered in the reserve mesenchyme and/or cartilage layers of the antler growth center, and are likely to play a role in regulating antler development. ,, MicroRNA sequencing has also been conducted in parallel with the transcriptome sequencing of antlers with extreme heavy and light weights; these researchers found 14 genes and 6 microRNAs linked to antler weight, and show a specific regulatory network encompassing the differentially expressed genes and microRNAs …”

Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development

“…In 2011, Salmena et al proposed the competitive endogenous RNA (ceRNA) hypothesis that protein-coding RNAs and lncRNAs can act as ceRNAs to communicate by competitively binding to miRNAs sites [17,18]. According to the ceRNA hypothesis, many investigators have devoted themselves to elucidating the ceRNA roles of lncRNAs in skeletal muscle myogenesis by constructing ceRNA networks [19][20][21][22].…”