Identification of novel reference genes using sika deer antler transcriptome expression data and their validation for quantitative gene expression analysis

Liu, Meichen; Yao, Baojin; Zhang, Hui; Guo, Huanyu; Hu, Dongyang; Wang, Qun; Zhao, Yu

doi:10.1007/s13258-014-0193-x

Cited by 10 publications

(5 citation statements)

References 30 publications

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“…Therefore, the selection of a suitable reference gene to study specific objects or experimental conditions is an important factor for gene expression analysis by RT-qPCR. Recently, with the rapid development of new biotechnology, transcriptome sequencing has been applied to identify new reference genes in various species, including monkey [ 10 ], buckwheat [ 11 ], crazyweed [ 12 ], deer [ 13 ], rice [ 14 ], and oilseed rape [ 15 ], and the results show that the new reference genes are more stably expressed and that the orthologs of these genes are suitable reference genes in different species that have a close relationship [ 11 ]. Therefore, examination of transcriptome-sequencing data may be a useful method to identify more reliable reference genes for RT-qPCR studies on specific fauna or under different experimental conditions.…”

Section: Introductionmentioning

confidence: 99%

Selection and evaluation of new reference genes for RT-qPCR analysis in Epinephelus akaara based on transcriptome data

et al. 2017

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Groupers are an economically important fish species in world fishery markets. Because many studies using RT-qPCR have addressed gene expression in groupers, appropriate reference genes are required to obtain reliable and accurate results. In this study, the most suitable reference genes were identified from eleven candidate genes of one of the most valuable species, Epinephelus akaara, in a range of different experimental conditions. Using the software packages geNorm, NormFinder, BestKeeper and refFinder, three traditionally used reference genes, β-actin (β-ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and beta-2-microglobulin (B2M), were identified as not suitable for E. akaara gene expression studies, whereas two newly identified reference genes, conserved oligomeric Golgi complex subunit 5 (Cog5) and brefeldin a-inhibited guanine nucleotide-exchange protein 1 (ARFGEF1), could be universally applied under all the tested conditions. These data provide the foundation for more precise results in RT-qPCR studies of gene expression in E. akaara and other Epinephelus species.

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Section: Introductionmentioning

confidence: 99%

Selection and evaluation of new reference genes for RT-qPCR analysis in Epinephelus akaara based on transcriptome data

et al. 2017

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“…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. ,,, …”

Section: Deer Antler Biomolecules Discovered From Other Approachesmentioning

confidence: 99%

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

Dong

Coates

2021

J. Proteome Res.

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The ability to activate and regulate stem cells during wound healing and tissue regeneration is a promising field that is resulting in innovative approaches in the field of regenerative medicine. The regenerative capacity of invertebrates has been well documented; however, in mammals, stem cells that drive organ regeneration are rare. Deer antlers are the only known mammalian structure that can annually regenerate to produce a tissue containing dermis, blood vessels, nerves, cartilage, and bone. The neural crest derived stem cells that drive this process result in antlers growing at up to 2 cm/day. Deer antlers thus provide superior attributes compared to lower-order animal models, when investigating the regulation of stem cell-based regeneration. Antler stem cells can therefore be used as a model to investigate the bioactive molecules, biological processes, and pathways involved in the maintenance of a stem cell niche, and their activation and differentiation during organ formation. This review examines stem cell-based regeneration with a focus on deer antlers, a neural crest stem cell-based mammalian regenerative structure. It then discusses the omics technical platforms highlighting the proteomics approaches used for investigating the molecular mechanisms underlying stem cell regulation in antler tissues.

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“…However, a limited number of studies can be found in the literature that evaluated the stability of expression of various genes using more than two approaches in red deer and none in the antler blood. In recent years, increasing evidence has shown that two or more reference genes need to be evaluated for stable expression for use in normalizing expression data 25 . In an experimental design with multiple samples, a balance needs to be reached between the use of multiple genes in multiple samples and the degree of accuracy required 26 .…”

Section: Introductionmentioning

confidence: 99%

Evaluation of candidate reference genes for quantitative real-time PCR normalization in blood from red deer developing antlers

Broggini

Abril

Carranza

et al. 2022

Sci Rep

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Sexual selection favors male traits that increase their ability to monopolize the breeding access to several females. Deer antlers are cranial appendages that regenerate annually in males. Throughout life, the phenology of antler growth advances and antler mass increases until the stag reaches, between 8 and 10 years old, maximum body mass and highest reproductive success. The molecular mechanisms of antler development are of great interest in both evolutionary and regenerative medicine studies. To minimize errors in the assessment of gene expression levels by qRT-PCR, we analyzed the stability of a panel of eight candidate reference genes and concluded that qRT-PCR normalization to three stable genes is strongly convenient in experiments performed in red deer antler blood. To validate our proposal, we compared the expression level of three genes linked to red deer antler growth (ANXA2, APOD and TPM1) in fifteen male red deer classified as young (up to 4 years old) and adults (4–6 years old). Our data confirms that B2M, ACTB and RPLP0 are valuable reference genes for future gene expression studies in red deer antler blood, which would provide increased insight into the effects of intrinsic factors that determine antler development in red deer.

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Identification of novel reference genes using sika deer antler transcriptome expression data and their validation for quantitative gene expression analysis

Cited by 10 publications

References 30 publications

Selection and evaluation of new reference genes for RT-qPCR analysis in Epinephelus akaara based on transcriptome data

Selection and evaluation of new reference genes for RT-qPCR analysis in Epinephelus akaara based on transcriptome data

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

Evaluation of candidate reference genes for quantitative real-time PCR normalization in blood from red deer developing antlers

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