Cold exposure induces the acquisition of brown adipocyte gene expression profiles in cattle inguinal fat normalized with a new set of reference genes for qRT-PCR

Cao, Kan; Hao, Dan; Wang, J.; Peng, Wenwen; Yan, Ying; Cao, Handi; Sun, Fenghua; Chen, Hong

doi:10.1016/j.rvsc.2017.02.021

Cited by 12 publications

(6 citation statements)

References 35 publications

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“…Among them, CTNNB1 and PFDN5 genes have the lowest coefficient of variation. In addition, we selected four reference genes ( TBP , PPIA , HPRT , and RPLP0 ) according to previous studies in white and brown adipose tissue [ 24 , 25 , 26 ]. Four traditional reference genes were also used, including GAPDH , 18SrRNA , YWHAZ , and ACTB genes [ 27 , 28 , 29 ].…”

Section: Resultsmentioning

confidence: 99%

Using RNA-Seq to Identify Reference Genes of the Transition from Brown to White Adipose Tissue in Goats

Wang

Chen

Song

et al. 2020

Animals

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Brown adipose tissues have unique non-shivering thermogenesis functions, can be found in newborn ruminate animals, and then are gradually replaced by white adipose tissues in adulthood. For the purpose of exploring the intrinsic mechanism underlying the conversion process from brown (BAT) to white adipose tissue (WAT), it is necessary to utilize Quantitative PCR (qPCR) to study gene expression profiling. In this study, we identified reference genes that were consistently expressed during the transformation from goat BAT to WAT using RNA-seq data. Then, twelve genes were evaluated as candidate reference genes for qPCR in goat perirenal adipose tissue using three tools (geNorm, Normfinder, and BestKeeper). In addition, the selected reference genes were used to normalize the gene expression of PGC-1α and GPAT4. It was found that traditional reference genes, such as GAPDH, RPLP0, HPRT1, and PPIA were not suitable for target gene normalization. In contrast, CTNNB, PFDN5, and EIF3M, selected from RNA sequencing data, showed the least variation and were recommended as the best reference genes during the transformation from BAT to WAT.

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Section: Resultsmentioning

confidence: 99%

Using RNA-Seq to Identify Reference Genes of the Transition from Brown to White Adipose Tissue in Goats

Wang

Chen

Song

et al. 2020

Animals

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“…Many studies of the selection of RGs in bovine adipose tissue have been published. − Nevertheless, in no studies analyses were performed on samples arising from cattle treated with PDN.…”

Section: Resultsmentioning

confidence: 99%

Reference Gene Selection and Prednisolone Target Gene Expression in Adipose Tissues of Friesian Cattle

Divari

Berio

Biolatti

et al. 2017

J. Agric. Food Chem.

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Corticosteroids are frequently used in livestock production, and their use is permitted by the European Union for therapeutic purposes only. However, small doses of corticosteroids are often administered in meat-producing animals to improve zootechnical performance. Prednisolone is one of the most commonly used corticosteroids with a growth-promoting purpose in animal husbandry. This study proposes to identify a gene whose expression is significantly regulated by prednisolone in visceral and subcutaneous adipose tissues. The analysis was conducted on Friesian cattle treated with prednisolone (30 mg day). The reference gene expression stability and optimal number for gene expression normalization were calculated. Family with sequence similarity 107 member A (FAM107A) and pyruvate dehydrogenase kinase 4 are the prednisolone target genes identified in adipose tissue. FAM107A was downregulated by ∼2.9-fold by prednisolone in subcutaneous adipose tissue. This result suggests that FAM107A could be a possible indirect biomarker of prednisolone treatment in cattle and encourages a deeper investigation in this direction.

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“…In another report, COX7A1 was identified as an indirect target of HIF1A via Activin/Nodal signaling providing intriguing indications of potential COX7A1 involvement in key phenotypic and metabolic differences between embryonic and adult cells [ 44 ]. Consistent with its role in metabolism, COX7A1 regulation has been implicated in diabetes [ 45 ] and is induced during browning of white adipose [ 46 , 47 ].…”

Section: Discussionmentioning

confidence: 99%

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells

West¹,

Labat²,

Sternberg³

et al. 2017

Oncotarget

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Here we present the application of deep neural network (DNN) ensembles trained on transcriptomic data to identify the novel markers associated with the mammalian embryonic-fetal transition (EFT). Molecular markers of this process could provide important insights into regulatory mechanisms of normal development, epimorphic tissue regeneration and cancer. Subsequent analysis of the most significant genes behind the DNNs classifier on an independent dataset of adult-derived and human embryonic stem cell (hESC)-derived progenitor cell lines led to the identification of COX7A1 gene as a potential EFT marker. COX7A1, encoding a cytochrome C oxidase subunit, was up-regulated in post-EFT murine and human cells including adult stem cells, but was not expressed in pre-EFT pluripotent embryonic stem cells or their in vitro-derived progeny. COX7A1 expression level was observed to be undetectable or low in multiple sarcoma and carcinoma cell lines as compared to normal controls. The knockout of the gene in mice led to a marked glycolytic shift reminiscent of the Warburg effect that occurs in cancer cells. The DNN approach facilitated the elucidation of a potentially new biomarker of cancer and pre-EFT cells, the embryo-onco phenotype, which may potentially be used as a target for controlling the embryonic-fetal transition.

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Cold exposure induces the acquisition of brown adipocyte gene expression profiles in cattle inguinal fat normalized with a new set of reference genes for qRT-PCR

Cited by 12 publications

References 35 publications

Using RNA-Seq to Identify Reference Genes of the Transition from Brown to White Adipose Tissue in Goats

Using RNA-Seq to Identify Reference Genes of the Transition from Brown to White Adipose Tissue in Goats

Reference Gene Selection and Prednisolone Target Gene Expression in Adipose Tissues of Friesian Cattle

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells

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