Abstract
The extent to which mammalian cells share similar transcriptomes remains unclear. Notwithstanding, such cross-species gene expression inquiries have been scarce for defined cell types and most lack the dissection of gene regulatory landscapes. Therefore, the work was aimed to determine C-MYC relative expression across mammalian fibroblasts (Ovis aries and Bos taurus) via cross-species RT-qPCR and comprehensively explore its regulatory landscape by in silico tools. The prediction of transcription factor binding sites in C-MYC and its 2.5 kb upstream sequence revealed substantial variation, thus indicating evolutionary-driven re-wiring of cis-regulatory elements. C-MYC and its downstream target TBX3 were up-regulated in Bos taurus fibroblasts. The relative expression of C-MYC regulators [RONIN (also known as THAP11), RXRβ, and TCF3] and the C-MYC-associated transcript elongation factor CDK9 did not differ between species. Additional in silico analyses suggested Bos taurus-specific C-MYC exonization, alternative splicing, and binding sites for non-coding RNAs. C-MYC protein orthologs were highly conserved, while variation was in the transactivation domain and the leucine zipper motif. Altogether, mammalian fibroblasts display evolutionary-driven C-MYC relative expression that should be instructive for understanding cellular physiology, cellular reprogramming, and C-MYC-related diseases.
Highlights
Cell types arise by stepwise acquisition of specific gene expression programs during development and have stable cellular phenotypes throughout organism adulthood[1]
One such report has found that the expression of two TFs (TLR4 and ZFX) were up-regulated in Bos taurus (B. taurus) fibroblasts compared to Ovis aries (O. aries) counterparts using rigorous reverse transcription quantitative PCR (RT-qPCR) n ormalization[12]
The TF-binding sites (TFBS) prediction for C-MYC, RXRβ, and TCF3 demonstrated species-specific variation, reinforcing the notion of evolutionary-driven re-wiring of cis-regulatory elements (CRE)
Summary
Cell types arise by stepwise acquisition of specific gene expression programs during development and have stable cellular phenotypes throughout organism adulthood[1]. Cross-species gene expression analysis becomes an attractive strategy to assist unraveling evolutionary-driven differences in the gene expression regulatory landscape[8] This comparative transcriptomic approach— largely based upon RNA sequencing—has been informative, most of them account for analysis carried out with whole organs[7,9]. One such report has found that the expression of two TFs (TLR4 and ZFX) were up-regulated in Bos taurus (B. taurus) fibroblasts compared to Ovis aries (O. aries) counterparts using rigorous reverse transcription quantitative PCR (RT-qPCR) n ormalization[12] The dissection of such differences between closely related species may be fruitful due to the expected similarities in their gene expression regulatory landscapes[11,12]. Integrative analysis coupling gene expression analysis and TFBS mapping should contribute toward elucidating evolutionary-driven divergences in gene regulatory landscapes
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