Pluripotency transcription factor levels in sheep embryos correlate with mRNA regulatory elements

•Pluripotency genes have dynamic mRNA levels during sheep early embryogenesis.•Gene expression patterns of pluripotency genes correlate with mRNA 3′UTR elements.•RNA methylation scores correlate with pluripotency gene levels in sheep embryos. Pluripotency-associated transcription factors (PATF) contribute to cell fate decisions in embryos, cellular reprogramming, and the derivation of stem cells. PATF hold species-specific mRNA fluctuations during early development but the regulatory determinants remain largely unknown in sheep. The aim of this study was to prospect correlations between PATF gene expression patterns and mRNA regulatory features. The relative expression of PATF was investigated in sheep embryos by RT-qPCR and mRNAs were investigated for cis-regulatory elements and N6-methyladenosine (m6A) RNA methylation using bioinformatics. Four PATF gene expression patterns emerged with relatively distinct mRNA regulatory modes. RXRβ and TCF3 were detected in oocytes and mRNAs had variable 3′untranslated region (3′UTR) length. Three mRNAs (DPPA3, THAP11, and ZFX), which had similar abundance among developmental stages, frequently had short 3′UTRs and polyadelylation sites. NR5A2 and SP1 levels increased at the cleavage-stage but diminished in morulae, thus showing long 3′UTRs with multiple polyadelylation and m6A sites. Finally, mRNA abundance was low in oocytes and up-regulated in morulae (UTF1 and ZNF281) without a distinctive regulatory mode. Hence, sheep embryos hold PATF gene expression that correlates with mRNA 3′UTR length and the number of polyadenylation and m6A sites. These findings may lead to modulating sheep PATF to enhance reprogramming and stem cell derivation.