Molecular cloning of PRD-like homeobox genes expressed in bovine oocytes and early IVF embryos

• Published in: BMC genomics 2024-11, Vol.25 (1), p.1048-16, Article 1048
• Main Authors: Yaşar, Barış, Boskovic, Nina, Ivask, Marilin, Weltner, Jere, Jouhilahti, Eeva-Mari, Vill, Piibe, Skoog, Tiina, Jaakma, Ülle, Kere, Juha, Bürglin, Thomas R, Katayama, Shintaro, Org, Tõnis, Kurg, Ants
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Amino acids; Analysis; Animal genetics; Animals; Annotations; Anopheles; Biological activity; Blastocyst - metabolism; Bos taurus; Bovine; Cattle; Cloning; Cloning, Molecular; Datasets; DNA binding proteins; Embryogenesis; Embryonic development; Embryonic Development - genetics; Embryonic growth stage; Embryos; Fertilization in Vitro; Functional analysis; Gametocytes; Gene expression; Gene Expression Regulation, Developmental; Gene regulation; Genes; Genes, Homeobox; Genetic aspects; Genetic research; Genetic transcription; Genomes; Genomic analysis; Genomics; Homeobox; Homeodomain; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; In vitro fertilization; Nucleotide sequence; Nucleotides; Oocytes; Oocytes - metabolism; Patient outcomes; Peptides; PRD-like (PRDL) domain; Predictions; Preimplantation embryo development; Proteins; Reproduction; RNA; RNA editing; RNA sequencing; Transcription activation; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription initiation
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10969-w

Embryonic genome activation (EGA) is a critical step in early embryonic development, as it marks the transition from relying on maternal factors to the initiation of transcription from embryo's own genome. The factors associated with EGA are not well understood and need further investigation. PRD-like (PRDL) homeodomain transcription factors (TFs) are considered to play crucial roles in this early event during development but these TFs have evolved differently, even within mammalian lineages. Different numbers of PRDL TFs have been predicted in bovine (Bos taurus); however, their divergent evolution requires species-specific confirmation and functional investigations. In this study, we conducted molecular cloning of mRNAs for the PRDL TFs ARGFX, DUXA, LEUTX, NOBOX, TPRX1, TPRX2, and TPRX3 in bovine oocytes or in vitro fertilized (IVF) preimplantation embryos. Our results confirmed the expression of PRDL TF genes in early bovine development at the cDNA level and uncovered their structures. For each investigated PRDL TF gene, we isolated at least one homeodomain-encoding cDNA fragment, indicative of DNA binding and thus potential role in transcriptional regulation in developing bovine embryos. Additionally, our cDNA cloning approach allowed us to reveal breed-related differences in bovine, as evidenced by the identification of a high number of single nucleotide variants (SNVs) across the PRDL class homeobox genes. Subsequently, we observed the prediction of the 9aa transactivation domain (9aaTAD) motif in the putative protein sequence of TPRX3 leading us to conduct functional analysis of this gene. We demonstrated that the TPRX3 overexpression in bovine fibroblast induces not only protein-coding genes but also short noncoding RNAs involved in splicing and RNA editing. We supported this finding by identifying a shared set of genes between our and published bovine early embryo development datasets. Providing full-length cDNA evidence for previously predicted homeobox genes that belong to PRDL class improves the annotation of the bovine genome. Updating the annotation with seven developmentally-important genes will enhance the accuracy of RNAseq analysis with datasets derived from bovine preimplantation embryos. In addition, the absence of TPRX3 in humans highlights the species-specific and TF-specific regulation of biological processes during early embryo development.