在牛卵母细胞和早期试管婴儿胚胎中表达的 PRD 样同源基因的分子克隆。

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY BMC Genomics Pub Date : 2024-11-06 DOI:10.1186/s12864-024-10969-w
Barış Yaşar, Nina Boskovic, Marilin Ivask, Jere Weltner, Eeva-Mari Jouhilahti, Piibe Vill, Tiina Skoog, Ülle Jaakma, Juha Kere, Thomas R Bürglin, Shintaro Katayama, Tõnis Org, Ants Kurg
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引用次数: 0

摘要

背景:胚胎基因组激活(EGA)是早期胚胎发育的关键一步,因为它标志着胚胎从依赖母体因素过渡到从胚胎自身基因组启动转录。与 EGA 相关的因素尚不十分清楚,需要进一步研究。PRD样(PRDL)同源转录因子(TFs)被认为在发育过程中的这一早期事件中起着至关重要的作用,但这些TFs的进化方式各不相同,甚至在哺乳动物的品系中也是如此。在牛(Bos taurus)中预测了不同数量的 PRDL TFs;然而,它们的不同进化需要物种特异性的确认和功能研究:在这项研究中,我们对牛卵母细胞或体外受精(IVF)植入前胚胎中的 PRDL TFs ARGFX、DUXA、LEUTX、NOBOX、TPRX1、TPRX2 和 TPRX3 的 mRNA 进行了分子克隆。我们的研究结果在 cDNA 水平上证实了 PRDL TF 基因在牛早期发育中的表达,并揭示了它们的结构。对于每个被研究的 PRDL TF 基因,我们都分离出了至少一个编码 homeodomain 的 cDNA 片段,这表明它们能与 DNA 结合,从而在牛胚胎发育过程中发挥潜在的转录调控作用。此外,我们的 cDNA 克隆方法还揭示了牛的品种相关差异,PRDL 类同源染色体基因中大量单核苷酸变异(SNV)的发现就是证明。随后,我们在 TPRX3 的推测蛋白序列中发现了 9aa 转录激活结构域(9aaTAD),从而对该基因进行了功能分析。我们证实,TPRX3 在牛成纤维细胞中的过表达不仅会诱导蛋白编码基因,还会诱导参与剪接和 RNA 编辑的短非编码 RNA。我们通过鉴定我们的数据集与已发表的牛早期胚胎发育数据集之间的一组共享基因来支持这一发现:结论:为以前预测的属于 PRDL 类的同源染色体基因提供全长 cDNA 证据改进了牛基因组的注释。用七个发育上重要的基因更新注释将提高对来自牛胚胎植入前的数据集进行 RNAseq 分析的准确性。此外,人类中 TPRX3 的缺失凸显了早期胚胎发育过程中生物过程的物种特异性和 TF 特异性调控。
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Molecular cloning of PRD-like homeobox genes expressed in bovine oocytes and early IVF embryos.

Background: 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.

Results: 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.

Conclusions: 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.

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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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