Elucidating the evolution of fast-evolving homeobox genes and their role in mammalian preimplantation embryonic development

同源盒基因编码的转录因子（TFs）具有60个氨基酸（aa）的dna结合同源结构域，在早期胚胎模式和细胞命运规范中经常发挥关键作用。在过去，快速进化的同形盒基因在很大程度上被忽视了，但现在却成为进化发育生物学一个令人兴奋的领域的中心。ETCHbox基因是胎盘哺乳动物特有的一组同源盒基因，我将以ETCHbox基因为模型来回答关于快速进化的同源盒基因的进化和功能的一些问题。有趣的是，这些基因只在人类胚胎发育的8和16个细胞阶段表达，然后再也没有被利用过。我将首先通过阐明这些基因在胚胎中的表达位置以及它们的转录靶标来更好地理解这些基因的功能。然后，我将了解它们对胚胎发育的重要性，使用CRISPR/Cas9基因编辑来创建功能丧失的突变牛胚胎。接下来，关于它们进化的问题将被解决。对人类和牛基因的比较将测试它们在快速进化过程中是否改变或维持了它们的功能，而rna测序数据的分析将有助于了解它们是否具有先前存在的功能，还是正在执行与基因一起出现的新功能。总的来说，这将更好地理解ETCHbox基因在哺乳动物胚胎发育中的作用，并阐明快速进化的同源盒基因的快速进化背后的过程。动物健康——高达56%的牛胚胎在囊胚阶段之前就丢失了，这种不育是一个重要问题，因为它是动物被淘汰的最大原因。这项工作旨在更全面地了解参与囊胚前发育的基因，从而确定导致这种早期胚胎丢失的因素。这项工作也与3r一致，因为选择牛作为模型是因为牛能够从屠宰场获得卵母细胞，而不牺牲任何动物，除了用于肉类生产的动物。

Summary for a non-specialist audience: Homeobox genes encode transcription factors (TFs) with a characteristic 60 amino acid (aa) DNA-binding homeodomain, which frequently play critical roles in early embryo patterning and cell fate specification. Fast-evolving homeobox genes have in the past been largely overlooked, but are now at the centre of an exciting area of evolutionary developmental biology. I will use the ETCHbox genes, which are a group of homeobox genes unique to the placental mammals, as a model to answer a number of questions about fast-evolving homeobox genes' evolution and function. Intriguingly, these genes are expressed only at the 8- and 16-cell stages of human embryonic development and then never utilised again. I will firstly aim to gain a better understanding of the function of these genes by elucidating where they are expressed in the embryo, and what their transcriptional targets are. I will then look to understand their importance to embryonic development, using CRISPR/Cas9 gene editing to create loss of function mutant bovine embryos. Next, questions regarding their evolution will be tackled. Comparisons between human and bovine genes will test whether they have changed or maintained their function during their rapid evolution, and analysis of RNA-sequencing data will help understand whether they have taken on a pre-existing function, or are performing a novel function that emerged with the genes. Overall, this will provide a better understanding of the role ETCHbox genes play in mammalian embryonic development, and illuminate the processes behind the rapid evolution of fast-evolving homeobox genes.BBSRC priority areas addressed: Animal health - up to 56% cattle embryos are lost before the blastocyst stage, and this infertility is an important issue because it is the largest cause of animal culling. This work aims to give a more complete understanding of the genes involved in pre-blastocyst development, which may identify contributing factors to this early embryo loss. This work is also consistent with the 3Rs, because cattle were selected as a model due to the ability to obtain oocytes from abattoirs without the sacrifice of any animals on top of those used for meat production.