The Homeobox Genes of <i>Caenorhabditis elegans</i> and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis

Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.

同源框基因（homeobox gene）对多细胞真核生物的发育发挥关键调控作用。本研究构建了秀丽隐杆线虫（Caenorhabditis elegans）所有同源框基因的修订列表，并为此前未命名的基因提供了统一命名规范。我们的分析显示，在103个同源框基因中，有70个与人类同源框基因存在共直系同源关系；另有14个基因演化高度分化，即便在其他隐杆线虫属（Caenorhabditis）物种中也未发现明确的直系同源基因。其中1个同源框基因可编码12个同源结构域，另外3个高度分化的同源框基因则编码一种新型双同源结构域，我们将其命名为HOCHOB。为阐明转录因子在发育过程中如何调控细胞命运，亟需获取精准的时空表达数据。我们依托自主研发的成像框架Endrov，针对60余个同源框基因以及一批其他发育调控基因，通过绿色荧光蛋白（GFP）报告系统获取了其在胚胎发生过程中的时空表达谱。在成像记录阶段，我们引入动态反馈机制自动调整相机曝光时长，以此突破相机硬件限制，拓展了成像动态范围。本研究将该新型成像框架应用于同源框基因表达模式的检测，并对这些表达模式进行了系统性分析。我们开发的表达数据分析与定量方法不仅适用于秀丽隐杆线虫，还可推广应用至其他模式生物系统乃至组织培养系统。