Diversity of human and mouse homeobox gene expression in development and adult tissues.
Diversity of human and mouse homeobox gene expression in development and adult tissues.
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DOI：
10.1186/s12861-016-0140-y
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发表时间：
2016-11-03
影响因子：
--
通讯作者：
Holland PW
中科院分区：
文献类型：
--
作者：
Dunwell TL;Holland PW
同源盒基因编码多种转录因子，涉及广泛的生物过程，包括但不限于胚胎细胞命运规范和模式。尽管许多研究报道了特定的同源盒型基因的表达，但缺乏对同源盒型基因的组织特异性的系统分析。在这里，我们分析了来自人类和小鼠发育阶段以及成人组织的公开转录组数据，以确定具有相似表达模式的同源盒基因组。我们计算了242个人类和278个小鼠同源盒位点在59个人类和12个小鼠成年组织的早期和晚期发育阶段的表达谱。这揭示了20个广泛表达的人类同源盒基因，主要来自TALE、CERS和ZF类。然而，大多数同源盒基因具有更大的组织特异性，使我们能够编制神经组织、免疫组织、生殖和发育样本以及许多器官系统的同源盒基因表达表。在小鼠发育过程中，我们提出了同源盒基因表达的四个不同阶段：卵母细胞到受精卵；都有;4细胞到囊胚；植入后早期到中期。最后的阶段变化以ANTP类基因的表达为标志。我们还利用这些数据比较了基于进化的基因类别之间的表达特异性，发现ANTP、PRD、LIM和POU同源盒基因类别具有最高的组织特异性，而HNF、TALE、CUT和CERS表达最广泛。同源盒基因包括一个大的超类，它们的表达模式也相应多样化，尽管在广义上与基于进化的分类有关。一些基因的普遍表达表明在一般细胞过程中起作用；相比之下，大多数人类同源盒基因具有更大的组织特异性，我们为特定的组织、器官和发育阶段编制了有用的同源盒数据集。从人类8细胞阶段到桑葚阶段，一组真核动物特异性同源盒基因的鉴定表明，新基因在进化中具有新的发育作用。本文的在线版本（doi:10.1186/s12861-016-0140-y）包含补充材料，授权用户可以使用。
Homeobox genes encode a diverse set of transcription factors implicated in a vast range of biological processes including, but not limited to, embryonic cell fate specification and patterning. Although numerous studies report expression of particular sets of homeobox genes, a systematic analysis of the tissue specificity of homeobox genes is lacking. Here we analyse publicly-available transcriptome data from human and mouse developmental stages, and adult human tissues, to identify groups of homeobox genes with similar expression patterns. We calculate expression profiles for 242 human and 278 mouse homeobox loci across a combination of 59 human and 12 mouse adult tissues, early and late developmental stages. This revealed 20 human homeobox genes with widespread expression, primarily from the TALE, CERS and ZF classes. Most homeobox genes, however, have greater tissue-specificity, allowing us to compile homeobox gene expression lists for neural tissues, immune tissues, reproductive and developmental samples, and for numerous organ systems. In mouse development, we propose four distinct phases of homeobox gene expression: oocyte to zygote; 2-cell; 4-cell to blastocyst; early to mid post-implantation. The final phase change is marked by expression of ANTP class genes. We also use these data to compare expression specificity between evolutionarily-based gene classes, revealing that ANTP, PRD, LIM and POU homeobox gene classes have highest tissue specificity while HNF, TALE, CUT and CERS are most widely expressed. The homeobox genes comprise a large superclass and their expression patterns are correspondingly diverse, although in a broad sense related to an evolutionarily-based classification. The ubiquitous expression of some genes suggests roles in general cellular processes; in contrast, most human homeobox genes have greater tissue specificity and we compile useful homeobox datasets for particular tissues, organs and developmental stages. The identification of a set of eutherian-specific homeobox genes peaking from human 8-cell to morula stages suggests co-option of new genes to new developmental roles in evolution. The online version of this article (doi:10.1186/s12861-016-0140-y) contains supplementary material, which is available to authorized users.
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