Blitz Ira L, Paraiso Kitt D, Patrushev Ilya, Chiu William T Y, Cho Ken W Y, Gilchrist Michael J
Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
Dev Biol. 2017 Jun 15;426(2):409-417. doi: 10.1016/j.ydbio.2016.07.002. Epub 2016 Jul 28.
Gene regulatory networks (GRNs) involve highly combinatorial interactions between transcription factors and short sequence motifs in cis-regulatory modules of target genes to control cellular phenotypes. The GRNs specifying most cell types are largely unknown and are the subject of wide interest. A catalog of transcription factors is a valuable tool toward obtaining a deeper understanding of the role of these critical effectors in any biological setting. Here we present a comprehensive catalog of the transcription factors for the diploid frog Xenopus tropicalis. We identify 1235 genes encoding DNA-binding transcription factors, comparable to the numbers found in typical mammalian species. In detail, the repertoire of X. tropicalis transcription factor genes is nearly identical to human and mouse, with the exception of zinc finger family members, and a small number of species/lineage-specific gene duplications and losses relative to the mammalian repertoires. We applied this resource to the identification of transcription factors differentially expressed in the early gastrula stage embryo. We find transcription factor enrichment in Spemann's organizer, the ventral mesoderm, ectoderm and endoderm, and report 218 TFs that show regionalized expression patterns at this stage. Many of these have not been previously reported as expressed in the early embryo, suggesting thus far unappreciated roles for many transcription factors in the GRNs regulating early development. We expect our transcription factor catalog will facilitate myriad studies using Xenopus as a model system to understand basic biology and human disease.
基因调控网络（GRNs）涉及转录因子与靶基因顺式调控模块中的短序列基序之间高度组合的相互作用，以控制细胞表型。指定大多数细胞类型的GRNs在很大程度上尚不清楚，并且是广泛关注的主题。转录因子目录是一种有价值的工具，有助于更深入地了解这些关键效应器在任何生物环境中的作用。在这里，我们展示了二倍体青蛙热带爪蟾转录因子的综合目录。我们鉴定出1235个编码DNA结合转录因子的基因，这与在典型哺乳动物物种中发现的数量相当。详细而言，除了锌指家族成员以及相对于哺乳动物基因库的少量物种/谱系特异性基因重复和丢失外，热带爪蟾转录因子基因的组成几乎与人类和小鼠相同。我们将此资源应用于鉴定原肠胚早期胚胎中差异表达的转录因子。我们发现转录因子在施佩曼组织者、腹侧中胚层、外胚层和内胚层中富集，并报告了218个在此阶段显示区域化表达模式的转录因子。其中许多转录因子此前尚未报道在早期胚胎中表达，这表明许多转录因子在调控早期发育的GRNs中具有迄今未被认识到的作用。我们期望我们的转录因子目录将促进使用爪蟾作为模型系统来理解基础生物学和人类疾病的众多研究。
