Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia.
PLoS One. 2011 Feb 28;6(2):e17286. doi: 10.1371/journal.pone.0017286.
The development of the mammalian kidney is well conserved from mouse to man. Despite considerable temporal and spatial data on gene expression in mammalian kidney development, primarily in rodent species, there is a paucity of genes whose expression is absolutely specific to a given anatomical compartment and/or developmental stage, defined here as 'anchor' genes. We previously generated an atlas of gene expression in the developing mouse kidney using microarray analysis of anatomical compartments collected via laser capture microdissection. Here, this data is further analysed to identify anchor genes via stringent bioinformatic filtering followed by high resolution section in situ hybridisation performed on 200 transcripts selected as specific to one of 11 anatomical compartments within the midgestation mouse kidney. A total of 37 anchor genes were identified across 6 compartments with the early proximal tubule being the compartment richest in anchor genes. Analysis of minimal and evolutionarily conserved promoter regions of this set of 25 anchor genes identified enrichment of transcription factor binding sites for Hnf4a and Hnf1b, RbpJ (Notch signalling), PPARγ:RxRA and COUP-TF family transcription factors. This was reinforced by GO analyses which also identified these anchor genes as targets in processes including epithelial proliferation and proximal tubular function. As well as defining anchor genes, this large scale validation of gene expression identified a further 92 compartment-enriched genes able to subcompartmentalise key processes during murine renal organogenesis spatially or ontologically. This included a cohort of 13 ureteric epithelial genes revealing previously unappreciated compartmentalisation of the collecting duct system and a series of early tubule genes suggesting that segmentation into proximal tubule, loop of Henle and distal tubule does not occur until the onset of glomerular vascularisation. Overall, this study serves to illuminate previously ill-defined stages of patterning and will enable further refinement of the lineage relationships within mammalian kidney development.
哺乳动物肾脏的发育在从老鼠到人之间是高度保守的。尽管在哺乳动物肾脏发育过程中，主要在啮齿动物物种中，已经有了相当多的关于基因表达的时间和空间数据，但仍然缺乏表达绝对特定于特定解剖部位和/或发育阶段的基因，我们将这些基因定义为“锚定”基因。我们之前使用激光捕获显微切割收集的解剖部位的微阵列分析生成了发育中老鼠肾脏基因表达图谱。在这里，通过严格的生物信息学过滤对这些数据进行进一步分析，以确定“锚定”基因，然后在 200 个转录本上进行高分辨率原位杂交，这些转录本被选择为特定于中孕期老鼠肾脏的 11 个解剖部位之一。在总共 6 个部位中鉴定出 37 个“锚定”基因，其中早期近端小管是“锚定”基因最丰富的部位。对这组 25 个“锚定”基因的最小和进化上保守的启动子区域进行分析，确定了转录因子 Hnf4a 和 Hnf1b、RbpJ（Notch 信号）、PPARγ:RxRA 和 COUP-TF 家族转录因子结合位点的富集。GO 分析也证实了这一点，该分析还将这些“锚定”基因确定为包括上皮细胞增殖和近端管状功能在内的过程的靶基因。除了定义“锚定”基因外，这种大规模的基因表达验证还鉴定出了另外 92 个部位丰富的基因，这些基因能够在空间或本体论上对肾器官发生过程中的关键过程进行亚部位化。这包括 13 个输尿管上皮基因，揭示了以前未被认识到的收集管系统的部位化，以及一系列早期管状基因，表明直到肾小球血管化开始，才发生近端小管、Henle 袢和远端小管的分段。总的来说，这项研究有助于阐明以前定义不明确的模式形成阶段，并将进一步细化哺乳动物肾脏发育过程中的谱系关系。
