Transcription profiling of mouse small intestinal crypt-villus axis

Genes encoding transcription factors function as hubs in gene regulatory networks because they encode DNA-binding proteins, which bind to promoters that carry their binding sites. In the present work we have studied gene regulatory networks defined by genes with transcripts belonging to different mRNA abundance classes in the small intestinal epithelial cell. The focus is the rewiring that occurs in transcription factor hubs in these networks during the differentiation of the small intestinal epithelial cell while it migrates along the crypt-villus axis and during its development from a fetal endodermal cell to a mature adult villus epithelial cell. We have generated transcriptome data for mouse small intestinal villus, crypt and fetal intestinal epithelial cells. In addition we have generated metabolome data from crypt and villus cells. Our results show that the intestinal crypt transcription factor hubs that are rewired during differentiation are involved in the cell cycle process (E2F, NF-Y) and stem cell maintenance (c-Myc). In contrast the villi are dominated by a HNF-4 villus hub, which is rewired during differentiation by the addition of network genes with relevance for lipoprotein synthesis and lipid absorption. Moreover, we have identified a villus NF-kB hub, which was revealed by comparison of the villus and endoderm transcriptomes. The rewiring of the NF-kB villus hub during intestinal development reflects transcriptional activity established by host and microflora interactions. To aid in the mining of our results we have developed a web portal (http://gastro.imbg.ku.dk/mousecv/) allowing easy linkage between the transcriptomic data, biological processes and functions. Experiment Overall Design: Four different sample categories were analyzed. Experiment Overall Design: 1) Small intestinal crypts isolated from 12-weeks old C57BL/6 mice. These samples are in triplicates. Experiment Overall Design: 2) Small intestinal villi isolated form 12-weeks old C57BL/6 mice. These samples are in triplicates. Experiment Overall Design: 3) Embryonic day 12 mesenchyme. These samples are in quadruplicate. each sample is derived from a pool of mesenchymes (10-40) Experiment Overall Design: 4) Embryonic day 12 endoderm. These samples are in quadruplicate. each sample is derived from a pool of endoderms (10-40)转录因子（transcription factor）编码基因在基因调控网络（gene regulatory network）中充当核心枢纽，因其编码的DNA结合蛋白（DNA-binding protein）可结合携带自身结合位点（binding site）的启动子（promoter）。本研究针对小肠上皮细胞中，转录本隶属于不同mRNA丰度类别的基因所构建的基因调控网络展开研究，重点关注两类过程中这些网络内转录因子枢纽的重布线调控：一是小肠上皮细胞沿隐窝-绒毛轴迁移分化的过程，二是其从胎儿内胚层细胞发育为成熟成人绒毛上皮细胞的全过程。 我们已获取小鼠小肠绒毛、隐窝及胎儿肠上皮细胞的转录组（transcriptome）数据，同时还获得了隐窝与绒毛细胞的代谢组（metabolome）数据。 本研究结果表明：分化过程中发生重布线的小肠隐窝转录因子枢纽，参与了细胞周期进程（E2F、NF-Y）与干细胞维持（c-Myc）相关的生物学过程。与之相对，绒毛调控网络以HNF-4绒毛枢纽为主导，该枢纽在分化过程中通过引入与脂蛋白合成及脂质吸收相关的网络基因而发生重布线。此外，通过对比绒毛与内胚层转录组数据，我们还鉴定出一个绒毛核因子κB（NF-κB）枢纽；该枢纽在肠道发育过程中的重布线，反映了宿主与菌群互作所确立的转录调控活性。 为便于研究者挖掘本研究的相关结果，我们开发了一个网络门户（web portal，http://gastro.imbg.ku.dk/mousecv/），可实现转录组数据、生物过程与功能之间的便捷关联。 实验总体设计：本研究共分析4类不同样本： 1. 从12周龄C57BL/6小鼠体内分离的小肠隐窝样本，设置3次生物学重复。 2. 从12周龄C57BL/6小鼠体内分离的小肠绒毛样本，设置3次生物学重复。 3. 胚胎第12天的间充质样本，设置4次生物学重复；每份样本取自10~40个间充质组织混合而成的混样。 4. 胚胎第12天的内胚层样本，设置4次生物学重复；每份样本取自10~40个内胚层组织混合而成的混样。