Tuteja Geetu, Chung Tisha, Bejerano Gill
Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
Placenta. 2016 Jan;37:45-55. doi: 10.1016/j.placenta.2015.11.001. Epub 2015 Nov 6.
Trophoblast invasion establishes adequate blood flow between mother and fetus in early placental development. However, little is known about the cis-regulatory mechanisms underlying this important process. We aimed to identify enhancer elements that are active during trophoblast invasion, and build a trophoblast invasion gene-enhancer network.
We carried out ChIP-Seq for an enhancer-associated mark (H3k27Ac) at two time points during early placental development in mouse. One time point when invasion is at its peak (e7.5) and another time point shortly afterwards (e9.5). We use computational analysis to identify putative enhancers, as well as the transcription factor binding sites within them, that are specific to the time point of trophoblast invasion.
We compared read profiles at e7.5 and e9.5 to identify 1,977 e7.5-specific enhancers. Within a subset of e7.5-specific enhancers, we discovered a cell migration associated regulatory code, consisting of three transcription factor motifs: AP1, Ets, and Tcfap2. To validate differential expression of the transcription factors that bind these motifs, we performed RNA-Seq in the same context. Finally, we integrated these data with publicly available protein-protein interaction data and constructed a trophoblast invasion gene-enhancer network.
The data we generated and analysis we carried out improves our understanding of the regulatory mechanisms of trophoblast invasion, by suggesting a transcriptional code exists in the enhancers of cell migration genes. Furthermore, the network we constructed highlights novel candidate genes that may be critical for trophoblast invasion.
在胎盘早期发育过程中，滋养层细胞侵入可在母体与胎儿之间建立充足的血流。然而，对于这一重要过程背后的顺式调控机制，我们知之甚少。我们旨在鉴定在滋养层细胞侵入过程中活跃的增强子元件，并构建一个滋养层细胞侵入基因-增强子网络。
我们在小鼠胎盘早期发育的两个时间点进行了与增强子相关标记（H3k27Ac）的染色质免疫沉淀测序（ChIP-Seq）。一个时间点是侵入处于高峰期时（e7.5），另一个时间点是随后不久（e9.5）。我们使用计算分析来鉴定特定于滋养层细胞侵入时间点的推定增强子及其内部的转录因子结合位点。
我们比较了e7.5和e9.5时的读数谱，以鉴定1977个e7.5特异性增强子。在e7.5特异性增强子的一个子集中，我们发现了一个与细胞迁移相关的调控密码，它由三个转录因子基序组成：AP1、Ets和Tcfap2。为了验证结合这些基序的转录因子的差异表达，我们在相同背景下进行了RNA测序。最后，我们将这些数据与公开可用的蛋白质-蛋白质相互作用数据整合，并构建了一个滋养层细胞侵入基因-增强子网络。
我们生成的数据和进行的分析表明细胞迁移基因的增强子中存在转录密码，从而增进了我们对滋养层细胞侵入调控机制的理解。此外，我们构建的网络突出了可能对滋养层细胞侵入至关重要的新候选基因。
