PDF(Pubmed)
Abstract：
BACKGROUND: Transcription factor (TF) proteins are a key component of the gene regulatory networks that control cellular fates and function. TFs bind DNA regulatory elements in a sequence-specific manner and modulate target gene expression through combinatorial interactions with each other, cofactors, and chromatin-modifying proteins. Large-scale studies over the last two decades have helped shed light on the complex network of TFs that regulate development in Drosophila melanogaster.
RESULTS: Here, we present a detailed characterization of expression of all known and predicted Drosophila TFs in two well-established embryonic cell lines, Kc167 and S2 cells. Using deep coverage RNA sequencing approaches we investigate the transcriptional profile of all 707 TF coding genes in both cell types. Only 103 TFs have no detectable expression in either cell line and 493 TFs have a read count of 5 or greater in at least one of the cell lines. The 493 TFs belong to 54 different DNA-binding domain families, with significant enrichment of those in the zf-C2H2 family. We identified 123 differentially expressed genes, with 57 expressed at significantly higher levels in Kc167 cells than S2 cells, and 66 expressed at significantly lower levels in Kc167 cells than S2 cells. Network mapping reveals that many of these TFs are crucial components of regulatory networks involved in cell proliferation, cell-cell signaling pathways, and eye development.
CONCLUSIONS: We produced a reference TF coding gene expression dataset in the extensively studied Drosophila Kc167 and S2 embryonic cell lines, and gained insight into the TF regulatory networks that control the activity of these cells.
RESULTS: Here, we present a detailed characterization of expression of all known and predicted Drosophila TFs in two well-established embryonic cell lines, Kc167 and S2 cells. Using deep coverage RNA sequencing approaches we investigate the transcriptional profile of all 707 TF coding genes in both cell types. Only 103 TFs have no detectable expression in either cell line and 493 TFs have a read count of 5 or greater in at least one of the cell lines. The 493 TFs belong to 54 different DNA-binding domain families, with significant enrichment of those in the zf-C2H2 family. We identified 123 differentially expressed genes, with 57 expressed at significantly higher levels in Kc167 cells than S2 cells, and 66 expressed at significantly lower levels in Kc167 cells than S2 cells. Network mapping reveals that many of these TFs are crucial components of regulatory networks involved in cell proliferation, cell-cell signaling pathways, and eye development.
CONCLUSIONS: We produced a reference TF coding gene expression dataset in the extensively studied Drosophila Kc167 and S2 embryonic cell lines, and gained insight into the TF regulatory networks that control the activity of these cells.
摘要：
背景：转录因子（TF）蛋白是控制细胞命运和功能的基因调节网络的关键组成部分。TFs以序列特异性方式结合DNA调控元件，并通过彼此的组合相互作用调节靶基因表达，辅因子，和染色质修饰蛋白。过去二十年的大规模研究有助于揭示调节果蝇发育的TFs复杂网络。
结果：这里，我们提出了一个详细的表征所有已知和预测的果蝇TFs在两个成熟的胚胎细胞系中的表达，Kc167和S2细胞。使用深度覆盖RNA测序方法，我们研究了两种细胞类型中所有707TF编码基因的转录谱。仅103个TFs在任一细胞系中没有可检测的表达,并且493TFs在至少一种细胞系中具有5或更大的读段计数。493个TFs属于54个不同的DNA结合域家族，具有zf-C2H2家族中的显著富集。我们确定了123个差异表达基因，57在Kc167细胞中的表达水平明显高于S2细胞，和66在Kc167细胞中的表达水平显著低于S2细胞。网络图显示，许多这些TF是参与细胞增殖的调节网络的关键组成部分，细胞-细胞信号通路，和眼睛发育。
结论：我们在广泛研究的果蝇Kc167和S2胚胎细胞系中产生了参考TF编码基因表达数据集，并深入了解了控制这些细胞活动的TF调控网络。
结果：这里，我们提出了一个详细的表征所有已知和预测的果蝇TFs在两个成熟的胚胎细胞系中的表达，Kc167和S2细胞。使用深度覆盖RNA测序方法，我们研究了两种细胞类型中所有707TF编码基因的转录谱。仅103个TFs在任一细胞系中没有可检测的表达,并且493TFs在至少一种细胞系中具有5或更大的读段计数。493个TFs属于54个不同的DNA结合域家族，具有zf-C2H2家族中的显著富集。我们确定了123个差异表达基因，57在Kc167细胞中的表达水平明显高于S2细胞，和66在Kc167细胞中的表达水平显著低于S2细胞。网络图显示，许多这些TF是参与细胞增殖的调节网络的关键组成部分，细胞-细胞信号通路，和眼睛发育。
结论：我们在广泛研究的果蝇Kc167和S2胚胎细胞系中产生了参考TF编码基因表达数据集，并深入了解了控制这些细胞活动的TF调控网络。
