Spatial clustering and common regulatory elements lead to TGF-β induced concerted gene expression. Spatial clustering and common regulatory elements lead to TGF-β induced concerted gene expression

Cellular responses require temporally concerted transcriptional regulation of multiple genes. A single-input-module motif with one transcription factor regulating multiple target genes can generate the coordinated gene expression. In eukaryotic cells, the local environment of a gene characterized by histone modifications, DNA methylations, and the three-dimensional chromosome structure also regulates its transcriptional activity. To examine how the local environment and transcriptional factor regulation is coupled, we performed combined analysis of time-course RNA-seq data of TGF-β treated MCF10A cells and corresponding epigenome and Hi-C data. We discovered, genes co-regulated by a common transcription factor has tendency to be close both in the linear DNA sequence and spatially. Specifically, we identified local spatial organization of over a hundred of AP1-regulated genes, and competition between hetero- and homo-dimeric AP1 fine-tunes the complex structure leading to differential expression of downstream genes sharing similar local environment. We suggest this spatial organization as a general regulation principle. Overall design: Gene expression profiling of MCF10A cells with 7 different duration of TGF-beta inducing as well as one control group without inducing, each time point with 3 biological replicates.

细胞应答过程需要对多个基因进行时序协同的转录调控。由单个转录因子（transcription factor）调控多个靶基因的单输入模块基序，可实现协调一致的基因表达。在真核细胞中，以组蛋白修饰（histone modifications）、DNA甲基化（DNA methylations）及三维染色体结构（three-dimensional chromosome structure）为特征的基因局部微环境，同样可调控其转录活性。为探究基因局部微环境与转录因子调控如何协同耦合，我们对经转化生长因子β（TGF-β）处理的MCF10A细胞的时序RNA测序（RNA-seq）数据，以及配套的表观基因组（epigenome）和Hi-C（Hi-C）数据开展了联合分析。我们发现，受同一转录因子共同调控的基因，在线性DNA序列与空间位置上均呈现彼此邻近的趋势。具体而言，我们鉴定出百余个受AP1调控的基因的局部空间组织模式；异二聚体与同二聚体AP1之间的竞争可对该复杂结构进行微调，进而使共享相似局部微环境的下游基因产生差异表达。我们认为该空间组织模式可作为一种通用的调控原则。实验整体设计：对经转化生长因子β（TGF-β）诱导不同时长（共7个时间梯度）的MCF10A细胞开展基因表达谱分析，同时设置未诱导的对照组；每个时间点均设置3次生物学重复。