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. 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.