Figure 2

Non-trivial composition structures arising due to enhancers bound by multiple transcription factors. (a) A biologically plausible mechanism revealing the occurrence of non-trivial composition structures in transcriptional gene regulation. Multiple transcription factors (TFs) can bind to the promoter as well as the enhancer region(s) of a target gene. The enhancers and promoters bound by TFs then act as transcriptional regulators (TRs) of their target genes, resulting in non-trivial composition structures. (b) A schematic representation of the composition structure \(\{ 2, 3 \}\) arising in subfigure (a). The target gene is regulated by an active promoter that is bound by 2 TFs, and an active enhancer that is bound by 3 TFs. (c) Scatter plot showing the number of active enhancers bound by a given number of TFs in the HepG2 cell line in humans. We found that 32.68% of the active enhancers in HepG2 are bound by at least 2 TFs. (d) Scatter plot showing the number of active enhancers bound by a given number of TFs in the K562 cell line in humans. We found that 44.31% of the active enhancers in K562 are bound by at least 2 TFs. The x and y axes in part (c) and (d) are in \(\log\) scale. These results suggest that non-trivial composition structures are prevalent in gene regulatory networks.