Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

The transcription factor NF-κB, which plays an important role in cell fate determination, is involved in the activation of super-enhancers (SEs). However, the biological functions of the NF-κB SEs in gene control are not fully elucidated. We investigated the characteristics of NF-κB-mediated SE activity using fluorescence live-cell imaging of RelA, single-cell transcriptome, and chromatin accessibility analyses in anti-IgM-stimulated B cells. Cell stimulation induced nuclear foci formation of RelA and gene expression in a switch-like manner. The gained SEs induced a higher fold-change expression and enhanced cell-to-cell variability in transcriptional response. These properties were correlated with the number of gained cis-regulatory interactions, while switch-like gene induction was associated with the number of NF-κB binding sites in SE. Our study suggests that NF-κB SEs have unique roles for quantitative control of gene expression through direct binding to accessible DNA and enhanced DNA contacts.