TCF3 transcription factor isoforms E12 and E47 activate endogenous SCX while repressing pCMV-driven transgene expression.

The Basic Helix-Loop-Helix transcription factors (bHLH TFs) modulate gene expression by binding to enhancers and promoters. Their expression and protein levels are tightly regulated due to their involvement in tissue development. TCF3 is a type I bHLH TF that can homodimerize and heterodimerize with type II tissue-specific bHLH TFs, including SCX. After adjusting for the squelching transcriptional artifact associated with strong promoter-driven overexpression, we found that both splicing isoforms of TCF3 (E12 and E47) negatively modulated the CMV promoter. Contrastingly, E47 had a strong positive effect on the endogenous SCX locus, whereas E12 was milder. These findings reveal the locus-dependent regulatory activities of TCF3 isoforms and highlight a previously unrecognized interaction between bHLH TFs and the widely used CMV promoter.