Broad-stroke regulation by DNA sequence-specific transcription factors

Sequence-specific transcription factors (TFs) regulate gene expression in all living organisms. An established function of TFs is to activate or repress transcription of target genes by binding to specific DNA sequence motifs at their promoters. However, in metazoans, accumulating evidence shows widespread TF binding to DNA outside of promoters, binding in the absence of cognate sequence motifs, and functioning without direct DNA binding. Here, we examine findings that support TFs regulating transcription with limited dependence on DNA sequence or at steps post initiation, particularly during promoter-proximal RNA polymerase II (Pol II) pausing. We suggest that mechanisms enabling TF binding outside of cognate sequence motifs, including cofactor- and chromatin-context-dependent binding, condensate-mediated interactions, and contacts with paused Pol II complexes, are critical for coordinating transcription across the genome, and we discuss their potential biological roles. While TFs fundamentally regulate transcription of genes by reading DNA, this function extends beyond promoter-centric and strictly sequence-dependent paradigms.