Biochemical and epigenomic dissection of TFIIE function reveals gene-selective requirement in human transcription

The general transcription factor TFIIE is believed to be universally required for RNA polymerase II (Pol II)-mediated transcription initiation. However, our biochemical assays and ENCODE ChIP-seq data suggest a more gene-selective role. Using Mediator-depleted HeLa nuclear extracts, we show that TFIIE can be less critical for transcription in the presence of endogenous nuclear components, whereas purified systems of GTFs, Pol II, and Mediator reveal TFIIE to be required for transcription. This conditional requirement led us to hypothesize that TFIIE acts only at a subset of promoters in vivo. Analysis of ENCODE datasets from K562 cells identified transcription start sites (TSS) classified as TFIIE-only by peak calling, lacking annotated TBP, ZZZ3, or MED1, alongside promoters co-bound by all. When we inspected the bigWig signal tracks, they revealed additional co-enrichment not captured by peak calls, suggesting that TFIIE-only sites reflect classification thresholds and not strict exclusivity. Heatmap analyses of TFIIE-bound promoters revealed selective co-enrichment with TBP, ZZZ3 and weaker enrichment with MED1, supporting a non-canonical pre-initiation complex configuration. Gene ontology analysis of these TFIIE-enriched promoters shows strong correlation to chromatin-related processes, suggesting that TFIIE coordinates transcription initiation with chromatin organization and genome stability.