Temporal analysis of two inducible human genes reveals post-transcriptional H3K4me3 deposition.

Abstract

Histone H3 lysine 4 trimethylation (H3K4me3) is an established hallmark of active promoters, yet the temporal hierarchy between its deposition and transcriptional initiation remains incompletely understood. Here, we employ temporal dynamic analysis of inducible human inflammatory genes to demonstrate that H3K4me3 accumulation lags significantly behind transcriptional onset. At the TNF-α and IL-1β loci, H3K4me3 enrichment succeeds the rapid recruitment of RNA polymerase II, NF-κB, and p300, appearing kinetically decoupled from the initial establishment of histone acetylation. We find that H3K4me3 deposition is attenuated by transcriptional inhibition, characterizing it as a downstream event rather than a prerequisite for initial activation. Furthermore, MLL1-mediated reduction of H3K4me3 does not impair transcriptional induction, demonstrating that this mark is dispensable for the primary onset of expression at these loci. At the constitutively active MYC locus, H3K4me3 persists after transcriptional inhibition, indicating temporal uncoupling between transcription and H3K4me3 maintenance. Our findings provide a detailed kinetic characterization of H3K4me3 loading and suggest that at these inducible genes, this modification serves as a consequence of, rather than a trigger for, transcriptional initiation.