Ablation of histone H1.4 reveals the focal regulation of AP-1 directed enhancers

Nucleosomes are flanked by histone H1's, which bind linker DNA and aid chromatin compaction. The specific role of linker histone Has remained elusive due to complex compensatory mechanisms among H1 variants. H1.4 ablation resulted in robust changes in nascent transcription and gene expression, with critical pathways upregulated (RAR, TNF-α/NF-κB) and extracellular matrix and collagen genes repressed. Alternations to chromatin accessibility intersected extragenic and intronic regions, overlapped sites of known enhancer chromatin, and were of enhancer size. These sites exhibited concomitant and concordant changes to epigenetic marks (H3K27ac/H3K4me1). Sites, which gained accessibility contained binding motifs for basal factors (TBP, SRF), localized to polycomb, heterochromatin, and quiescent/low chromatin, and gained active RNA transcription in ΔH1.4 cells. However, the AP-1 motif was enriched at sites that lost accessibility, consistent with the gene expression changes. This places histone H1.4 as a hitherto underappreciated regulator of transcriptional response patterns and a dynamic member of regulatory chromatin.