H1.3 depletion in AML cells prompts H1.2 redistribution, chromatin remodeling and cell cycle defects.

Linker histone H1 variants play critical, yet distinct, roles in chromatin organization and gene regulation. However, their specificity in cancer cells is not well understood. Our previous studies have shown that acute myeloid leukemia (AML) patients who were H3K27me3HIST1-positive exhibited lower H1.3 expression and a favorable outcome. These results imply that the H1.3 linker histone may play an unknown role in AML progression. In this study, we investigated the function of the H1.3 variant in AML cells. Through chromatin mapping and transcriptomic analyses, we revealed that H1.3 was enriched in regions with a high GC content and colocalized with the repressive mark H3K27me3. This supports its role in chromatin compaction and transcriptional repression. Knockout of H1.3 induced specific changes in gene expression profiles and chromatin dynamics, characterized by a changed in H1.2 localization, which was redistributed from its usual chromatin regions to H1.3 regions. Consequently, we observed chromatin alterations associated with changes in gene programs affecting interferon-related signaling and cell cycle regulation. Overall, our study revealed a mechanistic connection between H1.3 variant imbalance, immune response activation, and cell cycle regulation, with implications for our understanding of epigenetic regulation in AML cells.