HIRA-SETDB1-H3K9me3 axis regulates chromatin architecture in leukemia cells

Histone cell cycle regulator A (HIRA) confers chromatin accessibility and regulates developmental hematopoiesis. Previously, we showed that HIRA expression is higher in patient samples from chronic myeloid leukemia (CML) compared to samples from healthy individuals. However, the underlying mechanism that connects HIRA with chromatin reorganization and pathogenesis of leukemia associated with abnormal hematopoiesis remains unexplained. We developed a HIRA-knockdown K562 CML cell line model for this study, as this cell line showed a maximal expression of HIRA in the myeloid lineage. A proteome-wide analysis demonstrated the association of HIRA with components of chromatin organization in K562 cells. Fluorescence Recovery After Photobleaching and fluorescence lifetime imaging microscopy-forster resonance energy transfer microscopy and molecular interaction studies revealed increased chromatin compaction and altered spatial distribution of chromatin towards the nuclear periphery upon downregulation of HIRA in K562 cells. Mechanistically, enhanced chromatin compaction was attributed to increased histone H3K9me3 and HP1α levels mediated by histone methyltransferase SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1). The enrichment of histone H3.3 and the reduction in H3K27me3 levels, resulting from the loss of enzyme unit Enhancer of Zeste Homolog 2 recruitment at the SETDB1 and HP1α promoters in HIRA-knockdown cells, led to an increase in their expression. This HIRA-SETDB1-H3K9me3 axis contributed to restricted cell proliferation along with loss in expression of the Breakpoint Cluster Region protein- Abelson Tyrosine-Protein Kinase 1 fusion protein that causes CML. Thus, loss of HIRA promotes global chromatin condensation and redistribution, thereby regulating the Breakpoint Cluster Region protein- Abelson Tyrosine-Protein Kinase 1 expression and cell proliferation. Our findings highlight how elevated HIRA expression contributes to the pathogenesis of CML and establish a regulatory axis that could be further explored for therapeutic interventions.