PML-RARa induces dynamic changes in genome architecture during leukemic transformation

Acute Promyelocytic Leukemia (APL) is a fatal subtype of leukemia driven by the translocation between genes encoding the Promyelocytic Leukemia (PML) protein and the Retinoic Acid Receptor alpha (RARa) protein. We use mouse hematopoietic progenitor cells expressing PML-RARa and dissect the dynamic changes in the epigenome, transcriptome and genome architecture triggered by the expression of this oncogenic transcription factor during leukemic transformation. We find that PML-RARa induces a continuum of topologic and transcriptional alterations, mostly affecting distal regulatory elements. Furthermore, we identify Klf4 ? a master regulator of hematopoietic differentiation ? as an early mis-regulated gene during leukemogenesis, and deconstruct the dynamic alterations in long-range interactions, histone modifications and transcriptional output triggered by PML-RARa expression at the Klf4 locus. Our study provides a comprehensive overview of the dynamic genomic and transcriptomic alterations induced by PML-RARa, which ultimately block hematopoietic differentiation and induce leukemic transformation. Overall design: ChIP-seq (29 samples), RNA-seq (12 samples), and Hi-C (10 samples) of Bone marrow lineage negative hematopoietic stem/progenitor cells. Stage 0 cells are GFP+ cells transformed with empty vector, Stage I cells are transformed with PML-RARa-3xFlag vector (both after sorting by FACS). Stage II cells are Stage I cells plated in methylcellulose supplemented with cytokines and stem cell factor, and serially re-plated for 2 weeks. Stage III are Stage I cells plated in methylcellulose supplemented with cytokines and stem cell factor, and serially re-plated for 4 weeks. Stage IV cells are bone marrow blasts from mice in which Stage I cells were transplanted via tail vein injection into lethally irradiated (9 Gy) syngeneic animals (129SvEv). (ChIP-seq) There is an specific Input for each experiment of H3K27ac, except in Stage IV, in which the Input for the rest of histone marks is applicable for H3K27ac too.