Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence by repressing MYC pathway activation [RXR_CnR]

Hematopoietic stem cells (HSCs) maintain homeostasis and fitness by balancing self-renewal and differentiation. Alterations to the symmetry of HSC divisions reduce quiescence and induce myeloid/megakaryocyte-biased hematopoiesis. Here, we show that HSC self-renewal, fitness, and function are preserved by the master transcription factor retinoid X receptor (RXR). We demonstrate that dual lack of hematopoietic RXRα and RXRβ induces HSC asymmetric cell division resulting in HSC exhaustion and age-associated myeloproliferative disease. Characterization of transcriptomic and epigenetic changes in RXR-deficient HSCs demonstrated chromatin opening, acquisition of a premature aging-like HSC signature, MYC pathway upregulation, and RNA intron retention. Myc haploinsufficiency completely prevents the loss of RXR-deficient HSC activity. Our study unveils the critical relevance of RXR for HSC homeostasis and fitness. Here, we performed cleavege under target and release using nuclease followed by library preparation and subsequent next generation sequecing (CUT&RUNseq). HSCs (Lin-cKit+Sca1+CD48-CD150+) and MPPs (Lin-cKit+Sca1+CD150-) were sorted, bound to Concanavalin A magnetic bead, permeabilized using digitonin. The Concanvalin A bound and digitonin permeabilized cells were treated with RXRa Ab followed by proteinA-MNase (pA-MNase) and targeted digestion in presence of CaCl2. The CUT&RUN released DNA fragments were extracted using QIAGEN MinElute Reaction Cleanup kits, and were used for library preparation prepared using NEBNext Ultra II DNA library preparation kit for Illumina and NEBNext multiplex Oligoes for Illumina. Libraries followed next generation paired end sequencing.