Transcriptional regulation by SETBP1 and SETBP1(D/N) in mouse hematopoietic stem and progenitor cells

Global gene expression changes induced by Setbp1 and Setbp1(D/N) in purified mouse hematopoietic stem and progenitor cells were characterized by RNA-seq analysis; ChIP-seq studies to identify cooperation between SETBP1/SETBP1(D/N) and MLL1 in regulating gene transcription in hematopoietic stem and progenitor cells. For characterizing gene expression changes, Lin-Sca-1+c-kit+(LSK) cells from bone marrow of C57BL/6 mice were infected with control empty pMYs retrovirus (pMYs-IRES-GFP, 2105) or pMYs virus expressing Setbp1 cDNA (pMYs-Setbp1-IRES-GFP, WT) or Setbp1(D/N) cDNA (pMYs-Setbp1(D/N)-IRES-GFP, DN). After a brief expansion in methylcellulose medium, the transduced cells were purified based on GFP expression and their expression proflies analyzed by RNA-seq. For identifying cooperation in transcriptional regulation, LSK cells were infected with pMYs-3xFLAG-Setbp1-IRES-GFP (2PL) or pMYs-3xFLAG-Setbp1(D/N)-IRES-GFP (DPL) virus and genomic occupancy of SETBP1 (M2), SETBP1(D/N) (M2), Mll1 (MLN), H3K4me3, and H4K16ac analyzed by ChIP-seq.