Specific interactions of transcription factors (TFs) with their targets are crucial for specifying gene expression programs during cell differentiation. How specificity is maintained despite limited selectivity of individual TF-DNA interactions is not fully understood. RUNX1 TF is among the most frequently mutated genes in human leukemia and an important regulator of megakaryopoiesis. We used megakaryocytic cell lines to characterize the network of RUNX1 targets and cooperating TFs in differentiating megakaryocytes and demonstrated how dynamic partnerships between RUNX1 and cooperating TFs facilitated regulatory plasticity and specificity during this process. After differentiation onset, RUNX1 directly activated a large number of genes through interaction with preexisting and de novo binding sites. Recruitment of RUNX1 to de novo occupied sites occurred at H3K4me1-marked preprogrammed enhancers. A significant number of these de novo bound sites lacked RUNX motif but were occupied by AP-1 TFs. Reciprocally, AP-1 TFs were up-regulated by RUNX1 after 12-O-tetradecanoylphorbol-13-acetate induction and recruited to RUNX1-occupied sites lacking AP-1 motifs. At other differentiation stages, additional combinatorial interactions occurred between RUNX1 and its coregulators, GATA1 and ETS. The findings suggest that in differentiating megakaryocytic cell lines, RUNX1 cooperates with GATA1, AP-1, and ETS to orchestrate cell-specific transcription programs through dynamic TF partnerships. (Blood. 2011;117(1): e1-e14) IntroductionThe RUNX transcription factors (TFs) are key regulators of cell lineage and differentiation in several important developmental pathways. They regulate transcription in a context-dependent manner through binding to the consensus core DNA sequence PyGPyGGT. 1 RUNX1 functions as key regulator in embryonic and adult hematopoiesis. 2 Consistent with its important roles, haploinsufficiency, resulting from heterozygous loss-of-function mutations, is associated with familial platelet disorder and predisposition to acute myeloid leukemia (FPD-AML). 3,4 Sporadic heterozygous mutations in RUNX1 are also leukemogenic. 5,6 RUNX1 resides on human chromosome 21, and chromosomal translocations involving RUNX1, including 8;21,3;21,and 12;21, are among the most frequent leukemia-associated translocations. 7 In addition, patients with Down syndrome (DS), the phenotypic manifestation of trisomy 21, have 500 fold-increased risk of developing acute megakaryoblastic leukemia (DS-AMKL/AML-M7) relative to normal persons. 8 RUNX1 plays an important role in megakaryopoiesis, the process leading to production of megakaryocytes, the polyploid precursors of platelets. 9,10 Megakaryocytes share a common precursor with erythrocytes known as the megakaryocyte erythroid progenitor, which gives rise to both megakaryocytic and erythroid lineages. 9,10 Overexpression of RUNX1 in myeloid cell lines induces megakaryocytic differentiation, 11,12 whereas induced Runx1 deficiency in bone marrow results in impaired megakaryocytic maturation a...

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RUNX1 transcription factor (TF) is a key regulator of megakaryocytic development and when mutated is associated with familial platelet disorder and predisposition to acute myeloid leukemia (FPD-AML). We used mice lacking Runx1 specifically in megakaryocytes (MK) to characterized Runx1-mediated transcriptional program during advanced stages of MK differentiation. Gene expression and chromatin-immunoprecipitation-sequencing (ChIP-seq) of Runx1 and p300 identified functional Runx1 bound MK enhancers. Runx1/p300 co-bound regions showed significant enrichment in genes important for MK and platelet homeostasis. Runx1 occupied genomic regions were highly enriched in RUNX and ETS motifs and to a lesser extent in GATA motif. Megakaryocytic specificity of Runx1/P300 bound enhancers was validated by transfection mutagenesis and Runx1/P300 co-bound regions of two key megakaryocytic genes Nfe2 and Selp were tested by in vivo transgenesis. The data provides the first example of genome wide Runx1/p300 occupancy in maturating primary FL-MK, unravel the Runx1-regulated program controlling MK maturation in vivo and identify a subset of its bona fide regulated genes. It advances our understanding of the molecular events that upon RUNX1mutations in human lead to the predisposition to familial platelet disorders and FPD-AML.

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