A Distal Single Nucleotide Polymorphism Disrupts Development-Dependent Long-Range Transcriptional Regulation of the PU.1 Gene through the Chromatin-Remodeling Protein SATB1 in Acute Myeloid Leukemia.
Authors: Steidl Ulrich , Steidl Christian , Ebralidze Alexander , Chapuy Bjoern , Han Hye-Jung , Will Britta , Rosenbauer Frank , Becker Annegret , Wagner Katharina , Koschmieder Steffen , Kobayashi Susumu , Costa Daniel B. , Schulz Thomas , O’Brien Karen B. , Verhaak Roel G.W. , Delwel Ruud , Haase Detlef , Trumper Lorenz , Krauter Juergen , Kohwi-Shigematsu Terumi , Griesinger Frank , Tenen Daniel G. 
Published: October 2019

Abstract
Expression of the transcription factor PU.1 is dependent on a highly conserved upstream regulatory element (URE) located 14 kilobases upstream of the transcriptional start site. The proximal promoter of PU.1 alone, without this enhancer, displays 100-fold reduced promoter activity and is not capable of driving PU.1 expression in transgenic mice. Targeted disruption of the URE reduces PU.1 expression by 80% and leads to AML in mice. However, the mechanisms mediating the long-range regulatory function of the URE are largely unknown. Here, we identified a binding site of the chromatin-remodeling special AT-rich sequence-binding protein 1 (SATB1). Utilizing EMSA and ChIP, we found that SATB1 binds to the URE in myeloid U937 cells. Luciferase assays demonstrated 7-fold reduced reporter activity upon disruption of the SATB1 site. Lentiviral overexpression of SATB1 in primary murine Lin−, Kit+ progenitor cells led to an upregulation of PU.1 expression. We did not observe this effect in URE−/− progenitors indicating that the PU.1 regulatory function of SATB1 is mediated by the URE. Inhibition of SATB1 by siRNA in U937 cells led to a decrease in PU.1 expression. This inhibitory effect was not seen in myeloid URE−/− cells. To address the question at which stages during myeloid development SATB1 regulates PU.1, we sorted KSL-HSC, CMP, GMP, and MEP of SATB1 knockout mice and determined PU.1 expression levels. Interestingly, PU.1 expression was 88% and 80% reduced in SATB1−/− GMP and MEP, while KSL-HSC and CMP did not show significantly changed PU.1 levels. This finding indicates a stage-specific regulatory function of SATB1 during myelopoiesis. When we sequenced the URE in human individuals with AML we identified a SNP that abates binding of SATB1 and leads to decreased PU.1 expression in GMP and MEP. While the overall frequency of the homozygous SNP was not significantly changed in AML patients compared with healthy controls, this SNP was 2.3-fold more frequent in patients with AML with complex karyotype than in AML with normal karyotype (p<0.05). These findings suggest a role of this SNP in leukemia progression, in that the SNP acts as a modifier and favors a specific AML subtype, complex karyotypic AML. In conclusion, we have shown that the chromatin-remodeling protein SATB1 binds to the URE and acts as a development-dependent long-range transcriptional regulator of the PU.1 gene. Further, we have identified a SNP within this distal enhancer that is associated with a subtype of leukemia and exerts a deleterious effect through remote transcriptional dysregulation in specific progenitor subtypes.