GSE125246
Functional characterization of the clonal hematopoiesis and myeloproliferative neoplasm associated polymorphism rs621940 located downstream of GFI1B
Transcription factor GFI1B suppresses its own gene expression, and deregulated GFI1B expression contributes to myeloid neoplasms. The DNA polymorphism rs621940 located 8 kb downstream of GFI1B predisposes for clonal hematopoiesis and myeloproliferative neoplasms. Whether rs621940 affects GFI1B expression is unknown. We observed clear GFI1B binding around the rs621940 locus in megakaryoblast MEG-01 cells using ChIP-seq. Pull-downs using DNA-sequences with either rs621940-allele followed by protein identification using mass spectrometry detected 24 differentially bound proteins in MEG-01 cells, but GFI1B was not among these. Also, GFI1B auto-repression was not different between either rs621940-allele in transient gene reporter assays. Deletion of an 1.6 kb fragment encompassing rs621940 in K562 cells did not alter GFI1B expression nor GFI1B auto-repression. In primary peripheral blood mononuclear cells from healthy donors, absolute GFI1B expression did not differ consistently between the rs621940 alleles. Finally, GFI1B haplotyping using long range DNA sequencing detected 3' non-coding polymorphisms on the same chromosome as the rs621940 polymorphism. Yet, targeted deep RNA sequencing did not detect consistent effects of  rs621940 on allelic GFI1B expression. These studies find no evidence that rs621940 affects GFI1B expression nor GFI1B auto-repression. Overall design: ChIP-seq analysis of th GFI1B proteins in MEG01 cells was performed using illumina high-throughput sequencing