Harvard Catalyst Profiles

More than 40 coding variants within the DNA-binding domain of the transcription factor KLF1 have been associated with a wide spectrum of red blood cell disorders and rare blood cell traits, spanning phenotypes such as clinically unremarkable blood group types and the benign hereditary persistence of fetal hemoglobin, to more severe diseases such as nonspherocytic hemolytic anemia and congenital dyserythropoietic anemia. To investigate possible differences in the gene regulatory effects of these variants that may result in differences in gene dysregulation, we created and profiled an allelic series of KLF1 coding variants. Briefly, by CRISPR/Cas9-mediated genome editing, we have created isogenic cell lines of KLF1 missense variants in the K562 human erythroleukemic cell line. We then performed protein-binding microarrays (PBMs), CUT&RUN, ATAC-seq, and RNA-seq on this allelic series, in order to determine the effects of these KLF1 variants on in vitro DNA binding activity, genomic occupancy in cells, chromatin accessibility, and gene expression. This project will focus on integrative computational analysis of these collected functional genomic datasets in order to better understand the relationship between the altered DNA binding activities of these KLF1 variants and their effects on gene regulation. This project has the potential to also involve some wetlab experiments to investigate the associated cellular phenotypes. The student working on this project will take a lead role on the computational analysis and potential wetlab experimentation, and will contribute the results to a manuscript in preparation. Students interested in this opportunity should have prior experience in analyzing genomic datasets and Illumina sequencing data.