Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression

Pinpointing functional noncoding DNA sequences and defining their contributions to health-related traits is a major challenge for modern genetics. We developed a high-throughput framework to map noncoding DNA functions with single-nucleotide resolution in four loci that control erythroid fetal hemoglobin (HbF) expression, a genetically determined trait that modifies sickle cell disease (SCD) phenotypes. Specifically, we used the adenine base editor ABEmax to introduce 10,156 separate A center dot T to G center dot C conversions in 307 predicted regulatory elements and quantified the effects on erythroid HbF expression. We identified numerous regulatory elements, defined their epigenomic structures and linked them to low-frequency variants associated with HbF expression in an SCD cohort. Targeting a newly discovered gamma-globin gene repressor element in SCD donor CD34(+) hematopoietic progenitors raised HbF levels in the erythroid progeny, inhibiting hypoxia-induced sickling. Our findings reveal previously unappreciated genetic complexities of HbF regulation and provide potentially therapeutic insights into SCD. An ABEmax-based screen identifies regulatory noncoding nucleotides in four loci that control erythroid fetal hemoglobin (HbF) expression. Targeting a repressor element raises HbF levels in cells from patients with sickle cell disease.

Automated summary

This study identifies regulatory noncoding nucleotides in four loci controlling erythroid fetal hemoglobin (HbF) expression, revealing the genetic complexities of HbF regulation and providing potential therapeutic insights into sickle cell disease (SCD). Targeting a repressor element raises HbF levels in cells from SCD patients.