A Long Noncoding RNA from the Hbs1l-Myb Intergenic Region on Chr6q23 Regulates Human Fetal Hemoglobin Expression

The HBS1L-MYB intergenic polymorphisms on chr6q23 is a HbF QTL.  A distal enhancer located at ~84 kb upstream of MYB has been found by GWAS, and characterized using insertional mutation, 3C analysis, and gene editing. This enhancer contains a 3-bp deletion polymorphism (rs66650371) surrounded by binding sites for erythroid-specific transcription factors, and is likely the functional motif. RNA polymerase 2 occupancy and a 50-bp RNA transcript adjacent to rs66650371 led us to hypothesize that this transcript is part of a long noncoding RNA (lncRNA).  We characterized a novel 1283 bp lncRNA (HMI-LNCRNA), which was transcribed from this MYB enhancer and contained binding sites for TAL1/E47, GATA, and RUNX1. Increased expression was seen in erythroblasts from cord blood CD34+ cells, Most non-hematopoietic tissues had minimal expression. HMI-LNCRNA expression was higher in erythroblasts from adult peripheral blood CD34+ cells which expressed more HBB, compared with erythroblasts from cord blood CD34+ cells which expressed much more HBG. HMI-LNCRNA expression was higher in HUDEP-2 cells, an immortalized human adult-like erythroid cells which expressed only HBB compared to HUDEP-1 cells which expressed predominantly HBG.  Down-regulation of HMI-LNCRNA expression resulted in 200-fold increase in HBG mRNA.  HBG mRNA expression in these cells amounted to 20% of the total HBB and HBG mRNA. The changes in HBG mRNA levels were associated with corresponding changes in γ globin. HMI-LNCRNA is likely an enhancer RNA, or eRNA.  Its down-regulation can result in markedly increase in HBG expression making it a potential therapeutic target for HbF induction treatment in β hemoglobinopathies.