Exploring the Functional Role of an Alternative mRNA Transcript of the EPO Gene

Abstract

Erythropoietin (EPO) is the key regulator of erythropoiesis and stimulates the proliferation and differentiation of erythroid progenitor cells into mature erythrocytes. In a previous study, we identified a frame-shift mutation in the EPO gene that causes familial erythrocytosis with elevated erythropoietin (EPO) levels by initiating excess production of EPO protein from an alternative EPO mRNA [1]. This alternative non-coding mRNA is transcribed from a promoter (P2) located in intron 1, whereas the full length mRNA that encodes the EPO protein is transcribed from the P1 promoter located upstream of exon 1. Large parts of intron 1 sequences, including the P2 transcript are conserved among different species (Figure 1A), suggesting that the P2 transcript could have an as yet unknown physiological function. To study the putative function of the P2 transcript, we performed experiments in a human cell line, Hep3B, which can produce EPO. We used the CRISPR/Cas9 system to generate mutant Hep3B clones with targeted deletions in intron 1 of the EPO gene. Close to the P2 transcription start site in intron 1, we identified three GATA-consensus motifs that might act as promoter elements for the P2 transcript. In the first round of CRISPR/Cas9 mutagenesis, we targeted the first two GATA elements and expected to knock down the expression of the P2 transcript. Targeted Hep3B cells were sorted and deposited as single cells to derive clones that were genotyped by next generation sequencing. We obtained 2 clones with homozygous deletions in EPO intron 1 and one clone that was compound heterozygous (Figure 1A). In these Hep3B clones we assessed EPO mRNA expression by qPCR and EPO protein levels in the supernatant by ELISA (Figure 1B). Unexpectedly, the P2 transcript was still detectable in all three clones carrying deletions in intron 1 that eliminated GATA boxes 1 and 2 (data not shown). EPO P1 mRNA expression and EPO protein levels in the supernatant were slightly reduced in most of the clones. These data indicate that the GATA box 1 and 2 motifs are not required for generating the P2 transcript. We have now performed a second round of CRISPR/Cas9 mutagenesis. In one series we targeted all three GATA-motifs through a 186 bp deletion, and in a second series we targeted a highly conserved region upstream of the GATA boxes by a 93 bp deletion (Figure 1A). We obtained 4 clones homozygous for the 93 bp deletion and the clones for the 186 bp deletion are currently being expanded. The analysis of EPO mRNA and protein in these additions CRISPR/Cas9 clones will be presented. Our study shows that the GATA motifs 1 and 2 are not required for function of the P2 promoter in intron 1 of the EPO gene. However, deleting these two motifs in two different cell clones decreased the P1 full-length EPO mRNA expression and EPO protein production in Hep3B cells by 70.2% and 37.2%, respectively. Additional clones with deletion of all three GATA motifs and a highly conserved region upstream of the GATA boxes will likely provide more insights into the physiological role of the P2 transcript.