Alternative polyadenylation links RNA processing to iron metabolism in human erythropoiesis

TL;DR

This study shows how RNA processing, specifically alternative polyadenylation, connects to iron metabolism during red blood cell formation and how it may be linked to a blood disorder called polycythemia vera.

Contribution

The study identifies a novel regulatory axis involving CPSF6, APA, and iron metabolism in erythropoiesis and links its dysregulation to polycythemia vera.

Findings

Seven distinct APA dynamic patterns were identified during erythropoiesis, with genes involved in iron metabolism showing stage-specific APA changes.

CPSF6 depletion impaired heme synthesis and caused intracellular iron deficiency by shortening 3′UTRs of iron metabolism regulators.

CPSF6 and APA-regulated iron metabolism genes were upregulated in polycythemia vera patients, correlating with erythroid hyperproliferation.

Abstract

Erythropoiesis requires precise coordination of transcriptional and co-/post-transcriptional programs, yet the role of alternative polyadenylation (APA) in this process remains poorly understood. Here, we profiled the genome-wide dynamic APA landscape during erythropoiesis using single-cell RNA sequencing (scRNA-seq). Through clustering and functional enrichment analysis, seven distinct APA dynamic patterns were identified, with genes showing stage-specific APA changes enriched in erythroid lineage differentiation, heme synthesis, and iron metabolism. Combining motif analysis near polyadenylation sites (PASs) and APA regulators expression profiling, we observed that cleavage and polyadenylation specificity factor 6 (CPSF6), a critical APA regulator, exhibited significant variation. Functional assays demonstrated that CPSF6 facilitates erythropoiesis, as its depletion impaired heme synthesis and intracellular iron deficiency. Mechanistically, CPSF6 depletion shortened the 3′UTR length of iron metabolism regulators (FAM210B, IREB2, TFRC), which was accompanied by reduced expression of these genes. Clinically, CPSF6 and these APA-regulated iron metabolism-related genes were aberrantly upregulated in polycythemia vera (PV) patients, correlating with erythroid hyperproliferation. Collectively, our findings support a CPSF6-APA-iron homeostasis axis as an important co-/post- transcriptional regulatory mechanism in erythropoiesis, and implicate its dysregulation in the pathogenesis of PV, offering novel molecular targets for therapeutic intervention in myeloproliferative neoplasms.

Graphical Abstract

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