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Transcriptional repression of embryonic globin gene by SKI on the distal repressive element [RNA-seq]

ABSTRACT: The regulation of α-like globin gene expression, particularly the embryonic ζ-globin gene (HBZ), remains poorly understood compared to the well-characterized β-globin switch. To systematically identify transcriptional regulators of HBZ, we developed an HBZ-P2A-GFP reporter system in erythroid cell lines (K562 and HUDEP-2) and performed a CRISPR/Cas9 screen targeting 1,639 transcription factors. We identified SKI as a potent repressor of HBZ. Genetic ablation of SKI significantly upregulated HBZ without impairing erythropoiesis, whereas its overexpression suppressed HBZ. Inducible expression and degradation assays confirmed that SKI directly represses HBZ transcription. RNA-seq revealed that SKI deletion specifically activates HBZ with minimal effects on other erythroid genes. ChIP-seq demonstrated SKI binding at key distal enhancers (HS-10 and HS-40), partially overlapping with BCL11A. Dual knockout of SKI and BCL11A synergistically enhanced HBZ expression. Base editing of the SKI-binding site at HS-10 also increased HBZ expression, and a nearby natural variant (chr16:143207_G/A) was identified in α-thalassemia patients with elevated ζ-globin. Our findings establish SKI as a direct transcriptional repressor of HBZ and reveal a synergistic regulatory mechanism with BCL11A. This work provides new insights into globin gene regulation and suggests potential therapeutic strategies for α-thalassemia through targeted activation of ζ-globin.

ORGANISM(S): Homo sapiens

PROVIDER: GSE307350 | GEO | 2026/02/28

REPOSITORIES: GEO

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Project description:Basak A, Munschauer M, Lareau CA, Montbleau KE, Ulirsch JC, Hartigan CR, Schenone M, Lian J, Wang Y, Huang Y, Wu X, Gehrke L, Rice CM, An X, Christou HA, Mohandas N, Carr SA, Orkin SH, Chen JJ, Lander ES, and Sankaran VG. Increased production of the beta-like gamma-globin genes that form fetal hemoglobin can ameliorate the severity of sickle cell disease and beta-thalassemia, the major hemoglobin disorders. BCL11A is a key repressor of the gamma-globin genes and is expressed in a developmental stage-specific manner to regulate the physiologic fetal-to-adult hemoglobin switch. Despite extensive studies, the upstream mechanisms underlying the developmental expression of BCL11A and hemoglobin switching in humans have remained mysterious. Here we show that BCL11A is regulated at the level of mRNA translation during human hematopoietic development. While BCL11A mRNA is comparably expressed at all developmental stages in erythroid cells, robust protein expression only occurs in adult erythroid cells. Importantly, at the earlier stages of development, the observed reduction in protein expression is attributable to decreased synthesis and not increased degradation of BCL11A. While BCL11A protein is not well synthesized at these earlier stages of development, its mRNA curiously continues to be associated with ribosomes. Through unbiased proteomic analyses in erythroid cells, we demonstrate that the RNA-binding protein LIN28B, which is developmentally expressed in a reciprocal pattern to BCL11A, directly interacts with ribosomes. We show that the observed suppression of BCL11A protein translation is mediated by LIN28B through a direct interaction with BCL11A mRNA and independent of its role in let-7 microRNA biogenesis. Finally, we show that BCL11A is the major functional target in LIN28B-mediated fetal hemoglobin induction. Our results reveal a previously unappreciated regulatory mechanism underlying human hemoglobin switching and illuminate opportunities for developing improved treatments for sickle cell disease and beta-thalassemia.

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Transcriptional repression of embryonic globin gene by SKI on the distal repressive element [RNA-seq]

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