Super-enhancer-associated long noncoding RNA lnc-SPI1U mediates SPI1 feedback regulation by interacting with HNRNPH1 and HNRNPF

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Abstract
Long noncoding RNAs (lncRNAs) have been extensively studied for their regulatory roles in gene expression; however, relatively little is known about those specifically associated with super-enhancers (SEs)—genomic elements crucial for maintaining cell identity and function. This study profiles acute promyelocytic leukemia (APL)-specific SE-associated lncRNAs (SE-lncRNAs) using H3K27ac ChIP-seq and RNA-seq data from TCGA and Beat AML cohorts, identifying 44 SE-lncRNAs potentially involved in APL pathogenesis. Among these, we characterized a novel SE-lncRNA, RP11-750H9.5, located upstream of the SPI1 gene encoding the hematopoietic transcription factor PU.1, and designated it as lnc-SPI1U. Functional assays demonstrated that lnc-SPI1U suppressed differentiation, apoptosis and ATRA-induced cell proliferation inhibition, contrasting with the established role of SPI1 in promoting differentiation. Mechanistically, lnc-SPI1U interacted with heterogeneous nuclear ribonucleoproteins HNRNPH1/F, destabilizing SPI1 mRNA. Furthermore, we found that the induction of lnc-SPI1U during myeloid differentiation was dependent on PU.1, which established a feedback loop to fine-tune SPI1 expression at the optimal level for myeloid differentiation. In APL, the PML/RARα fusion protein inhibited PU.1-dependent transactivation of lnc-SPI1U by hijacking the SE region that overlapped with lnc-SPI1U locus. Our study provides mechanistic insight into how SE-lncRNAs contribute to the precise regulation of transcription factor activity during myeloid differentiation.

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