Super-Enhancer-Associated Long Noncoding RNA Lnc-SPI1U Participates in PU.1 Feedback Regulation By Interacting with HNRNPH1 and Hnrnpf

Super-enhancers (SEs) are essential regulatory elements that orchestrate the precise transcriptional regulation of cell-type- and state-specific-gene expression during hematopoietic differentiation. The role of SEs on the regulation of long noncoding RNAs (lncRNAs) during myeloid differentiation remains poorly understood. In this study, we illustrated the landscape of SE-associated lncRNAs in acute promyelocytic leukemia (APL) by integrating 20 datasets of H3K27Ac ChIP-seq and 379 datasets of RNA-seq from the TCGA and Beat AML databases. We identified 44 lncRNAs that are located in close proximity to SEs, which may play a pivotal role in the pathogenesis APL. Among these, we designated the lncRNA RP11-750H9.5, which is found upstream of the SE region of the SPI1 gene encoding key hematopoietic transcription factor PU.1, as lnc-SPI1U. Our data found that lnc-SPI1U was involved in the regulatory loop of PU.1 during all-trans retinoic acid (ATRA)-induced differentiation. The lnc-SPI1U transcript and its genomic locus functionally play distinct roles in SPI1 gene expression. lnc-SPI1U inhibited cell differentiation and apoptosis while promoting cell proliferation during ATRA-induced myeloid differentiation. This effect was mediated by destabilizing SPI1 mRNA in concert with HNRNPH1 and HNRNPF interactions. Conversely, the genomic deletion at the lnc-SPI1U locus diminished SPI1 activation. Further analysis of transcriptional regulation illustrated that PU.1 induced the expression of lnc-SPI1U by binding to its promoter and enhancer regions, and the induction of lnc-SPI1U by ATRA was dependent on PU.1. These findings suggest that lnc-SPI1U might function as a "brake" to modulate PU.1 level and participate in PU.1 feedback regulation, thereby accurately fine-tuning the expression of PU.1 at the optimal level for myeloid differentiation. However, the PML/RARα fusion protein, characteristic of APL, disrupted the lnc-SPI1U-SPI1 regulatory circuit by hijacking the lnc-SPI1U genomic region, leading to the inhibition of SPI1 activation. Our findings emphasize the significant role of SE-associated lncRNAs, such as lnc-SPI1U, in the gene regulatory networks involved in hematopoietic differentiation.