Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages

Alternative promoters are critical for lineage-specific gene expression; however, their systematic roles in hematopoiesis remain unclear. Here, we analyze 532 RNA sequencing (RNA-seq) datasets to construct a high-resolution promoter activity landscape. We identify 1,074 high-impact promoters, including novel lineage-specific switches in Pou2f1 and Ikzf1. Pou2f1 P1 is active in T/NK cells/monocytes, while P2 is B-cell-/progenitor-specific. Ikzf1 P1 is active in B cells/monocytes, and P2 is T-cell-specific. CRISPRi-mediated repression validated their lineage-specific functions. We further pinpoint the following driving transcription factors: Spi1 (Ikzf1 P1), Foxo1 (Ikzf1 P2), Yy1 (Pou2f1 P1), and Pax5 (Pou2f1 P2). This study provides novel insights into promoter-mediated regulation in hematopoietic lineages and a foundation for targeting promoter-specific mechanisms in disease.