Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC.

ABSTRACT: Pre-transcriptional regulation through alternative promoter usage is a critical yet underexplored mechanism influencing gene expression in Triple-Negative Breast Cancer (TNBC), a highly aggressive and heterogeneous breast cancer subtype. While short-read RNA sequencing data are widely available, they offer limited resolution in accurately capturing transcript-level diversity. To overcome this, we focused on promoter-level quantification to infer active promoter usage and investigate transcriptional regulation dynamics in TNBC. Using RNA-seq data from 360 TNBC tumors and 88 adjacent normal tissues, we identified TNBC-specific and subtype-enriched Active Alternative Promoters (AAPs). Integration with H3K4me3 and H3K27ac ChIP-seq data confirmed a key promoter switching event in the HDAC9 gene

SUBMITTER: Jit S 

PROVIDER: S-EPMC12575860 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature