Alternative promoter usage during organ development

Dynamic gene expression is crucial for mammalian organ development, influencing organ-specific functions and responses. A significant number of mammalian protein-coding genes are regulated by multiple distinct promoters, suggesting that the choice of promoter is as critical as its transcriptional output. However, the role of alternative promoters in organ development remains largely unexplored. In this study, we utilized RNA-seq data from 313 mouse samples across various developmental stages in seven major organs to identify active promoters. Our analyses revealed between 967 and 3,237 developmentally dynamic promoters (DDPs) in each organ. These DDPs encompass not only major promoters with the highest activity within a gene but also alternative promoters with lower activity, which are often overlooked in traditional gene-level analyses. Notably, we found that alternative DDPs can be independently regulated compared to their major counterparts, suggesting the involvement of unique transcriptional regulatory mechanisms. Furthermore, we observed that increased alternative promoter usage plays a pivotal role in driving organ-specific functions and gene expression alterations. Our findings underscore the importance of alternative promoter usage in shaping organ identity and function, providing new insights into the regulatory complexity of organogenesis.