Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome

Promoter shifting, characterized by alterations in Transcription Start Site (TSS) coordinates, is a well-documented phenomenon. The impact and statistical significance of promoter shifting can be assessed through analysis of Cap Analysis of Gene Expression (CAGE) data. This phenomenon is associated with developmental stage transitions, tissue differentiation, and cellular responses to environmental stimuli. Differential promoter usage suggests nonconstitutive expression of the regulated gene, indicative of focused promoter utilization. Conversely, housekeeping genes are typically characterized by stable expression levels driven by multiple dispersed promoters and are commonly expressed across a wide range of tissues. However, our findings demonstrate that many ubiquitously expressed genes utilize single, focused promoters and undergo significant promoter shifting, adding a layer of complexity to the definition of a housekeeping gene. Differential gene expression is commonly used to study gene responses to external stimuli in cells and tissues. Here, we employ an alternative approach based on differential promoter usage, identifying genes exhibiting significant promoter shifting as signatures of tissue response and phenotypic effects. Our results suggest that variations in chicken growth rate are regulated by nutrient metabolism rates, mediated through differential promoter usage of relevant genes.