An Integrated Database for Exploring Alternative Promoters in Animals

Abstract

Alternative promoter (AP) events, as a major pre-transcriptional mechanism, can initiate different transcription start sites to generate distinct mRNA isoforms and regulate their expression. At present, hundreds of thousands of APs have been identified across human tissues, and a considerable number of APs have been demonstrated to be associated with complex traits and diseases. Recent researches have also proven important effects of APs on animals. However, the landscape of APs in animals has not been fully recognized. In this study, 102,349 AP profiles from 23,077 samples across 12 species were systematically characterized. We further identified tissue-specific APs and investigated trait-related promoters among various species. In addition, we analyzed the associations between APs and enhancer RNAs (eRNA)/transcription factors (TF) as a means of identifying potential regulatory factors. Integrating these findings, we finally developed Animal-APdb, a database for the searching, browsing, and downloading of information related to Animal APs. Animal-APdb is expected to serve as a valuable resource for exploring the functions and mechanisms of APs in animals.

Fig. 1

Flow charts of Animal-APdb. (a) Data collection and processing of Animal-APdb. (b) Main modules of Animal-APdb. (c) Database construction of Animal-APdb.

Fig. 2

Data summary and technical validation of Animal-APdb. (a) The number of APs identified for each species in Animal-APdb. (b) The number of tissue-specific APs identified for each species in Animal-APdb. (c) The total number of AP genes annotated in Animal-APdb compared to those annotated in EPD. (d) Comparison of human AP genes annotated by EPD, proActiv, and Animal-APdb. (e) Distribution of distances between APs for genes annotated exclusively in EPD and those annotated in both EPD and proActiv.