TISdb: a database for alternative translation initiation in mammalian cells

• Published in: Nucleic acids research Vol. 42; no. Database issue; pp. D845 - D850
• Main Authors: Wan, Ji, Qian, Shu-Bing
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2014
• Subjects: Animals; Codon, Initiator; Databases, Genetic; Genome; Humans; Internet; Mice; Open Reading Frames; Peptide Chain Initiation, Translational; V. Human genome, model organisms, comparative genomics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkt1085

Proper selection of the translation initiation site (TIS) on mRNAs is crucial for the production of desired protein products. Recent studies using ribosome profiling technology uncovered a surprising variety of potential TIS sites in addition to the annotated start codon. The prevailing alternative translation reshapes the landscape of the proteome in terms of diversity and complexity. To identify the hidden coding potential of the transcriptome in mammalian cells, we developed global translation initiation sequencing (GTI-Seq) that maps genome-wide TIS positions at nearly a single nucleotide resolution. To facilitate studies of alternative translation, we created a database of alternative TIS sites identified from human and mouse cell lines based on multiple GTI-Seq replicates. The TISdb, available at http://tisdb.human.cornell.edu, includes 6991 TIS sites from 4961 human genes and 9973 TIS sites from 5668 mouse genes. The TISdb website provides a simple browser interface for query of high-confidence TIS sites and their associated open reading frames. The output of search results provides a user-friendly visualization of TIS information in the context of transcript isoforms. Together, the information in the database provides an easy reference for alternative translation in mammalian cells and will support future investigation of novel translational products.