TISdb: a database for alternative translation initiation in mammalian cells

Abstract

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.

Figure 1.

An example of TIS search results for ACTG1 from both human and mouse genomes. (A) Summary table of TIS information for ACTG1. The coordinates correspond to the first position of the start codon. The genome coordinates are consistent with hg19 (human) or mm10 (mouse). (B) Multiple alignment of TIS context. A window of −3 and +4 nt around an upstream TIS of mouse ACTG1 is displayed. The height in the ‘Placental Cons’ represents the degree of conservation for each base in the window. The orthologous sequences of 10 vertebrate species are shown for multiple alignment.

Figure 2.

The image of predicted ORFs associated with the identified TIS sites is shown for ACTG1. All isoforms of the transcript are displayed. From left to right, the transcript structure consists of the 5′ UTR (grey), CDS (green) and 3′ UTR (grey). Each ORF is represented as a line between an identified TIS and a predicted stop codon (black square). The ORF is color coded according to reading frames (red, frame 0; purple, frame 1; blue, frame 2). The TIS codon sequence composition is shown together with the coordinates relative to the transcription start site.