Journal
NUCLEIC ACIDS RESEARCH
Volume 42, Issue D1, Pages D845-D850Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt1085
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Funding
- National Institutes of Health [1 DP2 OD006449-01, 1R01AG042400-01A1]
- Ellison Medical Foundation [AG-NS-0605-09]
- DOD Exploration-Hypothesis Development Award [W81XWH-11-1-0236]
- National Institutes of Health
- NATIONAL INSTITUTE ON AGING [R01AG042400] Funding Source: NIH RePORTER
- OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH [DP2OD006449] Funding Source: NIH RePORTER
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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.
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