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49396 Bos taurus sequence windows |
Cis-acting mRNA elements that program ribosomes to shift translational reading frame were first discovered in viruses. These programmed -1 ribosomal frameshift (-1 PRF) signals are composed of a heptameric "slippery site" followed by an mRNA pseudoknot secondary structure. 1 Viruses typically use -1 PRF as a genome condensation strategy; enabling them to encode multiple proteins from a single unaltered mRNA. Historically, because of their relative simplicity, many molecular regulatory elements have been first discovered in viruses: -1 PRF is no different. We developed a computational method to identify putative -1 PRF signals in eukaryotic genomic sequences. Subsets of these sequences were shown to stimulate significant -1 programmed frameshifting using dual-luciferase reporter constructs. 2 Analysis of these signals suggests that, after a frameshifting event, ribosomes would be directed to translate premature termination codons. These should promote mRNA destabilization via the nonsense-mediated mRNA decay (NMD) pathway. We previously showed that a viral -1 PRF signal cloned in a similar context can function as an mRNA destabilizing element. 3 This suggests that regulation of -1 PRF may be used to regulate cellular gene expression by controlling mRNA stability. In addition, ribosome stalling induced by strong mRNA structures can also promote mRNA degradation via 'No-go decay,' suggesting that our computational approach may be capable of identifying a class of mRNA destabilizing elements independent of -1 PRF. This online database is focused on cataloging programmed ribosomal frameshift signals (PRF) in eukaryotic genomes. Please search for a gene of interest or select one of the links above to get started. Most of the sequence information from this database came from either the Yeast Genome Project or the Mammalian Gene Collection. It is possible to search for any word(s) from the NCBI or SGD gene description as well as the canonical gene name. Thus searching for 'RPL' or 'ribosome' are likely candidates for looking at ribosomal genes.
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