Abstract
Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such, they substantially influence the stability of mRNA and the amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A’s allowing for one mismatched base. The PATACSDB database is accessible at:http://sysbio.ibb.waw.pl/patacsdb. The source code is available athttp://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.
Highlights
The classical view of the genetic information flow inside living cells—the transcription from DNA to RNA and translation of mRNA into protein—is a subject of continous modification for both direction of the flow and the number of players involved
The past studies were focused on transcriptional regulation, but more recently the regulation of gene expression at the level of translation drew researchers’ attention
Translational regulation generally controls the amount of protein synthesised from a given mRNA through several mechanisms, targeting recruitment of ribosomes to
Summary
The classical view of the genetic information flow inside living cells—the transcription from DNA to RNA and translation of mRNA into protein—is a subject of continous modification for both direction of the flow and the number of players involved. How to cite this article Habich et al (2016), PATACSDB—the database of polyA translational attenuators in coding sequences. They occasionally lead to ribosome sliding on mRNA transcript which results in production of additional frameshifted product next to the known and well annotated gene protein product.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
