Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources - PubMed (original) (raw)

Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources

Francis Doyle et al. Methods Mol Biol. 2008.

Abstract

The untranslated regions (UTRs) of many mRNAs contain sequence and structural motifs that are used to regulate the stability, localization, and translatability of the mRNA. It should be possible to discover previously unidentified RNA regulatory motifs by examining many related nucleotide sequences, which are assumed to contain a common motif. This is a general practice for discovery of DNA-based sequence-based patterns, in which alignment tools are heavily exploited. However, because of the complexity of sequential and structural components of RNA-based motifs, simple-alignment tools are frequently inadequate. The consensus sequences they find frequently have the potential for significant variability at any given position and are only loosely characterized. The development of RNA-motif discovery tools that infer and integrate structural information into motif discovery is both necessary and expedient. Here, we provide a selected list of existing web-accessible algorithms for the discovery of RNA motifs, which, although not exhaustive, represents the current state of the art. To facilitate the development, evaluation, and training of new software programs that identify RNA motifs, we created the UAlbany training UTR (TUTR) database, which is a collection of validated sets of sequences containing experimentally defined regulatory motifs. Presently, eleven training sets have been generated with associated indexes and "answer sets" provided that identify where the previously characterized RNA motif [the iron responsive element (IRE), AU-rich class-2 element (ARE), selenocysteine insertion sequence (SECIS), etc.] resides in each sequence. The UAlbany TUTR collection is a shared resource that is available to researchers for software development and as a research aid.

PubMed Disclaimer

Cited by

Engineering Structurally Interacting RNA (sxRNA).
Doyle F, Lapsia S, Spadaro S, Wurz ZE, Bhaduri-McIntosh S, Tenenbaum SA. Doyle F, et al. Sci Rep. 2017 Mar 28;7:45393. doi: 10.1038/srep45393. Sci Rep. 2017. PMID: 28350000 Free PMC article.
Informatic resources for identifying and annotating structural RNA motifs.
George AD, Tenenbaum SA. George AD, et al. Mol Biotechnol. 2009 Feb;41(2):180-93. doi: 10.1007/s12033-008-9114-z. Epub 2008 Nov 1. Mol Biotechnol. 2009. PMID: 18979204 Free PMC article. Review.
Intracellular spatial transcriptomic analysis toolkit (InSTAnT).
Kumar A, Schrader AW, Aggarwal B, Boroojeny AE, Asadian M, Lee J, Song YJ, Zhao SD, Han HS, Sinha S. Kumar A, et al. Nat Commun. 2024 Sep 6;15(1):7794. doi: 10.1038/s41467-024-49457-w. Nat Commun. 2024. PMID: 39242579 Free PMC article.
RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing.
Piao M, Sun L, Zhang QC. Piao M, et al. Genomics Proteomics Bioinformatics. 2017 Oct;15(5):267-278. doi: 10.1016/j.gpb.2017.05.002. Epub 2017 Oct 12. Genomics Proteomics Bioinformatics. 2017. PMID: 29031843 Free PMC article. Review.
Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT).
Kumar A, Schrader AW, Boroojeny AE, Asadian M, Lee J, Song YJ, Zhao SD, Han HS, Sinha S. Kumar A, et al. Res Sq [Preprint]. 2023 Jan 27:rs.3.rs-2481749. doi: 10.21203/rs.3.rs-2481749/v1. Res Sq. 2023. PMID: 36747718 Free PMC article. Updated. Preprint.

Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources - PubMed (original) (raw)