Abstract
Gene expression regulatory elements are scattered in gene promoters and pre-mRNAs. In particular, RNA elements lying in untranslated regions (5′ and 3′UTRs) are poorly studied because of their peculiar features (i.e., a combination of primary and secondary structure elements) which also pose remarkable computational challenges. Several years ago, we began collecting experimentally characterized UTR regulatory elements, develo** the specialized database UTRsite. This paper describes the detailed guidelines to annotate cis-regulatory elements in 5′ and 3′ UnTranslated Regions (UTRs) by computational analyses, retracing all main steps used by UTRsite curators.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Wang C, Zhang MQ, Zhang Z (2013) Computational identification of active enhancers in model organisms. Genomics Proteomics Bioinformatics 11:142–150
Keene JD (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8:533–543
Piva F, Giulietti M, Burini AB et al (2012) SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. Hum Mutat 33:81–85
Piva F, Giulietti M, Nocchi L et al (2009) SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans. Bioinformatics 25:1211–1213
Giulietti M, Piva F, D’Antonio M et al (2013) SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res 41:D125–D131
Grillo G, Turi A, Licciulli F et al (2010) UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 38:D75–D80
Mathews DH, Moss WN, Turner DH (2010) Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol 2:a003665
Hamilton RS, Davis I (2011) Identifying and searching for conserved RNA localisation signals. Methods Mol Biol 714:447–466
Sarnowska E, Grzybowska EA, Sobczak K et al (2007) Hairpin structure within the 3′UTR of DNA polymerase beta mRNA acts as a post-transcriptional regulatory element and interacts with Hax-1. Nucleic Acids Res 35:5499–5510
Johnson M, Zaretskaya I, Raytselis Y et al (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:W5–W9
Morgenstern B (2004) DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res 32:W33–W36
Smith C, Heyne S, Richter AS et al (2010) Freiburg RNA tools: a web server integrating INTARNA, EXPARNA and LOCARNA. Nucleic Acids Res 38:W373–W377
Grillo G, Licciulli F, Liuni S et al (2003) PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res 31:3608–3612
Pesole G, Liuni S, D’Souza M (2000) PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics 16:439–450
Grzybowska EA, Zayat V, Konopinski R et al (2013) HAX-1 is a nucleocytoplasmic shuttling protein with a possible role in mRNA processing. FEBS J 280:256–272
Nowak R, Siedlecki JA, Kaczmarek L et al (1989) Levels and size complexity of DNA polymerase beta mRNA in rat regenerating liver and other organs. Biochim Biophys Acta 1008:203–207
Konopinski R, Nowak R, Siedlecki JA (1996) Alternative polyadenylation of the gene transcripts encoding a rat DNA polymerase beta. Gene 176:191–195
Hofacker IL (2007) RNA consensus structure prediction with RNAalifold. Methods Mol Biol 395:527–544
Nawrocki EP, Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29:2933–2935
Wei D, Alpert LV, Lawrence CE (2011) RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. Bioinformatics 27:2486–2493
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Giulietti, M., Grillo, G., Liuni, S., Pesole, G. (2015). A Guideline for the Annotation of UTR Regulatory Elements in the UTRsite Collection. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 1269. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2291-8_21
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2291-8_21
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2290-1
Online ISBN: 978-1-4939-2291-8
eBook Packages: Springer Protocols