RNAtips: analysis of temperature-induced changes of RNA secondary structure

Although multiple biological phenomena are related to temperature (e.g. elevation of body temperature due to an illness, adaptation to environmental temperature conditions, biology of coldblooded versus warm-blooded organisms), the molecular mechanisms of these processes remain to be understood. Perturbations of secondary RNA structures may play an important role in an organism’s reaction to temperature change—in all organisms from viruses and bacteria to humans. Here, we present RNAtips (temperature-induced perturbation of structure) web server, which can be used to predict regions of RNA secondary structures that are likely to undergo structural alterations prompted by temperature change. The server can also be used to: (i) detect those regions in two homologous RNA sequences that undergo different structural perturbations due to temperature change and (ii) test whether these differences are specific to the particular nucleotide substitutions distinguishing the sequences. The RNAtips web server is freely accessible without any login requirement at http://rnatips.org.

[1]  F. Narberhaus,et al.  Molecular basis for temperature sensing by an RNA thermometer , 2006, The EMBO journal.

[2]  Martin Ester,et al.  Density‐based clustering , 2019, WIREs Data Mining Knowl. Discov..

[3]  Hans-Peter Kriegel,et al.  A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise , 1996, KDD.

[4]  E. Nudler,et al.  New insights into the mechanism of heat shock response activation , 2008, Cellular and Molecular Life Sciences.

[5]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[6]  Robert Tibshirani,et al.  Genome-wide measurement of RNA folding energies. , 2012, Molecular cell.

[7]  J. Mergny,et al.  Analysis of thermal melting curves. , 2003, Oligonucleotides.

[8]  P. Doty,et al.  Heterogeneity in Deoxyribonucleic Acids: I. Dependence on Composition of the Configurational Stability of Deoxyribonucleic Acids , 1959, Nature.

[9]  Carl T Wittwer,et al.  High-resolution DNA melting analysis for simple and efficient molecular diagnostics. , 2007, Pharmacogenomics.

[10]  Emma Kreuger,et al.  Temperature-controlled Structural Alterations of an RNA Thermometer* , 2003, Journal of Biological Chemistry.

[11]  D. Thatcher,et al.  Denaturation of proteins and nucleic acids by thermal-gradient electrophoresis. , 1981, The Biochemical journal.

[12]  Dieter Braun,et al.  Melting curve analysis in a snapshot , 2007 .

[13]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[14]  Markus Ringnér,et al.  Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast , 2005, PLoS Comput. Biol..

[15]  G. Storz.  An RNA thermometer. , 1999, Genes & development.

[16]  E. Kandel,et al.  RNA-mediated response to heat shock in mammalian cells , 2006, Nature.

[17]  D. Braun,et al.  Thermophoretic melting curves quantify the conformation and stability of RNA and DNA , 2011, Nucleic acids research.

[18]  Fabian J Theis,et al.  Supplemental Material to : , 2012 .

[19]  P. Doty,et al.  Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. , 1962, Journal of molecular biology.

[20]  D. Riesner,et al.  Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. , 1987, Biophysical chemistry.

[21]  Torsten Waldminghaus,et al.  RNA thermometers. , 2006, FEMS microbiology reviews.