Abstract
The mechanism of RNA thermometers is a subject of growing interest. Also known as RNA thermosensors, these temperature-sensitive segments of the mRNA regulate gene expression by changing their secondary structure in response to temperature fluctuations. The detection of RNA thermometers in various genes of interest is valuable as it could lead to the discovery of new thermometers participating in fundamental processes such as preferential translation during heat-shock. RNAthermsw is a user-friendly webserver for predicting the location of RNA thermometers using direct temperature simulations. It operates by analyzing dotted figures generated as a result of a moving window that performs successive energy minimization folding predictions. Inputs include the RNA sequence, window size, and desired temperature change. RNAthermsw can be freely accessed at http://www.cs.bgu.ac.il/~rnathemsw/RNAthemsw/ (with the slash sign at the end). The website contains a help page with explanations regarding the exact usage.
Highlights
RNA thermometers are temperature-sensitive RNAs that regulate gene expression and have recently attracted growing attention [13]
It should be noted that as can be observed in the example that serves for validation of the method, which is the detection of a known RNA thermometer in Figures 3 & 4, the signal is not a consequence of having a longer sequence as input or simulating a larger difference in temperature because of a lower body temperature in Drosophila than in humans
A signal was still found for a potential RNA thermometer appearing in the HSP70 of Drosophila that does not appear in the HSP70 of humans
Summary
RNA thermometers are temperature-sensitive RNAs that regulate gene expression and have recently attracted growing attention [13]. RNA thermometers typically regulate genes required during either a heat shock or a cold shock response, but have implicated in other regulatory roles such as in pathogenicity and starvation [18]. Their conformational change and 3D structure have been investigated [4,5]. The motivation of RNAthermsw is to identify locations of RNA thermometers by the direct simulation of temperatures It relies on Vienna’s RNAfold [10] with energy parameters taken from the most recent Turner model [16]. The initial program was reported in [3] and is conceptually based on a sliding window with local folding predictions performed inside the moving window, as in [11]
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.
