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Collect of SO Ontologies
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New term request: Thermoregulator #404

Closed AntonPetrov closed 7 years ago

AntonPetrov commented 7 years ago

I would like to request a new term for Thermoregulator RNAs.

Background

These regulatory regions coordinate temperature-dependent gene expression. They are found in 5'UTRs, and their secondary structures change in response to temperature which affects the translation. More information can be found in this review.

Place in hierarchy

This term could sit in the same place as riboswitch in terms of is_a _mRNAregion and is part_of an mRNA.

Why we need this term

Once the term is created, we will attach it to the following RNA families in Rfam: http://rfam.xfam.org/search?q=thermoregulator

Please feel free to let me or @JoannaArgasinska know if you have any questions. Thank you!

AntonPetrov commented 7 years ago

I hope the description makes sense. Feel free to let me know if you need more information.

nicoleruiz commented 7 years ago

This looks good! Thank you for providing a review paper for us to reference. Do you have a definition to suggest?

AntonPetrov commented 7 years ago

Thank you @nicoleruiz! How about this:

A thermoregulator is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression.

nicoleruiz commented 7 years ago

I like the definition. I will use this for the new term. I do have a few questions though.

  1. Do you want to use the term thermoregulator? I scanned a few review papers and they all use the term RNA thermometer so it seems like that is the more popular term. I would like the new term to be the name that is most recognized by the community but I will also include alternate names as synonyms.
  2. Would it be useful for you if we created child terms like ROSE element or fourU element?
AntonPetrov commented 7 years ago

I agree, RNA thermometer seems to be more common than thermoregulator, so let's use it instead.

As far as creating child terms for specific RNA thermometers, I am not entirely convinced that it's necessary. Rfam currently has 31 thermometer families, including FourU and ROSE, so if one would have to create a child term for each of them. On the other hand I can see that it could be useful in some cases.

nicoleruiz commented 7 years ago

SO:0002168 RNA_thermometer has been added.