5' and 3' UTRs in RNA regulation

Question

[vin23]

Hello all, I am working on eukaryotic translation regulation. I am new to R and would like your help in solving a problem. I have a list of translationally regulated genes which are upregulated in Th2 cells. I would like to check what all properties are present in the UTRs (such as length of UTRs, GC content, secondary structures, etc.) in all these genes. I don't know how to go about this problem. I have extracted the 5' and 3' UTRs from UCSC for all the genes. I would like your help in performing a statistical analysis in all the properties of UTR using the UTRs extracted.

Thank you

[benformatics]

Why not calculate these things in R yourself using Biostrings? For secondary structure you may need to use RNA-fold

[vin23]

Thank you so much for the reply. Can you please elaborate on the same or provide me some reference that I can follow

Answer 1

[Rafael Soler]

Hello,

For the length, you actually have it in the downloaded sequences.

For the composition of the DNA: https://molbiol-tools.ca/DNA_composition.htm

For secondary structure: https://molbiol-tools.ca/Repeats_secondary_structure_Tm.htm

For promoters: https://molbiol-tools.ca/Promoters.htm

For DNA motifs: https://molbiol-tools.ca/DNA_Motifs.htm

And here you have the rest of the tools:https://molbiol-tools.ca/

Best

[vin23]

Thank you so much for your reply. I might have not mentioned it correctly, my mistake. But I want to compare the extracted UTRs and check for common features in them. I will still check these tools and see if it is helpful or not. Again thanks for providing with the list of tools

[Rafael Soler]

You are welcome! The first thing you can do is align the sequences with Jalview for example to check for common features. After this, you can analyze the UTR length, GC content and other statistics for the different UTRs with these tools.

You can also use HOMER to check if your gene list has a TF enriched in its UTR enhancer sequences: Analyze gene lists with promoter motif analysis

If you have any further questions, don't hesitate to ask!