can lnc-RNA target coding RNA?

Question

[ta_awwad]

Hello everyone, I have two divergent RNA transcripts one is coding and the other is non-coding .. is there any tool one can use to precisely calculate the complementarity between the non-coding and coding transcript if any?

thanks much TA

Answer 1

[EagleEye]

For you question "can lnc-RNA target coding RNA?", it is difficult to have a direct answer but you can have a look at these two articles.

1) H3K4me2 and WDR5 enriched chromatin interacting long non-coding RNAs maintain transcriptionally competent chromatin at divergent transcriptional units

2) MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

[Vasu]

I'm actually trying to use triplexator to find TTS and TFOs for a specific lncRNA. In the above mentioned papers I see in the second one they used triplexator tool to get TTS and TFOs for MEG3 lncRNA. I'm interested in knowing whether they have given the whole FATSA sequence of MEG3 as input or selected any region? From which database I can get the FASTA sequence of a lncRNA?

[EagleEye]

Sorry for late response, I forgot to reply.

Yes, compete sequence from MEG3 was used for the prediction. You can get DNA FASTA sequence of any lncRNA from GENCODE, "Fasta files" section from this link. Also UCSC and ENSEMBL can be an option to extract DNA FASTA sequences.

[Vasu]

thanks a lot for the answer.

[Vasu]

Could you please tell which command to use in linux to get FASTA sequence of MEG3/ any other lncRNA from gencode fasta file.

[GenoMax]

This should work

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' gencode.v29.lncRNA_transcripts.fa | grep MEG3 | tr "\t" "\n"

[Vasu]

Thanks a lot for the command.

[Vasu]

@EagleEye Do I need to use all the transcript (MEG3) sequences as input for triplexator?

[EagleEye]

What do you mean by "all transcript sequences" ? Are you referring to different isoforms ?

[Vasu]

What I mean is, MEG3 has multiple transcript IDs right. Do I need to use all or any specific transcript sequence is fine?

[EagleEye]

You must investigate all the transcript isoforms individually using triplexator.