Forum:RNA base modification

Question

[kaur.devbio]

Hello,

Does anybody know if the transcribed spacers (external or internal) also get its base modified (methylation and ѱ formation) the same way as rRNA 18S, 5.8S and 28S get?

[Whetting]

what do you mean by internal/external spacers?

[kaur.devbio]

Its external transcribed spacer (5'ETS and 3'ETS) of pre-rRNA and internal transcribed spacers.

[Whetting]

so you are asking whether ETS and ITS in rRNA is also modified?

e.g. check this paper PMC232341

[kaur.devbio]

Thanks for writing Whetting,

The paper you mentioned, in this the ETS they were talking about was not the one of pre-rRNA , its related to Intronic part of K18 gene. I am looking if like 18s rRNA, the 5'ETS also get its base modified?

Answer 1

[lsp03yjh]

You can use RMBase to find the genome-wide RNA modification sites identified from 404 transcriptome sequencing datasets (Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq). You can check whether there are modifications in pre-rRNA.

RMBase contains more than 100 modification types, such as m6A, m5C, 2'-O-Me and pseudouridine etc.