how do i know which long non coding RNA structures related with disease are solved experimentally ?
how do i know which long non coding RNA structures related with disease are solved experimentally ?
There might be very few with annotated structure as the interest in long nc RNAs seems such a recent trend. Just out of curiosity I searched and the first hit that came up in Google is lncRNAdb. I don't know how good this database is in comparison to other more general ones, maybe somebody else can comment on this. I searched lncRNAdb for 'structure' in the description field. There seems no way of finding that information in a programmatic way . So doing some 'text mining' on the first 3 retrieved entries I discovered there might be some candidates, e.g.: http://lncrnadb.com/Detail.aspx?TKeyID=140
Anyway, you might have to read the article again, so a pubmed search for smth like lncRNA AND structure might yield the same result.
My understanding is very few lncRNAs are predicted but rather are known from sequence data. If true, then the primary structure (i.e. the sequence string) is solved. Predicted folding of these long RNAs will be tough because of their length and because of haplotypes of genetic variation. To the latter point, a lncRNA with 8 SNPs falling in 2 LD blocks would generate at a minimum 4 haplo-isoforms (each LD block as major or minor allele, or 2 forms for each block, 2 x 2 = 4). As the number of SNPs and LD blocks goes up, the problem of predicting a secondary/tertiary structure becomes significantly more complex.
Considering their length and the fact that polymorphisms reside within, it would be rather complex to predict a tertiary structure. For now, literature suggests lncRNAs regulate mRNA availability for splicing and translation and so this interference can be predicted with primary sequence alone.
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casey thanks for fixing the url