Question

How Do I Know Which Lncrna Structures Are Solved Experimentally ?

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12.5 years ago

Hani ▴ 20

how do i know which long non coding RNA structures related with disease are solved experimentally ?

non rna biology structure • 3.0k views

ADD COMMENT • link updated 12.5 years ago by Larry_Parnell 16k • written 12.5 years ago by Hani ▴ 20

score 2 · Answer 1 · 2011-11-02

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.

score 1 · Answer 2 · 2011-11-02

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12.5 years ago

Larry_Parnell 16k

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.

ADD COMMENT • link 12.5 years ago by Larry_Parnell 16k

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ya even i think tertiary structure information is not available for long non coding RNAs.

ADD REPLY • link 12.5 years ago by Hani ▴ 20

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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.