Abstract
BackgroundThere are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat. These DNA sequences are absolutely conserved and show 100% identity with no insertions or deletions. About half of these UCRs are reported as transcribed and many correspond to long non-coding RNAs (lncRNAs).MethodsWe used custom microarrays with 962 probes representing sense and antisense sequences for the 481 UCRs to examine their expression across 374 normal samples from 46 different tissues and 510 samples representing 10 different types of cancer. The expression in embryonic stem cells of selected UCRs was validated by real time PCR.ResultsWe identified tissue selective UCRs and studied UCRs in embryonic and induced pluripotent stem cells. Among the normal tissues, the uc.283 lncRNA was highly specific for pluripotent stem cells. Intriguingly, the uc.283-plus lncRNA was highly expressed in some solid cancers, particularly in one of the most untreatable types, glioma.ConclusionOur results suggest that uc.283-plus lncRNA might have a role in pluripotency of stem cells and in the biology of glioma.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-014-0076-4) contains supplementary material, which is available to authorized users.
Highlights
There are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat
UCR expression arrays We studied the expression of UCRs using the Ohio State University Comprehensive Cancer Center (OSUCCC) custom microarray [18]
transcribed ultra-conserved region (T-UCR) expression in normal human tissues We tested the expression of UCRs in 374 samples from 46 types of normal tissues, belonging to 16 histological groups [25]
Summary
There are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat These DNA sequences are absolutely conserved and show 100% identity with no insertions or deletions. About half of these UCRs are reported as transcribed and many correspond to long non-coding RNAs (lncRNAs). The 'ultra-conserved' term was originally proposed for genomic regions longer than 200 bp that are absolutely conserved (100% homology with no insertions or deletions) in human, mouse, and rat genomes [2] Many of these elements possess tissuespecific enhancer activity [3,4,5] and others have been shown to associate with splicing regulators. Despite still having largely unknown roles, T-UCRs are thought to act as 'regulators' of other RNAs [10]
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