A large scale expression study associates uc.283-plus IncRNA with pluripotent stem cells and human glioma

Background: 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 (IncRNAs). Methods: We 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. Results: We identified tissue selective UCRs and studied UCRs in embryonic and induced pluripotent stem cells. Among the normal tissues, the uc.283 IncRNA was highly specific for pluripotent stem cells. Intriguingly, the uc.283-plus IncRNA was highly expressed in some solid cancers, particularly in one of the most untreatable types, glioma. Conclusion: Our results suggest that uc.283-plus IncRNA might have a role in pluripotency of stem cells and in the biology of glioma.