Human Transcribed Ultraconserved regions (T-UCRs) are long noncoding RNAs (LncRNAs) that are transcribed from 481 ultraconserved regions (UCRs) in the human genome (Braconi et al., 2011; Calin et al., 2007; Esteller, 2011; Lujambio et al., 2010). Recent genome-wide expression profiling studies demonstrated that some T-UCRs are aberrantly expressed in leukemia and several solid tumors, such as neuroblastoma (Braconi et al., 2011; Calin et al., 2007; Lujambio et al., 2010, Mestdagh et al., 2010). These results offer promise for the use of T-UCR expression patterns in the diagnosis and prognosis of specific human cancers.
Challenges for T-UCR Studies
• Previously, there has been no systematic discovery platform for novel T-UCRs
• Detection of potential T-UCRs can be inaccurate due to difficulties in designing specific probes
• Convenient tools to reveal the putative functional relationships between T-UCRs and their proximal protein-coding genes have been unavailable
• The annotation of UCR information in current databases is outdated.
Highlights
• 481 UCRs and their flanking regions using 60nt probes tiled at 40bp spacing: Enables the accurate detection and discovery of potentially novel T-UCRs.
• Comprehensive and Reliable potential T-UCR collection: Detects 153 potential T-UCRs predicted from the most updated transcriptome databases, such as RefSeq, UCSC knowngenes, and Ensembl.
• Accurate detection of RNA transcripts overlapping UCR loci and UCR-proximal genes: Helps researchers uncover potentially interesting functional relationships between T-UCRs and nearby protein-coding genes.
• Detailed annotation of UCRs, T-UCRs, and their relationships with cancer-associated genomic regions (CAGRs): Aids cancer researchers in the identification of potentially important biomarkers for diagnosis and prognosis.
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