Recent studies with tiling arrays have revealed more genomic transcription than 
previously anticipated. Whole new groups of non-coding transcripts (NCTs) have 
been detected. Some of these NCTs, including miRNAs, can regulate gene 
expression. To date, most known NCTs studied have been relatively short, but 
several important regulatory NCTs, including XIST, MALAT-1, BC1 and BC200, are 
considerably larger in length and represent a novel class of long, non-coding 
RNA species. Whole-genome tiling arrays were utilized to identify novel long 
NCTs across the entire human genome. Our results have identified a new group of 
long (>400 nt), abundantly expressed NCTs and have found that a subset of these 
are also highly evolutionarily conserved. In this report, we have begun to 
characterize 15 long, conserved NCTs. Quantitative real-time RT-PCR was used to 
analyze their expression in different normal human tissue and also in breast and 
ovarian cancers. We found altered expression of many of these NCTs in both 
cancer types. In addition, several of these NCTs have consistent mutations when 
sequences of normal samples were compared with a panel of cancer-derived cell 
lines. One NCT was found to be consistently mutated in a panel of endometrial 
cancers compared with matched normal blood. These NCTs were among the most 
abundantly expressed transcripts detected. There are probably many long, 
conserved NCTs, albeit with lower levels of expression. Although the function of 
these NCTs is currently unknown, our study indicates that they may play an 
important function in both normal cells and in cancer development.