Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes

To discover novel antisense transcripts encoded in the antisense strand of important genes, such as cancer-related genes, we conducted expression analyses of antisense transcripts using our custom microarray platform along with 2376 probes designed specifically to detect the potential antisense transcripts of 501 well-known genes suitable for cancer research.Using colon cancer tissue and normal tissue surrounding the cancer tissue obtained from 6 patients, we found that antisense transcripts without poly(A) tails are expressed from approximately 80% of these well-known genes. This observation is consistent with our previous finding that many antisense transcripts expressed in a cell are poly(A)-. We also identified 101 and 71 antisense probes displaying a high level of expression specifically in normal and cancer tissues respectively.Our microarray analysis identified novel antisense transcripts with expression profiles specific to cancer tissue, some of which might play a role in the regulatory networks underlying oncogenesis and thus are potential targets for further experimental validation. Our microarray data are available at http://www.brc.riken.go.jp/ncrna2007/viewer-Saito-01/index.html webcite.Non-coding RNAs are one class of RNAs that do not encode proteins but have specific cellular activities. Some non-coding RNAs are antisense RNAs encoded on the antisense strand of protein-coding genes. Recent progress in sequencing technologies has allowed the rapid sequence analysis of the large amount of RNAs that are transcribed in the cell. For example, the large-scale cDNA sequencing projects conducted by the FANTOM consortium revealed that a large proportion of the mouse genome is transcribed into RNAs and that many of these RNAs do not have protein-coding potential and thus are considered non-coding RNAs [1,2]. Studies using tiling arrays further support these observations and have revealed the presence of RNA-encoding regions in the genome by computational mappi