Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes
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Published on: August 31, 2018
Rintaro Saito1, Keisuke Kohno, Yuki Okada
1Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
Background:
Recent studies have identified thousands of sense-antisense gene pairs across different genomes by computational mapping of cDNA sequences. These studies have shown that approximately 25% of all transcriptional units in the human and mouse genomes are involved in cis-sense-antisense pairs. However, the number of known sense-antisense pairs remains limited because currently available cDNA sequences represent only a fraction of the total number of transcripts comprising the transcriptome of each cell type.
Methods:
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.
Results:
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.
Conclusion:
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.
Insights
Researchers discovered novel antisense transcripts in cancer tissues using microarray analysis. These transcripts, often lacking poly(A) tails, show cancer-specific expression and may be key targets for oncogenesis research.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Sense-antisense gene pairs are prevalent, with ~25% of human and mouse transcriptional units involved.
- Current knowledge of sense-antisense pairs is limited by incomplete transcriptome data.
Purpose of the Study:
- To discover novel antisense transcripts in cancer-related genes.
- To analyze the expression profiles of these transcripts in cancer versus normal tissues.
Main Methods:
- Custom microarray platform with 2376 probes targeting antisense transcripts of 501 cancer-related genes.
- Expression analysis using colon cancer and adjacent normal tissues from 6 patients.
Main Results:
- Antisense transcripts lacking poly(A) tails are expressed from ~80% of the studied genes.
- 101 and 71 antisense probes showed high expression specific to normal and cancer tissues, respectively.
Conclusions:
- Novel antisense transcripts with cancer-specific expression profiles were identified.
- These transcripts may be involved in oncogenesis regulatory networks.
- Identified transcripts are potential targets for experimental validation and cancer therapy development.
