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In silico prediction and experimental validation of natural antisense transcripts in two cancer-associated regions of
Laura Monti1, Raffaella Cinquetti, Alessandro Guffanti
1Department of Biotechnology and Molecular Sciences, University of Insubria, I-21100 Varese, Italy.
Abstract:
Antisense transcription has long been recognized as a mechanism involved in the regulation of gene expression. Therefore, several human diseases associated with abnormal patterns of gene expression might display antisense RNA-mediated pathogenetic mechanisms. Such issue could be particularly relevant for cancer pathogenesis, since deregulated gene expression has long been established as a hallmark of cancer cells. Herein, we report on a bioinformatic search for antisense transcription in two cancer-associated regions of human chromosome 6 (6q21 and 6q27). Natural antisense transcripts (NATs) for several genes in both genomic regions were predicted in silico and subsequently validated by strand-specific RT-PCR. Detailed experimental validation by quantitative real-time RT-PCR of five putative cancer related sense-antisense transcript pairs revealed a single candidate tumor suppressor gene (RPS6KA2) whose expression levels display marked cancer-related changes that are likely mediated by its antisense RNA in a breast cancer cell line model.
Insights
Natural antisense transcripts (NATs) regulate gene expression and are implicated in human diseases. This study identified NATs in chromosome 6 cancer regions, finding RPS6KA2 expression changes likely mediated by its antisense RNA in breast cancer.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Antisense transcription is a known gene expression regulator.
- Aberrant gene expression is a hallmark of cancer.
- Antisense RNA may play a role in cancer pathogenesis.
Purpose of the Study:
- To investigate antisense transcription in cancer-associated regions of human chromosome 6 (6q21 and 6q27).
- To identify natural antisense transcripts (NATs) potentially involved in cancer development.
Main Methods:
- Bioinformatic analysis to predict NATs in specific genomic regions.
- In silico prediction of NATs.
- Validation using strand-specific RT-PCR and quantitative real-time RT-PCR.
Main Results:
- NATs were predicted in silico for several genes in chromosome 6 regions.
- Experimental validation confirmed some NATs.
- One candidate tumor suppressor gene, RPS6KA2, showed cancer-related expression changes potentially mediated by its antisense RNA in a breast cancer model.
Conclusions:
- Antisense transcription is present in cancer-associated genomic regions of chromosome 6.
- NATs may contribute to cancer pathogenesis.
- RPS6KA2 is a potential tumor suppressor gene whose expression is regulated by its antisense RNA in breast cancer.
