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Published on: August 12, 2015
Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA
Wenqiang Yu1, David Gius, Patrick Onyango
1Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA.
Abstract:
Tumour suppressor genes (TSGs) inhibiting normal cellular growth are frequently silenced epigenetically in cancer. DNA methylation is commonly associated with TSG silencing, yet mutations in the DNA methylation initiation and recognition machinery in carcinogenesis are unknown. An intriguing possible mechanism for gene regulation involves widespread non-coding RNAs such as microRNA, Piwi-interacting RNA and antisense RNAs. Widespread sense-antisense transcripts have been systematically identified in mammalian cells, and global transcriptome analysis shows that up to 70% of transcripts have antisense partners and that perturbation of antisense RNA can alter the expression of the sense gene. For example, it has been shown that an antisense transcript not naturally occurring but induced by genetic mutation leads to gene silencing and DNA methylation, causing thalassaemia in a patient. Here we show that many TSGs have nearby antisense RNAs, and we focus on the role of one RNA in silencing p15, a cyclin-dependent kinase inhibitor implicated in leukaemia. We found an inverse relation between p15 antisense (p15AS) and p15 sense expression in leukaemia. A p15AS expression construct induced p15 silencing in cis and in trans through heterochromatin formation but not DNA methylation; the silencing persisted after p15AS was turned off, although methylation and heterochromatin inhibitors reversed this process. The p15AS-induced silencing was Dicer-independent. Expression of exogenous p15AS in mouse embryonic stem cells caused p15 silencing and increased growth, through heterochromatin formation, as well as DNA methylation after differentiation of the embryonic stem cells. Thus, natural antisense RNA may be a trigger for heterochromatin formation and DNA methylation in TSG silencing in tumorigenesis.
Insights
Natural antisense RNAs can silence tumour suppressor genes (TSGs) like p15 in cancer. This process involves heterochromatin formation and DNA methylation, potentially triggering gene silencing in tumorigenesis.
Area of Science:
- Molecular Biology
- Epigenetics
- Cancer Biology
Background:
- Tumour suppressor genes (TSGs) are crucial for inhibiting cell growth and are often epigenetically silenced in cancer.
- While DNA methylation is a known mechanism for TSG silencing, the role of non-coding RNAs, particularly antisense RNAs, is increasingly recognized.
- Antisense RNAs can interact with their sense counterparts, influencing gene expression and epigenetic modifications.
Purpose of the Study:
- To investigate the role of natural antisense RNAs in the epigenetic silencing of tumour suppressor genes in cancer.
- To elucidate the mechanism by which antisense RNA, specifically p15AS, silences the p15 gene in leukaemia.
- To determine if antisense RNA can initiate heterochromatin formation and DNA methylation leading to TSG silencing.
Main Methods:
- Analysis of p15 antisense (p15AS) and p15 sense expression in leukaemia samples.
- Generation of a p15AS expression construct to study its effects on p15 silencing in cis and trans.
- Treatment with methylation and heterochromatin inhibitors to assess their impact on p15AS-induced silencing.
- Expression of exogenous p15AS in mouse embryonic stem cells to evaluate its effects on p15 silencing and cellular growth.
Main Results:
- An inverse correlation was observed between p15AS and p15 sense expression in leukaemia.
- A p15AS expression construct induced p15 silencing via heterochromatin formation, independent of DNA methylation initially.
- The induced silencing persisted even after p15AS expression ceased, but was reversible with inhibitors.
- Expression of exogenous p15AS in mouse embryonic stem cells led to p15 silencing and increased growth, followed by DNA methylation upon differentiation.
Conclusions:
- Natural antisense RNAs, such as p15AS, can act as triggers for heterochromatin formation and DNA methylation.
- Antisense RNA-mediated silencing of TSGs is a significant mechanism in tumorigenesis.
- This study highlights a novel pathway for epigenetic regulation and TSG inactivation in cancer development.
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