Abstract 147: Epigenetic networks and promoter-associated long noncoding RNAs (paRNAs) in prostate cancer
Authors: Napoli Sara , Mapelli Sarah , Pisignano Giuseppina , Mitra Abhishek , Garcia-Escudero Ramon , Carbone Giuseppina M. R. , Catapano Carlo V. 
Published: August 2015

Long noncoding RNAs (lncRNAs) are emerging as important players in epigenetic mechanisms and human diseases, including cancer. paRNAs represent a class of lncRNAs transcribed in promoter-proximal regions of genes. However, their function is still unknown. In this study we examined the functional relationship between paRNAs and expression of neighboring genes. By analyzing Global Run On sequencing (GRO-Seq) data from different cell lines and experimental conditions we identified large numbers of nascent transcripts with both sense (S) and antisense (AS) orientation in the 2 kb upstream region of many genes. Interestingly, many paRNAs were found to be shared across different cell lines, denoting a conserved function. Furthermore, many paRNAs were dynamically linked to their neighboring gene expression, exhibiting concomitant changes in transcription in different experimental conditions. Although the overall mechanisms and network of co-acting elements may be highly complex, we defined subgroups of genes whose paRNAs behaved consistently in similar ways. This genome-wide analysis suggested that specific patterns of S and AS paRNAs might be associated with either transcriptional activation or repression of neighboring genes. To provide support to this hypothesis, we focused on CDH1, the gene encoding E-cadherin, an important tumor suppressor silenced in many epithelial cancers. We uncovered a complex paRNA-based epigenetic network controlling CDH1 transcription in normal and cancer cells. In addition to S and AS paRNAs, the network included the RNA interference protein Argonaute 1 (AGO1) and the epigenetic effector SUV39H1. Silencing of CDH1 in prostate cancer cells relied on binding of AGO1 to the S paRNA, which in turn recruited SUV39H1 and induced repressive histone modifications (H3K9me) at the CDH1 promoter. Notably, this mechanism was shared by other genes that were similarly silenced by AGO1 and SUV39H1 and reactivated by AGO1 and SUV39H1 knockdown in prostate cancer cells. Integrating GRO-seq data and ChIP-seq data we found that many AGO1 and SUV39H1 co-regulated genes showed evidence of bidirectional paRNAs and AGO1 binding in their promoters. Furthermore, many co-regulated genes had putative tumor suppressor function, were downregulated in human tumors and were associated with metastasis and poor clinical outcome. This study reveals the presence of complex RNA-based epigenetic networks that rely on transcription of bidirectional paRNAs and interaction with AGO1 and epigenetic effectors. paRNA-based networks can coordinate epigenetic silencing of critical tumor suppressors, like CDH1, and promote tumor development and progression. These findings give also new perspectives and insights on epigenetic mechanisms and identify paRNAs as novel targetable elements in the epigenetic machinery.

Citation Format: Sara Napoli, Sarah Mapelli, Giuseppina Pisignano, Abhishek Mitra, Ramon Garcia-Escudero, Giuseppina M. R. Carbone, Carlo V. Catapano. Epigenetic networks and promoter-associated long noncoding RNAs (paRNAs) in prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 147. doi:10.1158/1538-7445.AM2015-147