Abstract 3698: Identification of a regulatory long non-coding RNA adjacent to RFC4, a gene related to chromosomal instability, in a cell model of prostate cancer

Abstract

Between 70-80 % of human genome is transcribed, nevertheless it contains only 1.5% of protein-coding sequences while non-coding genome comprises almost 99%. Within the non-coding transcripts, a group of regulatory non-coding RNAs (ncRNAs) stands out in number: the long non-coding RNAs (lncRNAs), which are transcripts lacking coding potential and longer than 200 nucleotides. These transcripts are involved in different regulatory processes. In this study, our aim is to identify new lncRNAs involved in regulation of chromosomal instability (CIN) in a cell model of prostate cancer (PCa). Using RNA-seq data from two prostate cell lines: LNCaP (neoplastic, exhibits CIN) and PrEC (non-neoplastic, does not exhibit CIN) we have identified a lncRNA adjacent to the protein-coding gene RFC4, a gene involved in CIN in human cancers. This transcript, which we have provisionally named lncRNA-RFC4, exhibits differential expression between PrEC and LNCaP as seen in expression analyses from RNA-seq data. Afterwards, we performed qPCR experiments and found similar results as those seen in RNA-seq data analyses, lncRNA-RFC4 is downregulated in LNCaP, whereas the adjacent coding gene RFC4 is upregulated; the opposite is found in PrEC cell line. Western blot experiments confirmed that RFC4 protein abundance is higher in LNCaP. Our findings suggest that this transcript could have a possible repressor role on RFC4. In order to explore the regulatory mechanism, we performed cell fractionation and measured the abundance of lncRNA-RFC4 in each fraction using qPCR, we found that this transcript accumulates in the nucleus, specifically in the chromatin fraction, the nucleoplasm and cytoplasm fraction are not enriched with this lncRNA. In order to predict possible RNA-protein interactions we used an in-silico tool and found predicted interactions between lncRNA-RFC4 and two repressor proteins, CBX7 and SUZ12, part of the polycomb repressive complex 1 and 2 respectively, these interactions are yet to be confirmed experimentally. In conclusion, we have identified a chromatin-enriched lncRNA adjacent to RFC4, a CIN related gene, this ncRNA could play a repressive role on the adjacent gene though its interaction with the repressor proteins CBX7 and SUZ12, consequently, this transcript could be involved in a network controlling CIN in this cell model of PCa. Further experiments are needed to prove cis regulation of RFC4 by lncRNA-RFC4 and the molecular mechanism underlying this regulatory network. Citation Format: Rogelio Montiel Manriquez, Cristian Arriaga Canon, Laura Contreras Espinosa, Paula Alarcón Zendejas, Luis Alonso Herrera Montalvo. Identification of a regulatory long non-coding RNA adjacent to RFC4, a gene related to chromosomal instability, in a cell model of prostate cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3698.