Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs

Abstract

Cell signaling events triggered by androgen hormone in prostate cells is dependent on activation of the androgen receptor (AR) transcription factor. Androgen hormone binding to AR promotes its displacement from the cytoplasm to the nucleus and AR binding to DNA motifs, thus inducing activatory and inhibitory transcriptional programs through a complex regulatory mechanism not yet fully understood. In this work, we performed RNA-seq deep-sequencing of LNCaP prostate cancer cells and found over 7000 expressed long intergenic non-coding RNAs (lincRNAs), of which ∼4000 are novel lincRNAs, and 258 lincRNAs have their expression activated by androgen. Immunoprecipitation of AR, followed by large-scale sequencing of co-immunoprecipitated RNAs (RIP-Seq) has identified in the LNCaP cell line a total of 619 lincRNAs that were significantly enriched (FDR < 10%, DESeq2) in the anti-Androgen Receptor (antiAR) fraction in relation to the control fraction (non-specific IgG), and we named them Androgen-Receptor-Associated lincRNAs (ARA-lincRNAs). A genome-wide analysis showed that protein-coding gene neighbors to ARA-lincRNAs had a significantly higher androgen-induced change in expression than protein-coding genes neighboring lincRNAs not associated to AR. To find relevant epigenetic signatures enriched at the ARA-lincRNAs’ transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.

PVT1 signals an androgen-dependent transcriptional repression program in prostate cancer cells and a set of the repressed genes predicts high-risk tumors

“…1c, blue and red bars). Also interesting, prostate tumor suppressor lincRNA DRAIC [40], previously detected by us with RIP-seq as one of the other RNAs associated with AR [18], was confirmed here by RIP-qPCR ( Fig. 1d, blue and red bars), whereas negative control snRNA U1-19 was not associated with AR ( Fig.…”

“…Regarding the possible interplay between AR and lncRNAs, two studies have demonstrated AR association with HOTAIR [ 16 ], PCGEM and PRCNR1 [ 17 ] lncRNAs in PCa. Our group has recently shown that in LNCaP cells the AR is significantly associated with over six hundred other lncRNAs [ 18 ]. Interestingly, the oncogenic lncRNA PVT1 was one of the RNAs that was associated with AR, a finding that was not explored in that work [ 18 ].…”

“…Our group has recently shown that in LNCaP cells the AR is significantly associated with over six hundred other lncRNAs [ 18 ]. Interestingly, the oncogenic lncRNA PVT1 was one of the RNAs that was associated with AR, a finding that was not explored in that work [ 18 ]. PVT1 is a long intergenic non-coding RNA (lincRNA) that is overexpressed in twenty-five different tumor tissues [ 19 ] including prostate adenocarcinoma [ 19 , 20 ].…”

Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer

“…As a result AR signaling devolves from its normal control of cell growth and differentiation to favor growth promoting pathways 6,7 . In this manner AR signaling is "re-wired", often associated with distorted histone modifications and DNA methylation patterns that impact AR access to enhancer regions 8,9 . These observations fit with the emerging concept of oncogenic enhancer addiction 10,11 acting as a driver of lineage plasticity 12,13 .…”

Efeito do lincRNA >i<PVT1>/i< associado ao potenciador de zeste homólogo 2 (EZH2) e ao receptor de andrógeno (AR) sobre a expressão gênica em larga escala em células LNCaP de câncer de próstata

“…Com a descoberta dos RNAs longos não codificadores, descritos mais abaixo nesta introdução, os fatores que influenciam a transcrição gênica também passaram a incluí-los (Davidson and Britten 1979, Consortium, Birney et al 2007, Mercer, Dinger et al 2009, Consortium 2012, Rinn and Chang 2012, Cheetham, Gruhl et al 2013, Iyer, Niknafs et al 2015). Com relação ao AR, já há estudos demonstrando a associação do receptor de andrógeno aos RNA longos não codificadores HOTAIR, PCGEM, PRCNR1 (Yang, Lin et al 2013, Zhang, Zhao et al 2015) e nosso grupo mostrou recentemente que o AR se liga a um conjunto de algumas centenas de outros lncRNAs (daSilva, Beckedorff et al 2018).…”