Function of the p53-induced lncRNA LINC01021 in suppression of colorectal cancer

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Recent sequencing analyses revealed that the human genome encodes approximately 32.000 long-non-coding/lncRNAs. Therefore, this class of transcripts is similar in number as protein-coding mRNAs, but represents largely uncharted territory, which promises to have important functions in mediating tumor suppression. Alterations in lncRNA structure or regulation presumably contribute to the pathogenesis of human tumors. LncRNAs have a length of more than 200 nucleotides and fulfil diverse functions, mainly in the nucleus where they bind and affect chromatin-associated proteins to regulate gene expression, but LncRNAs also interact with other RNAs, e.g. microRNAs, and DNA. Notably, also the p53 transcription factor, which is encoded by the most commonly mutated tumor suppressor gene, regulates lncRNAs. However, the characterization and identification of p53-regulated lncRNAs is far from complete. Colorectal cancers (CRC) display p53 mutations in ca. 60% of all cases. In order to comprehensively study the function of p53 in CRC we recently determined the differential RNA, microRNA and protein expression after activation of a conditional p53 allele in SW480 CRC cells using RNA-Seq, miR-Seq and quantitative proteomics (pSILAC) analyses. In addition, we determined the global DNA binding pattern of p53 by a ChIP-Seq analysis. By the combination of these analyses, we identified LINC01021 as a novel p53-induced lincRNA, which reproducibly showed a dramatic induction by p53 (>600x) and suppressed proliferation, when expressed ectopically. More recently, we reported that deletion of LINC01021 increases sensitivity of CRC cell lines to chemotherapeutic drugs. Furthermore, in the CMS4 sub-set of CRC patients low expression of LINC01021 was associated with poor survival. Although, LINC01021 harbors tumor-relevant capacities the molecular mechanisms of its action are still poorly understood. Our preliminary results indicate that LINC01021 modulates the expression of a subset of p53-regulated genes. Here we intend to use genome- and proteome-wide, unbiased approaches to uncover the molecular mechanisms by which LINC01021 contributes to regulations within the p53 network. Protein interaction partners of LINC01021 will be identified by RNA pull-down and mass spectrometric analysis in order to determine the molecular mechanisms by which LINC0121 influences gene expression. The LINC01021 interacting proteins and their functional role in LINC01021-mediated gene regulation will be characterized in further detail. LINC01021-mediated gene regulations will be identified by ChIRP (chromatin isolation by RNA purification)-Seq analyses. The functional relevance of LINC01021-regulated genes and its interactions with proteins for p53-mediated tumor suppression will be determined. Taken together, these analyses aim to illuminate the mechanisms by which LINC01021 performs critical functions within the p53 network.