Determining the function and mechanism of the MALAT1 long non-coding RNA in co-transcriptional splicing

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PROJECT SUMMARY Many long non-coding RNAs (lncRNAs) have been shown to be mutated or aberrantly expressed in human cancers. One of the most common is a lncRNA called metastasis-associated lung adenocarcinoma transcript 1 (MALAT1). MALAT1 represents an ideal model to study the role of lncRNAs in driving cancer because its overexpression is associated with mis-regulation of splicing in lung adenocarcinoma, breast, pancreatic, colon, prostate and hepatocellular carcinomas. Second, studies in animal models have shown that MALAT1 acts as an oncogene and promotes aggressive tumors and metastasis. Despite the clear importance of MALAT1 as a critical driver of many cancers, the functional role of MALAT1 in normal cellular conditions is unknown. Splicing in mammals occurs through a predominantly co-transcriptional mechanism such that splicing factors are recruited to nascent pre-mRNAs as they are being transcribed by RNA Polymerase II. Although it is clear that the C-terminal domain (CTD) of RNA Polymerase II (RNA PolII) is required for efficient splicing, how splicing factors are recruited co-transcriptionally and interact with RNA PolII is unknown. Recently, our group showed that MALAT1 localizes to the genomic DNA of the majority of actively transcribed RNA PolII genes and that this localization occurs in a transcriptionally dependent manner. Additionally, MALAT1 is known to localize to nuclear speckles, a nuclear compartment that is enriched for splicing factors. Based on these results, we hypothesized that MALAT1 might act as the elusive molecular link connecting RNA PolII and the splicing machinery that is required for efficient co- transcriptional recruitment and splicing of mammalian pre-mRNA. I hypothesize that MALAT1 acts as a molecular scaffold between RNA Polymerase II and splicing machinery to coordinate co-transcriptional splicing. Aim 1 of this proposal will characterize factors that directly bind to MALAT1 to coordinate co-transcriptional splicing. Aim 2 will identify if MALAT1 expression is directly linked to splicing defects. Finally, in Aim 3, the relationship between MALAT1 abundance and cancer will be explored. Taken together, these results would provide a transformative understanding of transcription and splicing, how they are coordinated in the cell, and how these processes might be disrupted through MALAT1 – a single lncRNA – to drive cancer.