Transcriptional regulation by lncRNAs examined via TETRIS assay (2016)

Undergraduates: Allison Baker, Dr. Mauro Calabrese, Dr. Kaoru Inoue

Faculty Advisor: Mauro Calabrese
Department: Biology

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Long non-coding RNAs (lncRNAs) are a class of gene transcripts that do not code for a protein product, but instead interact in the cell as RNA. Recent studies have identified thousands of predicted lncRNAs in the human genome, and evidence increasingly suggests their importance in development and disease, yet few have a known function. Of these, many lncRNAs affect epigenetic states by regulating transcription, such as Xist, which silences genes in X chromosome inactivation. We developed a novel assay, called TETRIS (Transposable Element to Test RNA's effect on transcription in cis), to efficiently test the effect of lncRNAs on transcription of adjacent genes. The TETRIS assay was designed in tandem with a novel computational method that predicts lncRNA function based on sequence, and allows for streamlined testing of these predictions. TETRIS uses a transposable vector system to insert a gene cassette into the genome of cultured mammalian cells. Transfected cells have drug-inducible lncRNA expression and constitutive downstream luciferase expression, which quantitatively reports any effect on local transcription the lncRNA exerts. Initial testing of TETRIS yielded support for the predicted function in 4 of 10 lncRNAs. Continued improvements to the computational analysis and experimental design are in progress. The immediate goal of TETRIS is to connect lncRNA sequence and function, and ultimately to translate these insights into therapeutic interventions.