YBX1-dependent LNA-tRF-mediated modulation of transcript stability

In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by alpha-amanitine treatment, RNA extraction at time points 0 and 8hr post-treatment, and transcriptomic profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets whose stabilities are modulated due to tRF loss-of-function. We used alpha-amanitine mediated inhibition of RNA-polymerase to measure transcript stability across the entire transcriptome.