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bioRxiv · 10.1101/555540

Transcriptome stability profiling identifies novel and functional MIRNA targets in melanoma cells

Joshi, P.·Seki, T.·Bergano, A.·Marchica, J.·Kitamura, S.·Perera, R. J.
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Abstract

RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumor suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and in silico predictions, we identified both existing and novel direct miR-211 targets. We validated DUSP3 as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signaling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and in silico approaches.

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Joshi, P., Seki, T., Bergano, A., Marchica, J., Kitamura, S., Perera, R. J.. 2019-02-20. Transcriptome stability profiling identifies novel and functional MIRNA targets in melanoma cells. https://doi.org/10.1101/555540

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