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I am excited to present this work led by the very talented postdoc Jaeil Han in which we identify a ubiquitin ligase complex that promotes the degradation of microRNAs engaged with highly complementary targets. A detailed thread follows. https://science.sciencemag.org/content/early/2020/11/11/science.abc9546
2/For many years, we have been interested in the mechanisms through which cells degrade miRNAs, going all the way back to 2007 when a student in my lab, Hun-Way Hwang, discovered that, unlike most miRNAs, miR-29b is very unstable in cycling HeLa cells. https://science.sciencemag.org/content/315/5808/97
3/This taught us that cells can selectively regulate miRNA stability, but the mechanisms remained mysterious. In 2010, the Steitz @SteitzLab and Zamore @zamore_lab labs discovered target-directed miRNA degradation (TDMD), in which highly complementary targets trigger miRNA decay.
4/TDMD is associated with addition and removal of nucleotides from the miRNA 3’ end (aka tailing and trimming). Due in part to redundancy of factors that carry it out, however, it was unclear whether tailing and trimming is required for TDMD.
5/Recently, the Bartel, Shkumatava @AlenaShkumatava, and Nicassio labs identified endogenous target RNAs that robustly induced TDMD, opening the door to mechanistic dissection of this pathway.
6/Leveraging the robust CYRANO:miR-7 TDMD pair discovered by the Bartel lab, we applied a genome-wide CRISPR screening strategy that has become a mainstay of our lab. This revealed a cullin-RING ubiquitin ligase, containing the substrate adapter ZSWIM8, that is required for TDMD.
7/Further work provided evidence for a new model of TDMD in which the ZSWIM8 ubiquitin ligase directs proteasomal degradation of miRNA-containing complexes engaged with highly complementary targets, thereby releasing the miRNA for decay.
8/Importantly, tailing and trimming was not necessary for this pathway of TDMD, since miRNAs with a 2’-O-methyl group at the 3’ end still underwent TDMD in a ZSWIM8-dependent manner.
9/Finally, small RNA-seq of cell lines with ZSWIM8 deficiency demonstrated that the TDMD pathway acts broadly to regulate miRNA levels in diverse cell types.
10/These findings have important implications for our understanding of the mechanisms through which miRNA levels are controlled in development, physiology, and disease.
11/The independence of this pathway from tailing and trimming raises the possibility that other classes of silencing RNAs that carry 2’-O-methyl modifications, such as piRNAs and siRNAs, may be substrates of related turnover pathways that depend upon proteasomal decay.
12/Lastly, I want to highlight the related paper from the Bartel lab that was co-published in Science today and thank their group for their collegial interactions leading up to these publications. https://science.sciencemag.org/content/early/2020/11/11/science.abc9359
