SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress @cellcellpress.bsky.social @mitchguttman.bsky.social
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SPIDR uses a dramatically simplified split-and-pool based strategy to increase the throughput of CLIP by two orders of magnitude. SPIDR enables the rapid generation of consortium-level datasets within any molecular biology lab without the need for specialized training or equipment.
We show that SPIDR generates high quality data across a diverse range of RBPs, including transcription, splicing, translation, and miRNA biogenesis, all within a single experiment.
Single nucleotide binding maps generated by SPIDR can map known RNP structures at atomic resolution and identify novel components within RNP structures.
We identified an interaction between LARP1 and 18S rRNA located within the mRNA channel entry site on the 40S small ribosomal subunit and @jbquerido.bsky.social resolved this structure at 2.8 Å using single-particle cryo-EM.
We used SPIDR to identify mTOR-dependent changes and observed that 4EBP1 showed a dramatic increase in binding upon mTOR inhibition specifically at mRNAs containing a TOP-motif, suggesting a new model for how translational repression is selectively achieved upon mTOR inhibition.
This work was led by co-first authors Jimmy Guo and Erica Wolin with support from amazing teams from our lab @caltech.edu and the Jovanovic lab @columbiauniversity.bsky.social and @jbquerido.bsky.social lab with financial support from NHGRI, NSF, @genometdcc.bsky.social.
Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...
