Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

Street, Lena; Rothamel, Katherine; Brannan, Kristopher; Jin, Wenhao; Bokor, Benjamin; Dong, Kevin; Rhine, Kevin; Madrigal, Assael; Al-Azzam, Norah; Kim, Jenny Kim; Ma, Yanzhe; Abdou, Ahmed; Wolin, Erica; Doron-Mandel, Ella; Ahdout, Joshua; Mujumdar, Mayuresh; Jovanovic, Marko; Yeo, Gene W

doi:10.1101/2023.06.08.544225

Cited by 4 publications

(1 citation statement)

References 112 publications

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“…Following the initial evidence of splicing-associated protein enrichment after TRNAU1AP, SCAF8 and RTCA pulldown, we matched these experiments with ribonuclease-positive conditions as well as matching IgG controls in ±ribonuclease conditions to distinguish between direct proteinprotein interactions and RNA-mediated interactions (Fig. 4c,d) 51 . We applied a strict P value cutoff of 0.00000001 to visualize the most specific RBPs and splicing-associated proteins pulled down by each bait.…”

Section: Splicing Protein Enrichment In Pulldown Of Unexpected Hitsmentioning

confidence: 99%

Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion

Schmok,

Jain,

Street

et al. 2024

Nat Biotechnol

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RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification–mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.

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Section: Splicing Protein Enrichment In Pulldown Of Unexpected Hitsmentioning

confidence: 99%

Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion

Schmok,

Jain,

Street

et al. 2024

Nat Biotechnol

Self Cite

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Targeting RNA-protein interactions with small molecules: promise and therapeutic potential

Rhodes,

Balaratnam,

Yazdani

et al. 2024

Med Chem Res

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The therapeutic potential of targeting protein-RNA interactions has not been fully explored. While several approaches to block the interactions between various RNA and protein partners have been developed, rational efforts to target pre-assembled complexes have not been broadly pursued. This is despite the recent commercial success of risdiplam, and the high-resolution structure of the EIF4A-polypurine-Rocaglamide A ternary complex, which elucidates how compounds may recognize these pockets. These prominent examples indicate the viability of this approach, but important questions remain. For example, how abundant are these pockets in other protein-RNA complexes? Do such pockets have properties suitable for small molecule recognition? A broad analysis of 160 previously published RNP complexes confirmed that interfacial pockets in RNA-protein complexes are both abundant and have favorable properties that would make them good candidates for rational screening campaigns. These conclusions are expected to have important implications especially for those working on developing small molecules that bind directly to RNA structural elements.

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Mapping the future of oxidative RNA damage in neurodegeneration: Rethinking the status quo with new tools

Wheeler,

Madrigal,

Chaim

2024

Proc. Natl. Acad. Sci. U.S.A.

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Over two decades ago, increased levels of RNA oxidation were reported in postmortem patients with ALS, Alzheimer’s, Parkinson’s, and other neurodegenerative diseases. Interestingly, not all cell types and transcripts were equally oxidized. Furthermore, it was shown that RNA oxidation is an early phenomenon, altogether indicating that oxidative RNA damage could be a driver, and not a consequence, of disease. Despite all these exciting observations, the field appears to have stagnated since then. We argue that this is a consequence of the shortcomings of technologies to model these diseases, limiting our understanding of which transcripts are being oxidized, which RNA-binding proteins are interacting with these RNAs, what their implications are in RNA processing, and as a result, what their potential role is in disease onset and progression. Here, we discuss the limits of previous technologies and propose ways by which advancements in iPSC-derived disease modeling, proteomics, and sequencing technologies can be combined and leveraged to answer new and decades-old questions.

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Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

Cited by 4 publications

References 112 publications

Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion

Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion

Targeting RNA-protein interactions with small molecules: promise and therapeutic potential

Mapping the future of oxidative RNA damage in neurodegeneration: Rethinking the status quo with new tools

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