Gene W Yeo
Affiliation: University of California
- Markmiller S, Soltanieh S, Server K, Mak R, Jin W, Fang M, et al. Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. Cell. 2018;172:590-604.e13 pubmed publisher..Using three Drosophila ALS/FTD models, we identify SG-associated modifiers of neurotoxicity in vivo. Altogether, our results highlight SG proteins as central to understanding and ultimately targeting neurodegeneration. ..
- Van Nostrand E, Gelboin Burkhart C, Wang R, Pratt G, Blue S, Yeo G. CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. Methods. 2017;118-119:50-59 pubmed publisher..TAG-eCLIP enables eCLIP profiling of new native proteins where no suitable antibody exists, expanding the RBP-RNA interaction landscape. ..
- Brannan K, Yeo G. From Protein-RNA Predictions toward a Peptide-RNA Code. Mol Cell. 2016;64:437-438 pubmed publisher..Two reports now introduce proteome-wide approaches that identify the peptides that are crosslinked to RNA (Castello et al., 2016; He et al., 2016). ..
- Bos T, Nussbacher J, Aigner S, Yeo G. Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins. Adv Exp Med Biol. 2016;907:61-88 pubmed publisher..We also discuss how classic tethering assay approaches and insights gained from them have been empowered by more recent technological advances, including efficient genome editing and high-throughput RNA-sequencing. ..
- Washburn M, Kakaradov B, Sundararaman B, Wheeler E, Hoon S, Yeo G, et al. The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome. Cell Rep. 2014;6:599-607 pubmed publisher..These results raise the possibility that other dsRNA binding proteins, including the inactive human ADARs, regulate RNA editing through deaminase-independent mechanisms. ..
- Yeo G, Coufal N, Liang T, Peng G, Fu X, Gage F. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol. 2009;16:130-7 pubmed publisher..These findings suggest that FOX2 functions as a critical regulator of a splicing network, and we further show that FOX2 is important for the survival of human embryonic stem cells. ..
- Song Y, Botvinnik O, Lovci M, Kakaradov B, Liu P, Xu J, et al. Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. Mol Cell. 2017;67:148-161.e5 pubmed publisher..Systematic AS characterization in single cells redefines our understanding of AS complexity in cell biology. ..
- Kapeli K, Martinez F, Yeo G. Genetic mutations in RNA-binding proteins and their roles in ALS. Hum Genet. 2017;136:1193-1214 pubmed publisher..Here, we focus on several key RBPs involved in ALS-TDP-43, HNRNP A2/B1, HNRNP A1, FUS, EWSR1, and TAF15-and review our current understanding of how mutations in these proteins cause disease. ..
- Batra R, Nelles D, Pirie E, Blue S, Marina R, Wang H, et al. Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9. Cell. 2017;170:899-912.e10 pubmed publisher..Finally, we report a truncated RCas9 system compatible with adeno-associated viral packaging. This effort highlights the potential of RCas9 for human therapeutics. ..
- Sundararaman B, Zhan L, Blue S, Stanton R, Elkins K, Olson S, et al. Resources for the Comprehensive Discovery of Functional RNA Elements. Mol Cell. 2016;61:903-13 pubmed publisher..Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/). ..
- Martinez F, Pratt G, Van Nostrand E, Batra R, Huelga S, Kapeli K, et al. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. Neuron. 2016;92:780-795 pubmed publisher..Our findings provide a cellular resource and reveal RNA networks relevant to neurodegeneration, regulated by normal and mutant hnRNP A2/B1. VIDEO ABSTRACT. ..
- Van Nostrand E, Nguyen T, Gelboin Burkhart C, Wang R, Blue S, Pratt G, et al. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol. 2017;1648:177-200 pubmed publisher..These notes further refine the eCLIP methodology, simplifying robust RNA binding protein studies for all users. ..
- Brannan K, Jin W, Huelga S, Banks C, Gilmore J, Florens L, et al. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. Mol Cell. 2016;64:282-293 pubmed publisher..Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins. ..
- Lee S, Pratt G, Martinez F, Yeo G, Lykke Andersen J. Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. Mol Cell. 2015;59:413-25 pubmed publisher..Given the prevalence of helicases in RNA regulation, ATP hydrolysis may be a widely used activity in target RNA discrimination. ..