Gene W Yeo

Summary

Affiliation: University of California
Country: USA

Publications

  1. Nussbacher J, Tabet R, Yeo G, Lagier Tourenne C. Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions. Neuron. 2019;102:294-320 pubmed publisher
    ..Emerging therapeutic approaches to mitigate or reverse alterations of RNA binding proteins in neurological diseases are discussed. ..
  2. Tan F, Sathe S, Wheeler E, Nussbacher J, Peter S, Yeo G. A Transcriptome-wide Translational Program Defined by LIN28B Expression Level. Mol Cell. 2018;: pubmed publisher
    ..Post-transcriptional effects were scaled across the physiological LIN28 expression range. Together, these data highlight the central importance of RBP expression level and its ability to encode regulation. ..
  3. Yee B, Pratt G, GRAVELEY B, Van Nostrand E, Yeo G. RBP-Maps enables robust generation of splicing regulatory maps. RNA. 2018;: pubmed publisher
  4. Nussbacher J, Yeo G. Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels. Mol Cell. 2018;69:1005-1016.e7 pubmed publisher
    ..Our approach to identifying regulators of miR loci can be applied to any user-defined RNA annotation, thereby guiding the discovery of uncharacterized regulators of RNA processing. ..
  5. Nussbacher J, Batra R, Lagier Tourenne C, Yeo G. RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci. 2015;38:226-36 pubmed publisher
    ..Given that the disruption of RNA processing is increasingly implicated in neurological diseases, these approaches will continue to provide insights into the roles of RBPs in disease pathogenesis. ..
  6. Tan F, Yeo G. Blurred Boundaries: The RNA Binding Protein Lin28A Is Also an Epigenetic Regulator. Mol Cell. 2016;61:1-2 pubmed publisher
    ..Lin28A is best known as a post-transcriptional regulator of gene expression. In this issue, Zeng et al. (2016) show that Lin28A has an unexpected role as an epigenetic regulator of DNA. ..
  7. Nelles D, Fang M, O Connell M, Xu J, Markmiller S, Doudna J, et al. Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. 2016;165:488-96 pubmed publisher
    ..We also demonstrate time-resolved measurements of ACTB mRNA trafficking to stress granules. Our results establish RCas9 as a means to track RNA in living cells in a programmable manner without genetically encoded tags. ..
  8. Conway A, Van Nostrand E, Pratt G, Aigner S, Wilbert M, Sundararaman B, et al. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Rep. 2016;15:666-679 pubmed publisher
    ..Additionally, we show that IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles. ..
  9. Krach F, Batra R, Wheeler E, Vu A, Wang R, Hutt K, et al. Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS. Acta Neuropathol. 2018;136:405-423 pubmed publisher
    ..Our framework of transcriptome-pathology correlations identifies candidate genes with relevance to novel mechanisms of neurodegeneration. ..

More Information

Publications25

  1. 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. ..
  2. 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. ..
  3. 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). ..
  4. 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. ..
  5. Van Nostrand E, Huelga S, Yeo G. Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. Adv Exp Med Biol. 2016;907:1-28 pubmed publisher
  6. 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. ..
  7. 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. ..
  8. 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. ..
  9. 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. ..
  10. 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. ..
  11. 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/). ..
  12. 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. ..
  13. 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. ..
  14. Van Nostrand E, Shishkin A, Pratt G, Nguyen T, Yeo G. Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions. Methods. 2017;126:29-37 pubmed publisher
  15. 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. ..
  16. 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. ..