Gene W Yeo

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Misregulated RNA processing in amyotrophic lateral sclerosis
    Magdalini Polymenidou
    Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093 6070, USA
    Brain Res 1462:3-15. 2012
  2. pmc An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
    Gene W Yeo
    Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Struct Mol Biol 16:130-7. 2009
  3. pmc Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs
    Clotilde Lagier-Tourenne
    Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA
    Nat Neurosci 15:1488-97. 2012
  4. pmc Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing
    Shatakshi Pandit
    Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093 0651, USA
    Mol Cell 50:223-35. 2013
  5. pmc Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins
    Stephanie C Huelga
    Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
    Cell Rep 1:167-78. 2012
  6. pmc ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43
    Eveline S Arnold
    Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 110:E736-45. 2013
  7. doi request reprint Comprehensive identification of miRNA target sites in live animals
    Dimitrios G Zisoulis
    Department of Biology, University of California, La Jolla, San Diego, CA, USA
    Methods Mol Biol 732:169-85. 2011
  8. doi request reprint RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy
    Michael T Lovci
    Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 729:247-55. 2011
  9. pmc A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells
    Maria C N Marchetto
    The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 143:527-39. 2010
  10. doi request reprint A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells
    Andrew Hinton
    Pediatric Diabetes Research Center, Stem Cell Program, University of California, San Diego, La Jolla, California, USA
    Stem Cells Dev 19:797-807. 2010

Collaborators

Detail Information

Publications26

  1. pmc Misregulated RNA processing in amyotrophic lateral sclerosis
    Magdalini Polymenidou
    Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093 6070, USA
    Brain Res 1462:3-15. 2012
    ..Hence, ALS and FTLD converge in pathogenic pathways disrupting the regulation of RNA processing. This article is part of a Special Issue entitled RNA-Binding Proteins...
  2. pmc An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells
    Gene W Yeo
    Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Struct Mol Biol 16:130-7. 2009
    ..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...
  3. pmc Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs
    Clotilde Lagier-Tourenne
    Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA
    Nat Neurosci 15:1488-97. 2012
    ....
  4. pmc Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing
    Shatakshi Pandit
    Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093 0651, USA
    Mol Cell 50:223-35. 2013
    ..Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes...
  5. pmc Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins
    Stephanie C Huelga
    Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
    Cell Rep 1:167-78. 2012
    ..Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells...
  6. pmc ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43
    Eveline S Arnold
    Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 110:E736-45. 2013
    ..Thus, adult-onset motor neuron disease does not require aggregation or loss of nuclear TDP-43, with ALS-linked mutants producing loss and gain of splicing function of selected RNA targets at an early disease stage...
  7. doi request reprint Comprehensive identification of miRNA target sites in live animals
    Dimitrios G Zisoulis
    Department of Biology, University of California, La Jolla, San Diego, CA, USA
    Methods Mol Biol 732:169-85. 2011
    ..The bound RNA molecules are trimmed to the regions protected by Argonaute, subjected to a series of isolation and linker ligation steps and identified by high-throughput sequencing methods...
  8. doi request reprint RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy
    Michael T Lovci
    Department of Cellular and Molecular Medicine, Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 729:247-55. 2011
    ....
  9. pmc A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells
    Maria C N Marchetto
    The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Cell 143:527-39. 2010
    ..Our model recapitulates early stages of a human neurodevelopmental disease and represents a promising cellular tool for drug screening, diagnosis and personalized treatment...
  10. doi request reprint A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells
    Andrew Hinton
    Pediatric Diabetes Research Center, Stem Cell Program, University of California, San Diego, La Jolla, California, USA
    Stem Cells Dev 19:797-807. 2010
    ..Examination of potential mRNA targets showed that TIMM8A is repressed by ectopic miR-375 expression in pluripotent hESCs...
  11. pmc Alternative splicing events identified in human embryonic stem cells and neural progenitors
    Gene W Yeo
    Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, La Jolla, California, USA
    PLoS Comput Biol 3:1951-67. 2007
    ..In summary, a new methodology for exon array analysis was introduced, leading to new insights into the complexity of AS in human embryonic stem cells and their transition to neural stem cells...
  12. pmc Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model
    Hairi Li
    Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0651, USA
    Proc Natl Acad Sci U S A 105:20179-84. 2008
    ..This study provides a general guide for analysis of gene expression and alternative splicing by deep sequencing...
  13. pmc Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans
    Dimitrios G Zisoulis
    Department of Biology, Stem Cell Program, University of California, San Diego, La Jolla, California, USA
    Nat Struct Mol Biol 17:173-9. 2010
    ..Furthermore, our analyses revealed a striking enrichment of Argonaute binding sites in genes important for miRNA function, suggesting an autoregulatory role that may confer robustness to the miRNA pathway...
  14. pmc LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans
    Priscilla M Van Wynsberghe
    Department of Biology, University of California, San Diego, La Jolla, CA, USA
    Nat Struct Mol Biol 18:302-8. 2011
    ..We conclude that co-transcriptional interaction of LIN-28 with let-7 primary transcripts blocks Drosha processing and, thus, precocious expression of mature let-7 during early development...
  15. pmc Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment
    Wenqing Cai
    Sanford Burnham Medical Research Institute, La Jolla, California 92037, USA
    Genes Dev 27:2332-44. 2013
    ..This is the first demonstration that cues from the progenitor cell environment direct the subunit variant composition of SWI/SNF to remodel the transcriptional landscape for lineage-specific differentiation...
  16. pmc L1 retrotransposition in human neural progenitor cells
    Nicole G Coufal
    Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nature 460:1127-31. 2009
    ..These data suggest that de novo L1 retrotransposition events may occur in the human brain and, in principle, have the potential to contribute to individual somatic mosaicism...
  17. pmc Genome-wide approaches in the study of microRNA biology
    Melissa L Wilbert
    Department of Cellular and Molecular Medicine, Stem Cell Program, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
    Wiley Interdiscip Rev Syst Biol Med 3:491-512. 2011
    ..Here we review the genome-wide approaches that have allowed for the discovery of new miRNAs, the characterization of their targets, and a systems-level view of their impact...
  18. pmc Transcriptional signature and memory retention of human-induced pluripotent stem cells
    Maria C N Marchetto
    The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, California, USA
    PLoS ONE 4:e7076. 2009
    ..Moreover, the episomal reprogramming strategy represents a safe way to generate human iPSCs for clinical purposes and basic research...
  19. doi request reprint Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges
    Michael T Lovci
    1 Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA 2 Stem Cell Program, University of California, San Diego, La Jolla, California, USA 3 Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
    Nat Struct Mol Biol 20:1434-42. 2013
    ..Thus we demonstrate a previously unknown RNA-mediated mechanism for AS control by distally bound RNA-binding proteins. ..
  20. doi request reprint Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells
    Gene W Yeo
    Laboratory of Genetics, Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Hum Mol Genet 17:R67-75. 2008
    ..An integrative view of the different levels will hopefully provide much needed insight into understanding stem cell biology...
  21. pmc Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43
    Magdalini Polymenidou
    Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA
    Nat Neurosci 14:459-68. 2011
    ..Lastly, we found that TDP-43 autoregulates its synthesis, in part by directly binding and enhancing splicing of an intron in the 3' untranslated region of its own transcript, thereby triggering nonsense-mediated RNA degradation...
  22. doi request reprint Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice
    Sandrine Thuret
    Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Hippocampus 19:658-69. 2009
    ..Together, these results suggest that adult neurogenesis is correlated with spatial learning and visual recognition learning, possibly by modulating morphological plasticity in the dentate gyrus...
  23. doi request reprint Differential L1 regulation in pluripotent stem cells of humans and apes
    Maria C N Marchetto
    1 Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA 2
    Nature 503:525-9. 2013
    ..We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have continuing adaptive significance. ..
  24. pmc High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection
    Thomas J Stark
    Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA
    J Virol 86:226-35. 2012
    ..In addition to miRNAs, we also identified novel forms of virus-derived smRNAs, revealing greater complexity within the smRNA population during HCMV infection...
  25. pmc Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements
    Gene W Yeo
    Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, La Jolla, California, United States of America
    PLoS Genet 3:e85. 2007
    ..Our results demonstrate that ISREs are crucial building blocks in understanding general and tissue-specific AS regulation and the biological pathways and functions regulated by these AS events...
  26. pmc Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration
    Wei Zhu
    Molecular and Cell Biology Laboratory and Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Dev Growth Differ 54:673-85. 2012
    ....