Gil Ast

Summary

Affiliation: Tel Aviv University
Country: Israel

Publications

  1. ncbi The alternative genome
    Gil Ast
    Department of Human Genetics and Molecular Medicine, Tel Aviv University Medical School, Israel
    Sci Am 292:40-7. 2005
  2. ncbi Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome
    Noa Sela
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Biol 8:R127. 2007
  3. ncbi SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
    Britta Mersch
    Department of Molecular Biophysics, German Cancer Research Center DKFZ, Heidelberg, Germany
    BMC Genet 8:78. 2007
  4. ncbi How did alternative splicing evolve?
    Gil Ast
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nat Rev Genet 5:773-82. 2004
  5. ncbi Drug-targeting strategies for prostate cancer
    Gil Ast
    Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Israel
    Curr Pharm Des 9:455-66. 2003
  6. ncbi Phosphatidylserine increases IKBKAP levels in familial dysautonomia cells
    Hadas Keren
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    PLoS ONE 5:e15884. 2010
  7. ncbi The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates
    Noa Sela
    Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Genome Biol 11:R59. 2010
  8. ncbi Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons
    Rotem Sorek
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Mol Cell 14:221-31. 2004
  9. ncbi Multifactorial interplay controls the splicing profile of Alu-derived exons
    Oren Ram
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Mol Cell Biol 28:3513-25. 2008
  10. ncbi Intronic Alus influence alternative splicing
    Galit Lev-Maor
    Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS Genet 4:e1000204. 2008

Collaborators

Detail Information

Publications54

  1. ncbi The alternative genome
    Gil Ast
    Department of Human Genetics and Molecular Medicine, Tel Aviv University Medical School, Israel
    Sci Am 292:40-7. 2005
  2. ncbi Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome
    Noa Sela
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Biol 8:R127. 2007
    ..Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the mouse transcriptome...
  3. ncbi SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements
    Britta Mersch
    Department of Molecular Biophysics, German Cancer Research Center DKFZ, Heidelberg, Germany
    BMC Genet 8:78. 2007
    ..Thus, exonizations can have negative effects for the transcriptome of an organism...
  4. ncbi How did alternative splicing evolve?
    Gil Ast
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nat Rev Genet 5:773-82. 2004
    ..So, alternative splicing might have originated as a result of relaxation of the 5' splice site recognition in organisms that originally could support only constitutive splicing...
  5. ncbi Drug-targeting strategies for prostate cancer
    Gil Ast
    Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Israel
    Curr Pharm Des 9:455-66. 2003
    ..These latter genes on the level of DNA, RNA and protein products are the targets of several new approaches to prostate cancer therapy and are the focus of this review...
  6. ncbi Phosphatidylserine increases IKBKAP levels in familial dysautonomia cells
    Hadas Keren
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    PLoS ONE 5:e15884. 2010
    ..Our results suggest that PS has potential for use as a therapeutic agent for FD. Understanding its mechanism of action may reveal the mechanism underlying the FD disease...
  7. ncbi The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates
    Noa Sela
    Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Genome Biol 11:R59. 2010
    ..However, no extensive analysis has compared the effects of TEs on the transcriptomes of mammals, non-mammalian vertebrates and invertebrates...
  8. ncbi Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons
    Rotem Sorek
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Mol Cell 14:221-31. 2004
    ..Based on these findings, we identified 7810 Alus within the human genome that are prone to exonization. Mutations in these Alus may cause genetic disorders or contribute to human-specific protein diversity...
  9. ncbi Multifactorial interplay controls the splicing profile of Alu-derived exons
    Oren Ram
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Mol Cell Biol 28:3513-25. 2008
    ..These results shed light on the mechanism through which Alu elements enrich the primate transcriptome and allow a better understanding of the exonization process in general...
  10. ncbi Intronic Alus influence alternative splicing
    Galit Lev-Maor
    Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS Genet 4:e1000204. 2008
    ..Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptome...
  11. ncbi Overlapping splicing regulatory motifs--combinatorial effects on splicing
    Amir Goren
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 38:3318-27. 2010
    ....
  12. ncbi TEs or not TEs? That is the evolutionary question
    Keren Vaknin
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69987, Israel
    J Biol 8:83. 2009
    ..A recent paper in BMC Molecular Biology discusses the creation of new transcripts by transposable element insertion upstream of retrocopies and the involvement of such insertions in tissue-specific post-transcriptional regulation...
  13. ncbi Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene
    Maayan Amit
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    BMC Mol Biol 8:109. 2007
    ..We examined whether there is less selection against exonization of transposed elements in duplicated genes than in single-copy genes...
  14. ncbi Stress alters the subcellular distribution of hSlu7 and thus modulates alternative splicing
    Noam Shomron
    Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
    J Cell Sci 118:1151-9. 2005
    ..A possible spatial and temporal regulatory mechanism by which hSlu7 protein levels are regulated within the nucleus is suggested, thus implying a broad effect of hSlu7 on alternative splicing...
  15. ncbi The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution
    Nurit Gal-Mark
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS Genet 5:e1000717. 2009
    ..Overall, these findings expand our understanding of the role of TIA1/TIAR proteins in enhancing recognition of exons, in general, and Alu exons, in particular...
  16. ncbi RNA-editing-mediated exon evolution
    Galit Lev-Maor
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Biol 8:R29. 2007
    ..It was recently shown that Alu elements are also heavily changed by RNA editing in the human genome...
  17. ncbi TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates
    Asaf Levy
    Department of Molecular Genetics and Biochemistry, Tel Aviv University Medical School, Tel Aviv 69978, Israel
    Nucleic Acids Res 36:D47-52. 2008
    ..Publicly available query interfaces to TranspoGene and microTranspoGene are available at http://transpogene.tau.ac.il/ and http://microtranspogene.tau.ac.il, respectively. The entire database can be downloaded as flat files...
  18. ncbi Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons
    Sahar Gelfman
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 22:35-50. 2012
    ..Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery...
  19. ncbi The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons
    Galit Lev-Maor
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Science 300:1288-91. 2003
    ..We revealed a mechanism that governs 3' splice-site selection in these exons during alternative splicing. On the basis of these findings, we identified mutations that activated the exonization of a silent intronic Alu...
  20. ncbi Alternative approach to a heavy weight problem
    Amir Goren
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 18:214-20. 2008
    ....
  21. ncbi The "alternative" choice of constitutive exons throughout evolution
    Galit Lev Maor
    Department of Human Molecular Genetics, Tel Aviv University, Tel Aviv, Israel
    PLoS Genet 3:e203. 2007
    ..Our results uncover an evolutionary pathway that increases transcriptome diversity by shifting exons from constitutive to alternative splicing...
  22. ncbi Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    EMBO J 29:1629-36. 2010
    ..In this review we discuss evidence for the coupling between transcription and splicing, focusing on recent findings suggesting a link between chromatin structure and splicing, and highlighting challenges this emerging field is facing...
  23. ncbi Different levels of alternative splicing among eukaryotes
    Eddo Kim
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 35:125-31. 2007
    ....
  24. ncbi AluGene: a database of Alu elements incorporated within protein-coding genes
    Tal Dagan
    Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 32:D489-92. 2004
    ..The Alu elements are annotated with respect to coding region and exon/intron location. This design facilitates queries on Alu sequences, locations, as well as motifs and compositional properties via a one-stop search page...
  25. ncbi How prevalent is functional alternative splicing in the human genome?
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Trends Genet 20:68-71. 2004
    ..We conclude that a significant portion of cassette exons evident in EST databases is not functional, and might result from aberrant rather than regulated splicing...
  26. ncbi Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers
    Amir Goren
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Mol Cell 22:769-81. 2006
    ..This finding signifies the delicate positional effect of ESRs on alternative splicing regulation...
  27. ncbi A non-EST-based method for exon-skipping prediction
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 14:1617-23. 2004
    ..We show that a substantial fraction of the splice variants in the human genome could not be identified through current human EST or cDNA data...
  28. ncbi Alu exonization events reveal features required for precise recognition of exons by the splicing machinery
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 5:e1000300. 2009
    ..This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing...
  29. ncbi Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    Schraga H Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 18:88-103. 2008
    ....
  30. ncbi Characteristics of transposable element exonization within human and mouse
    Noa Sela
    Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 5:e10907. 2010
    ..Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes...
  31. ncbi Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing
    Moti Alberstein
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    RNA 13:1988-99. 2007
    ..Our results provide indications of a complex transcription regulation mechanism that controls the spatial and temporal expression of Slu7, presumably allowing regulation of tissue-specific alternative splicing events...
  32. ncbi Differential GC content between exons and introns establishes distinct strategies of splice-site recognition
    Maayan Amit
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Cell Rep 1:543-56. 2012
    ....
  33. ncbi Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements
    Asaf Levy
    Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 38:1515-30. 2010
    ..TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition...
  34. ncbi SROOGLE: webserver for integrative, user-friendly visualization of splicing signals
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 37:W189-92. 2009
    ..SROOGLE is available at http://sroogle.tau.ac.il, and may also be downloaded as a desktop version...
  35. ncbi Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans
    Noa Sela
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
    Biol Direct 3:41. 2008
    ..elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif...
  36. ncbi Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus
    Noam Shomron
    Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel 69978
    Mol Biol Cell 15:3782-95. 2004
    ..Altogether, this indicates that zinc-dependent nucleocytoplasmic shuttling might be the possible molecular basis by which hSlu7 protein levels are regulated within the nucleus...
  37. ncbi The emergence of alternative 3' and 5' splice site exons from constitutive exons
    Eli Koren
    Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 3:e95. 2007
    ..This model was validated experimentally on four exons, showing that they indeed originated from constitutive exons that acquired a new competing splice site during evolution...
  38. ncbi Alternative splicing and disease
    Eddo Kim
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    RNA Biol 5:17-9. 2008
    ..It may be that splicing silencers play a more prominent role in alternative splicing regulation than previously anticipated...
  39. ncbi Comparative analysis detects dependencies among the 5' splice-site positions
    Ido Carmel
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    RNA 10:828-40. 2004
    ..Our findings indicate the importance of U1 snRNA base-pairing to the exonic portion of the 5' splice site...
  40. ncbi Chromatin organization marks exon-intron structure
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    Nat Struct Mol Biol 16:990-5. 2009
    ..Our results suggest an RNA polymerase II-mediated cross-talk between chromatin structure and exon-intron architecture, implying that exon selection may be modulated by chromatin structure...
  41. ncbi Alternative splicing and evolution: diversification, exon definition and function
    Hadas Keren
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nat Rev Genet 11:345-55. 2010
    ....
  42. ncbi Alternative splicing: current perspectives
    Eddo Kim
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    Bioessays 30:38-47. 2008
    ....
  43. ncbi Intronic sequences flanking alternatively spliced exons are conserved between human and mouse
    Rotem Sorek
    Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 13:1631-7. 2003
    ..Our results suggest that the function of many of the intronic sequence blocks that are conserved between human and mouse is the regulation of alternative splicing...
  44. ncbi The importance of being divisible by three in alternative splicing
    Alon Magen
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 33:5574-82. 2005
    ..These findings suggest that alternative splicing of symmetrical and non-symmetrical exons is governed by different selective pressures and serves different purposes...
  45. ncbi SR proteins: a foot on the exon before the transition from intron to exon definition
    Oren Ram
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Trends Genet 23:5-7. 2007
    ..These results imply that SR proteins had already facilitated the splicing of weak introns before the evolution of alternative splicing...
  46. ncbi Alternative splicing of Alu exons--two arms are better than one
    Nurit Gal-Mark
    Department of Human Genetics and Molecular Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 36:2012-23. 2008
    ..Thus, the dimeric form of the Alu element fortuitously provides it with an evolutionary advantage, allowing enrichment of the primate transcriptome without compromising its original repertoire...
  47. ncbi Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation
    Guy Kol
    Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
    Hum Mol Genet 14:1559-68. 2005
    ..Mutations in the putative BS revealed a shift from constitutive to alternative splicing, and it also controls the inclusion/skipping ratio in alternative splicing. This suggests a role for BS sequences in regulated splicing...
  48. ncbi Insights into the connection between cancer and alternative splicing
    Eddo Kim
    Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Trends Genet 24:7-10. 2008
    ..We further show evidence suggesting that the lower levels of alternative splicing in cancerous tissues might be a result of disruption of splicing regulatory proteins...
  49. ncbi Boric acid reversibly inhibits the second step of pre-mRNA splicing
    Noam Shomron
    Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Ramat Aviv, Israel
    FEBS Lett 552:219-24. 2003
    ..The mechanism of action does not involve chelation of several metal ions; hindrance of 3' splice-site; or binding to hSlu7. This study presents a novel method for specific reversible inhibition of the second step of pre-mRNA splicing...
  50. ncbi Alu-containing exons are alternatively spliced
    Rotem Sorek
    Department of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 12:1060-7. 2002
    ..Presumably, evolutionary events that cause a constitutive insertion of an Alu sequence into an mRNA are deleterious and selected against...
  51. ncbi The U1 snRNP base pairs with the 5' splice site within a penta-snRNP complex
    Hadar Malca
    Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
    Mol Cell Biol 23:3442-55. 2003
    ..This fraction is functional in mRNA spliceosome assembly when supplemented with soluble nuclear proteins. The results argue that U1 can bind the 5' splice site in a mammalian preassembled penta-snRNP complex...
  52. ncbi Bioactivation of carbamate-based 20(S)-camptothecin prodrugs
    Neta Pessah
    School of Chemistry, Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
    Bioorg Med Chem 12:1859-66. 2004
    ..The described derivatives of CPT further our knowledge in the design of prodrugs for use in selective approaches for targeted chemotherapy...
  53. ncbi Detection and removal of biases in the analysis of next-generation sequencing reads
    Schraga Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
    PLoS ONE 6:e16685. 2011
    ..Collectively, our results highlight several important pitfalls, challenges and approaches in the analysis of NGS reads...
  54. ncbi Pre-mRNA splicing is a determinant of nucleosome organization
    Hadas Keren-Shaul
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 8:e53506. 2013
    ..Overall, these results suggest that splicing can affect chromatin organization...