gilastLab

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  • RNA
    RNA
  • Bioinformatics
    Bioinformatics
  • DNA
    DNA
  • Molecular Biology
    Molecular Biology
  • Chromatin Structure
    Chromatin Structure
  • Cancer Transcriptomics
    Cancer Transcriptomics
  • Genomics
    Genomics
  • Familial Dysautonomia (FD)
    Familial Dysautonomia (FD)
  • Genetic Study
    Genetic Study

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We are currently seeking highly motivated individuals who want to join us. Please contact us at gilast@post.tau.ac.il

 

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Publications

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publications

  1.  Shiran Naftelberg, Ziv Abramovitch, Shani Gluska, Sivan Yannai, Yuvraj Joshi, Maya Donyo, Keren Ben-Yaakov, Tal Gradus, Jonathan Zonszain, Chen Farhy, Ruth Ashery-Padan, Eran Perlson,Gil Ast (2016) Phosphatidylserine Ameliorates Neurodegenerative Symptoms and Enhances Axonal Transport in a Mouse Model of Familial Dysautonomia. PLOS Genetics. doi:10.1371/journal.pgen.1006486 [PDF]. 

  2. Hollander D*, Naftelberg S*, Lev-Maor G, Kornblihtt AR, Ast G. (2016) How are short exons flanked by long introns defined and committed to splicing? Trends Genet. doi:10.1016/j.tig.2016.07.003. [PDF]. *equal contribution.

  3. Hollander D, Donyo M*, Atias N*, Mekahel K, Melamed Z, Yannai S, Lev-Maor G, Shilo A, Schwartz S, Barshack I, Sharan R#, Ast G#. (2016) A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1. Genome Res. doi: 10.1101/gr.193169.115. [PDF]*equal contribution. #corresponding authors.
  4. Donyo M, Hollander D, Abramovitch Z, Naftelberg S, Ast G. (2016) Phosphatidylserine enhances IKBKAP transcription by activating the MAPK/ERK signaling pathway. Hum Mol Genet. doi: 10.1093/hmg/ddw011. [PDF].
  5. Naftelberg S, Schor IE, Ast G*, Kornblihtt AR*. (2015) Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure. Annu Rev Biochem. doi: 10.1146/annurev-biochem-060614-034242. [PDF]. *corresponding authors.
  6. Kfir N, Lev-Maor G, Glaich O, Alajem A, Datta A, Sze SK, Meshorer E, Ast G. (2015) SF3B1 Association with Chromatin Determines Splicing Outcomes. Cell Reports. DOI: http://dx.doi.org/10.1016/j.celrep.2015.03.048. [PDF].
  7. Lev-Maor G, Yearim A, Ast G. (2015) The alternative role of DNA methylation in splicing regulation. Trends Genet. DOI: http://dx.doi.org/10.1016/j.tig.2015.03.002. [PDF].
  8. Yearim A*, Gelfman S*, Shayevitch R, Melcer S, Glaich O, Mallm JP, Nissim-Rafinia M, Cohen AH, Rippe K, Meshorer E, Ast G. (2015) HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing. Cell Reports. DOI: http://dx.doi.org/10.1016/j.celrep.2015.01.038. [PDF]. *eqaul contribution. 
  9. Fuchs G*, Hollander D*, Voichek Y, Ast G, Oren M. (2014) Co-transcriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate. Genome Res. doi:10.1101/gr.176487.114. [PDF]. *equal contribution.
  10. Gelfman S, Ast G. (2013) When epigenetics meets alternative splicing: the roles of DNA methylation and GC architecture. Epigenomics. doi: 10.2217/epi.13.32. [PDF]
  11. Melamed Z, Levy A, Ashwal-Fluss R, Lev-Maor G, Mekahel K, Atias N, Gilad S, Sharan R, Levy C, Kadener S, Ast G. (2013) Alternative Splicing Regulates Biogenesis of miRNAs Located across Exon-Intron Junctions. Mol Cell. doi: 10.1016/j.molcel.2013.05.007. [PDF]
  12. Ramalho RF, Gelfman S, de Souza JE, Ast G, de Souza SJ, Meyer D. (2013) Testing for Natural Selection in Human Exonic Splicing Regulators Associated with Evolutionary Rate Shifts. J Mol Evol. DOI 10.1007/s00239-013-9555-2 [PDF]
  13. Bochner R, Ziv Y, Zeevi D, Donyo M, Abraham L, Ashery-Padan R, Ast G. (2013) Phosphatidylserine increases IKBKAP levels in a humanized knock-in IKBKAP mouse model. Hum Mol Genet. doi:10.1093/hmg/ddt126 [PDF]
  14. Gelfman S, Cohen N, Yearim A, and Ast G. (2013) DNA-methylation effect on co-transcriptional splicing is dependent on GC-architecture of the exon-intron structure. Genome Res. doi:10.1101/gr.143503.112 [PDF]
  15. Keren-Shaul H*, Lev-Maor G*, Ast G. (2013) Pre-mRNA Splicing Is a Determinant of Nucleosome Organization. PLoS ONE 8(1): e53506. doi:10.1371/journal.pone.0053506. [PDF]. *equal contribution.
  16. Amit M*, Donyo M*, Hollander D*, Goren A*, Kim E, Gelfman S, Lev-Maor G, Burstein D, Schwartz S, Postolsky B, Pupko T, Ast G. (2012) Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition. Cell Reports. doi:10.1016/j.celrep.2012.03.013. [PDF]. *equal contribution.
  17. Gelfman S, Burstein D, Penn O, Savchenko A, Amit M, Schwartz S, Pupko T, Ast G. (2012) Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res. 2012 Jan;22(1):35-50. Epub 2011 Oct 5. [PDF].
  18. Cheishvili D, Maayan C, Cohen-Kupiec R, Lefler S, Weil M, Ast G, Razin A. (2011) IKAP/Elp1 involvement in cytoskeleton regulation and implication for familial dysautonomia. Hum Mol Genet. 2011 Feb 11. [PDF].
  19. Schwartz S, Oren R, Ast G. (2011) Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One. 2011 Jan 31;6(1):e16685. [PDF].
  20. Keren H, Donyo M, Zeevi D, Maayan C, Pupko T and Ast G (2010) Phosphatidylserine Increases IKBKAP Levels in Familial Dysautonomia Cells. PLoS One. 2010 Dec 1;5(12):e15884. [PDF].
  21. Llorian M*, Schwartz S*, Clark TA, Hollander D, Tan LY, Spellman R, Gordon A, Schweitzer AC, de la Grange P, Ast G, Smith CW. (2010) Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB. Nat Struct Mol Biol. 2010 Sep;17(9):1114-23.Epub 2010 Aug 15. [PDF]*equal contribution.
  22. Sela N, Mersch B, Hotz-Wagenblatt, and Ast G. (2010) Characteristics of transposable element exonization within human and mouse. PLoS One. 2010 Jun 1;5(6):e10907. [PDF].
  23. Noa Sela, Eddo Kim, and Gil Ast (2010)The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol. 2010 Jun 2;11(6):R59. [PDF].
  24. Schraga Schwartz and Gil Ast (2010) Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. The EMBO Journal. 2010 Mar 26. [PDF].
  25. Keren H, Lev-Maor G, Ast G. (2010) Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet. 2010 Apr 8. [PDF].
  26. Goren A*, Kim E*, Amit M*, Vaknin K, Kfir N, Ram O, Ast G. (2010) Overlapping splicing regulatory motifs--combinatorial effects on splicing. Nucleic Acids Res. 2010 Jan 27. [PDF]. *equal contribution.
  27. Levy A, Schwartz S, Ast G. (2010) Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements. Nucleic Acids Res. 2010 Epub ahead of print. [PDF].
  28. Gal-Mark N*, Schwartz S*, Ram O, Eyras E, Ast G. (2009) The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution. PLoS Genet. 2009 Nov;5(11):e1000717. Epub 2009 Nov 13. [PDF]. *equal contribution.
  29. Vaknin K, Goren A and Ast G. (2009) TEs or not TEs? That is the evolutionary question. J.Biol. 2009 Oct 23. [PDF].
  30. Schwartz S, Meshorer E, Ast G. (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol. 2009 Aug 16. [Epub ahead of print] [PDF].
  31. Schwartz S, Hall E, Ast G. (2009) SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W189-92. Epub 2009 May 8. [PDF].
  32. Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, Ast G. (2009) Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol. 2009 Mar;5(3):e1000300. Epub 2009 Mar 6. [PDF].
  33. Sela N, Stern A, Makalowski W, Pupko T and Ast G.(2008) Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposableelement of C. elegans.Biol Direct. 2008 Oct 8;3:41. [Epub ahead of print] [PDF].
  34. Lev-Maor G, Ram O, Kim E, Sela N, Goren A, Levanon EY and Ast G. (2008) Intronic Alus influence alternative splicing. PLoS Genet. 2008 Sep 26;4(9):e1000204. [PDF].
  35. Kim E, Goren A and Gil Ast. (2008) Alternative splicing and disease. RNA Biol. 2008 Mar 22;5(1) [Epub ahead of print] [PDF].
  36. Ram O, Schwartz S and Gil Ast. (2008) Multifactorial interplay controls the splicing profile of Alu derived exons. Mol Cell Biol. 2008 Mar 10; [Epub ahead of print] [PDF].
  37. Gal-Mark N, Schwartz S and Gil Ast. (2008) Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Res. 2008 Feb 14 [PDF].
  38. Goren A*, Kim E*, Amit M*, Bochner R, Lev-Maor G, Ahituv N and Gil Ast. (2008) Alternative approach to a heavy weight problem. Genome Res. 2008 Feb [PDF]. *equal contribution.
  39. Kim E*, Goren A* and Gil Ast. (2008) Alternative splicing: current perspectives. Bioessays. 2008 Jan;30(1):38-47.[PDF]. *equal contribution.
  40. Kim E*, Goren A* and Gil Ast. (2008) Insights into the connection between cancer and alternative splicing. Trends Genet. 2008 Jan [PDF]. *equal contribution.
  41. Maayan Amit, Noa Sela, Hadas Keren, Ze'ev Melamed, Inna Muler, Noam Shomron, Shai Izraeli and Gil Ast. (2007) Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. BMC Molecular Biology 2007, 8:109 [PDF].
  42. Schraga Schwartz, Jo.o Silva, David Burstein, Tal Pupko, Eduardo Eyras and Gil Ast. (2007) Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 2007 Nov 21 [PDF].
  43. Lev-Maor G*, Goren A*, Sela N*, Kim E, Keren H, Doron-Faigenboim A, Leibman-Barak S, Pupko T, Ast G. (2007) The "Alternative" Choice of Constitutive Exons throughout Evolution. PLoS Genet. 2007 Nov 16;3(11):e203 [PDF]. *equal contribution.
  44. Mersch B, Sela N, Ast G, Suhai S, Hotz-Wagenblatt A. (2007) SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements. BMC Genet. 2007 Nov 6;8(1):78 [PDF].
  45. Asaf Levy*, Noa Sela* and Gil Ast. (2007) TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res.2007; doi: 10.1093/nar/gkm949. [PDF]. *equal contribution.
  46. Alberstein M*, Amit M*, Vaknin K, O'donnell A, Farhy C, Lerenthal Y, Shomron N, Shaham O, Sharrocks AD, Ashery-Padan R and Ast G. (2007) Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing. RNA. 2007 Sep 5. [PDF]. *equal contribution.
  47. Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A and Gil Ast. (2007) Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol. 2007 Jun;8(6):R127. [PDF]
  48. Cheishvili D, Maayan C, Smith Y, Ast G and Aharon Razin. (2007) IKAP/hELP1 deficiency in the cerebrum of familial dysautonomia patients results in down regulation of genes involved in oligodendrocyte differentiation and in myelination. Hum Mol Genet. 2007 Jun 25;(16):17. [PDF]
  49. Koren E, Lev-Maor G, and Gil Ast. (2007) The emergence of alternative 3' and 5' splice site exons from constitutive exons. PLoS Comput Biol. 2007 May 25;3(5):e95. [PDF]
  50. Galit Lev-Maor, Rotem Sorek , Erez Y Levanon, Nurit Paz, Eli Eisenberg and Gil Ast. (2007) RNA-editing-mediated exon evolution. Genome Biol. 2007;8(2):R29. [PDF]
  51. Kim E, Magen A, Ast G. (2007) Different levels of alternative splicing among eukaryotes. Nucleic Acids Res. 2007;35(1):125-31. [PDF]
  52. Ram O, Ast G. (2007) SR proteins: a foot on the exon before the transition from intron to exon definition. Trends Genet. 2007 Jan;23(1):5-7. [PDF]
  53. Goren A*, Ram O*, Amit M, Keren H, Lev-Maor G, Vig I, Pupko T, Ast G. (2006) Comparative analysis identifies exonic splicing regulatory sequences-the complex definition of enhancers and silencers.Mol Cell. 2006 Jun 23;22(6):769-81. [PDF]. *equal contribution.
  54. Magen A, Ast G. (2005) The importance of being divisible by three in alternative splicing. Nucleic Acids Research (2005)Vol. 33,No. 17: 5574.5582. [PDF]
  55. Kol G, Lev-Maor G, Ast G. (2005) Human-Mouse Comparative Analysis reveals that Branch-site plasticity contributes to splicing regulation. Human Molecular Genetics (2005) 14: 1559-1568.[PDF]
  56. Ast G. (2005) The Alternative Genome. Scientific American. 2005 Apr; Vol 292(4):58-65. [PDF] [Fig1] [Fig2]
  57. Noam Shomron*, Moti Alberstein*, Mika Reznik, Gil Ast (2005) Stress alters the subcellular distribution of hSlu7 and thus modulates alternative splicing. J Cell Sci. 2005 Feb 22. [PDF].*equal contribution
  58. Ast G. (2004) How did Alternative Splicing Evolve ? Nature Reviews Genetics. 2004 Oct;5(10):773-782. [PDF] supplementary material [PDF] [Fig1] [Fig2] [Fig3] [Fig4].
  59. Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R (2004) A Non-EST-Based Method for Exon-Skipping Prediction. Genome Res. 2004 Aug;14(8):1617-23. [PDF]
  60. Noam Shomron, Mika Reznik, Gil Ast. (2004) Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus, Mol. Biol. Cell  15(8):3782-3795 [PDF] .
  61. Rotem Sorek*, Galit Lev-Maor*, Mika Reznik*, Tal Dagan, Frida Belinky, Dan Graur, Gil Ast. (2004) Minimal conditions for exonization of intronic sequences: 5' splice site formation in Alu exons. Mol. Cell.  14(2) 221-31  [PDF] supplementary material [PDF] . *equal contribution.
  62. Ido Carmel, Saar Tal, Ida Vig, Gil Ast. (2004) Comparative Analysis Detects Dependencies Among the 5' Splice-Sites Positions. RNA, 10(5) 828-840[PDF].
  63. Pessah, N., Reznik, M., Shamis, M., Yantiri, F., Xin, H., Bowdish, K., Shomron, N., Ast, G., Shabat, D. (2004) Bioactivation of carbamate-based 20(S)-camptothecin prodrugs.Bioorganic; Medicinal Chemistry. 12 [PDF]
  64. Sorek, R., Shamir, R., Ast, G. (2004) How prevalent is functional alternative splicing in the human genome?. Trends in Genetics. Feb Vol. 20 No. 2 [PDF]
  65. Dagan, T*., Sorek*, R., Sharon*, E., Ast, G., Graur, D. (2004) AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Research, Vol. 32, D489-D492 *equal contribution [PDF]
  66. Shomron, N. Ast, G. (2003) Boric acid reversibly inhibits the second step of splicing. FEBS letters.Volume 552, Issue 2-3,pp. 219-224. [PDF]
  67. Sorek, R. Ast, G. (2003) Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 2003 Jul;13(7):1631-7. [PDF]
  68. Lev-Maor, G*, Sorek, R*, Shomron, N. Ast G. (2003) The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science. May 23:1288-1291. *equal contribution. [PDF] [reviewed] [Supporting material]
  69. Malca, H., Shomron, N., Ast, G. (2003) The U1 snRNP basepairs the 5 splice site within a penta-snRNP complex. Mol. Cell. Biol. May;23(10):3442-55 [PDF]
  70. Ast, G. (2003). Drug-targeting strategies for prostate cancer. Current Pharmaceutical Design.9: 455-466. [PDF]
  71. Shomron, N., Malca, H., Vig, I., Ast, G. (2002) Reversible inhibition of the second step of splicing suggests a possible role in zinc in the second step of splicing. Nucleic Acids Res. 30(19): 4127-4137. [PDF + supplement]
  72. Sorek, R., Ast, G., Graur, D. (2002) Alu-Containing Exons are Alternatively Spliced. Genome Res. 12: 1060-1067. [PDF]
  73. Ast, G., Pavelitz, T., Weiner, A.M. (2001) Sequences upstream of the branch site are required to form helix II between U2 and U6 snRNA in a trans-splicing reaction. Nucleic Acids Res. 29: 1741-1749. [PDF]
  74. Ast G, and Weiner, A.M. (1997a) Antisense oligonucleotide binding to U5 snRNP induces a conformational change that exposes the conserved loop of U5 snRNA. Nucleic Acids Res. 25, 3508-3513. [PDF]
  75. Ast, G. and Weiner, A.M. (1997b) A novel U1/U5 interaction suggests that U1 directs U5 small nuclear RNA to the 5' splice site. RNA 371-381.
  76. Ast, G. and Weiner, A.M. (1996) A U1/U4/U5 snRNP complex induced by a 2'-O-Methyl-oligribonucleotide complementary to U5 snRNA. Science 272, 881-884.[Abstract]
  77. Ast, G., Weismann, A., Goldblatt, D.,  Sperling, R., Mozes, E. and Sperling, J. (1994) An autoantibody derived from mice with experimental SLE is directed against  the essential splicing factor, SF53/4 - a possible role for lnRNP particles in autoimmune disorders. Internat.Immunol 6, 1087-1105.[Abstract]
  78. Richler, C., Ast, G., Goitein, R., Wahrman, J., Sperling, R. and Sperling, J. (1994) Splicing components are excluded from the transcriptionally inactive XY body in male meiotic nuclei. Mol. Biol. of the Cell 5, 1341-1352.
  79. Ast, G., Goldblatt, D., Offen, D., Sperling, J. and Sperling, R. (1991) A novel splicing factor is an integral component of 200S large nuclear ribonucleoprotein (lnRNP) particles. EMBO J. 10, 425-432.
  80. Ast, G., Goldblatt, D., Sperling, J. and Sperling, R. (1990) Identification of nuclear RNP proteins as pre-mRNA splicing factors.  Mol. Biol. Reports, 14, 193.[PubMed Link]
  81. Anglister, J., Jacob, C., Assulin, O., Ast, G., Pinker, R. and Arnon, R. (1988)NMR study of the complex between a synthetic peptide derived from Cholera toxin. Biochemistry 27, 717-724. [PubMed Link]

 

 

 

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