Itay Tirosh

Summary

Affiliation: Weizmann Institute of Science
Country: Israel

Publications

  1. ncbi request reprint A genetic signature of interspecies variations in gene expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
    Nat Genet 38:830-4. 2006
  2. ncbi request reprint The pattern and evolution of yeast promoter bendability
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Trends Genet 23:318-21. 2007
  3. pmc Transcriptional priming of cytoplasmic post-transcriptional regulation
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Transcription 2:258-62. 2011
  4. pmc Computational verification of protein-protein interactions by orthologous co-expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Bioinformatics 6:40. 2005
  5. doi request reprint Computational analysis of nucleosome positioning
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Methods Mol Biol 833:443-9. 2012
  6. pmc Widespread remodeling of mid-coding sequence nucleosomes by Isw1
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Herzl Street, Rehovot 76100, Israel
    Genome Biol 11:R49. 2010
  7. pmc Promoter architecture and the evolvability of gene expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
    J Biol 8:95. 2009
  8. pmc Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Genome Biol 8:R50. 2007
  9. doi request reprint A yeast hybrid provides insight into the evolution of gene expression regulation
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Science 324:659-62. 2009
  10. pmc Chromatin regulators as capacitors of interspecies variations in gene expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 6:435. 2010

Collaborators

Detail Information

Publications25

  1. ncbi request reprint A genetic signature of interspecies variations in gene expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
    Nat Genet 38:830-4. 2006
    ..TATA-dependent regulation may enhance the sensitivity of gene expression to genetic perturbations, thus facilitating expression divergence at particular genetic loci...
  2. ncbi request reprint The pattern and evolution of yeast promoter bendability
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Trends Genet 23:318-21. 2007
    ..Rigid DNA could influence nucleosome positioning and assist in the assembly of the transcriptional machinery at TATA-less promoters...
  3. pmc Transcriptional priming of cytoplasmic post-transcriptional regulation
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Transcription 2:258-62. 2011
    ..Here, I speculate that this is a widespread mode of regulation and discuss the potential mechanisms, advantages and implications of such a regulatory strategy...
  4. pmc Computational verification of protein-protein interactions by orthologous co-expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Bioinformatics 6:40. 2005
    ..Several methods have recently been suggested for this purpose including co-expression as a confidence measure for interacting proteins, but their performance is still quite poor...
  5. doi request reprint Computational analysis of nucleosome positioning
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Methods Mol Biol 833:443-9. 2012
    ..Potential pitfalls that may be encountered in such analysis and computational quality controls are further discussed in Subheading 3...
  6. pmc Widespread remodeling of mid-coding sequence nucleosomes by Isw1
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Herzl Street, Rehovot 76100, Israel
    Genome Biol 11:R49. 2010
    ..While the genome-wide effect of most remodelers has not been described, recent studies in Saccharomyces cerevisiae have shown that Isw2 prevents ectopic expression of anti-sense and suppressed transcripts at gene ends...
  7. pmc Promoter architecture and the evolvability of gene expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
    J Biol 8:95. 2009
    ..Here, we discuss how these promoter properties may confer an inherent capacity for flexibility of expression...
  8. pmc Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Genome Biol 8:R50. 2007
    ..However, functional divergence can also be attributed to changes in regulatory properties, such as protein localization or expression, which require only minor changes in gene sequence...
  9. doi request reprint A yeast hybrid provides insight into the evolution of gene expression regulation
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Science 324:659-62. 2009
    ..These results provide insights on the regulatory changes in cis and trans during the divergence of species and upon hybridization...
  10. pmc Chromatin regulators as capacitors of interspecies variations in gene expression
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 6:435. 2010
    ..Our results support the idea that regulatory proteins serve as capacitors that buffer gene expression against hidden genetic variability...
  11. pmc On the relation between promoter divergence and gene expression evolution
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 4:159. 2008
    ..Our analysis emphasizes the flexibility of promoter structure, and highlights the interplay between specific binding sites and general chromatin structure in the control of gene expression...
  12. pmc Inferring regulatory mechanisms from patterns of evolutionary divergence
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 7:530. 2011
    ..We review examples of this concept using yeast as a model system, and highlight a hybrid-based approach that is highly instrumental in this analysis...
  13. pmc Expression noise and acetylation profiles distinguish HDAC functions
    Leehee Weinberger
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Cell 47:193-202. 2012
    ....
  14. pmc Two strategies for gene regulation by promoter nucleosomes
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Genome Res 18:1084-91. 2008
    ..Analysis of nucleosome positioning in human promoters reproduces the main observations. Our results suggest two distinct strategies for gene regulation by chromatin, which are selectively employed by different genes...
  15. pmc Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 6:365. 2010
    ..Our results provide evolutionary insights to the genetic determinants and regulatory function of nucleosome positioning...
  16. pmc Coupled evolution of transcription and mRNA degradation
    Mally Dori-Bachash
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 9:e1001106. 2011
    ..These results suggest that an opposite coupling between the regulation of transcription and that of mRNA degradation has shaped the evolution of gene regulation in yeast...
  17. pmc Promoter nucleosome organization shapes the evolution of gene expression
    Dalia Rosin
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 8:e1002579. 2012
    ..Our results suggest that promoter organization constrains the early evolutionary dynamics and in this way biases the path of long-term evolution...
  18. pmc Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns
    Kyle Tsui
    Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada
    Mol Cell Biol 31:4348-55. 2011
    ..Thus, while some evolutionary changes in nucleosome occupancy contribute to gene expression divergence, nucleosome occupancy often diverges extensively with apparently little impact on gene expression...
  19. pmc Opposite GC skews at the 5' and 3' ends of genes in unicellular fungi
    Malcolm A McLean
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Genomics 12:638. 2011
    ..GC-skews have previously been linked to transcription in some eukaryotes. They have been associated with transcription start sites, with the coding strand G-biased in mammals and C-biased in fungi and invertebrates...
  20. pmc Extensive divergence of yeast stress responses through transitions between induced and constitutive activation
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 108:16693-8. 2011
    ..e., biological noise). Frequent compensatory changes and biological noise may explain how diverged expression responses support similar physiological responses...
  21. ncbi request reprint Comparative biology: beyond sequence analysis
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
    Curr Opin Biotechnol 18:371-7. 2007
    ..Here we review recent works applying comparative analysis to large-scale gene expression datasets and discuss the central principles and challenges of such approaches...
  22. pmc The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression
    Efrat Shema
    Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Genes Dev 22:2664-76. 2008
    ..Furthermore, frequent RNF20 promoter hypermethylation was observed in tumors. RNF20 may thus be a putative tumor suppressor, acting through selective regulation of a distinct subset of genes...
  23. doi request reprint Evolution of gene sequence and gene expression are not correlated in yeast
    Itay Tirosh
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Trends Genet 24:109-13. 2008
    ..Based on these findings, we discuss the possibilities of neutral evolution of gene expression and of different modes of evolution in unicellular versus multicellular organisms...
  24. pmc Autocorrelation analysis reveals widespread spatial biases in microarray experiments
    Amnon Koren
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Genomics 8:164. 2007
    ..A particular source of false data has been described, in which non-random placement of gene probes on the microarray surface is associated with spurious correlations between genes...
  25. pmc CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
    Adi Stern
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Genome Res 22:1985-94. 2012
    ..Our finding of global sharing of gut phages is surprising in light of the extreme genetic diversity of phages found in other ecological niches...