José E Pérez-Ortín

Summary

Affiliation: University of Valencia
Country: Spain

Publications

  1. pmc Genomic insights into the different layers of gene regulation in yeast
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biologicas, Universitat de Valencia, C Dr Moliner 50, 46100 Burjassot, Spain
    Genet Res Int 2011:989303. 2011
  2. pmc A complete set of nascent transcription rates for yeast genes
    Vicent Pelechano
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, Burjassot, Spain
    PLoS ONE 5:e15442. 2010
  3. pmc Regulon-specific control of transcription elongation across the yeast genome
    Vicent Pelechano
    Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, Burjassot, Spain
    PLoS Genet 5:e1000614. 2009
  4. doi request reprint Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de Valencia, Dr Moliner 50, E 46100 Burjassot, Valencia, Spain Electronic address
    J Mol Biol 425:3750-75. 2013
  5. doi request reprint Genome-wide studies of mRNA synthesis and degradation in eukaryotes
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biologicas, Universitat de Valencia, C Dr Moliner 50, E46100 Burjassot, Spain
    Biochim Biophys Acta 1819:604-15. 2012
  6. pmc The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast
    José García-Martínez
    Universitat de Valencia, Valencia, Spain
    Transcription 3:39-44. 2012
  7. ncbi request reprint Functional analysis of 12 ORFs from Saccharomyces cerevisiae chromosome II
    S Rodriguez-Navarro
    Departament de Bioquimica i Biologia Molecular, Facultat de Ciencies Biologiques, Universitat de Valencia, Spain
    Yeast 15:913-9. 1999
  8. ncbi request reprint A genomic view of mRNA turnover in yeast
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, Dr Moliner 50, 46100 Burjassot, Spain
    C R Biol 334:647-54. 2011
  9. doi request reprint Genomics of mRNA turnover
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biologicas, Dr Moliner 50 E46100 Burjassot, Spain
    Brief Funct Genomic Proteomic 6:282-91. 2007
  10. ncbi request reprint DNA chips for yeast biotechnology. The case of wine yeasts
    José E Pérez-Ortín
    Departamento de Bioquímica y Biología Molecular and Servicio de Chips de DNA, Universitat de Valencia, Spain
    J Biotechnol 98:227-41. 2002

Collaborators

Detail Information

Publications34

  1. pmc Genomic insights into the different layers of gene regulation in yeast
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biologicas, Universitat de Valencia, C Dr Moliner 50, 46100 Burjassot, Spain
    Genet Res Int 2011:989303. 2011
    ..A comparison between the datasets generated by them provides interesting genomic insights into the different layers of gene regulation in eukaryotes...
  2. pmc A complete set of nascent transcription rates for yeast genes
    Vicent Pelechano
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, Burjassot, Spain
    PLoS ONE 5:e15442. 2010
    ..Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell...
  3. pmc Regulon-specific control of transcription elongation across the yeast genome
    Vicent Pelechano
    Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, Burjassot, Spain
    PLoS Genet 5:e1000614. 2009
    ..This work demonstrates that the regulation of transcription elongation is a widespread, gene class-dependent phenomenon that also affects housekeeping genes...
  4. doi request reprint Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de Valencia, Dr Moliner 50, E 46100 Burjassot, Valencia, Spain Electronic address
    J Mol Biol 425:3750-75. 2013
    ..Some of these factors can regulate both transcription and decay rates, thereby maintaining proper mRNA homeostasis during eukaryotic cell life. ..
  5. doi request reprint Genome-wide studies of mRNA synthesis and degradation in eukaryotes
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biologicas, Universitat de Valencia, C Dr Moliner 50, E46100 Burjassot, Spain
    Biochim Biophys Acta 1819:604-15. 2012
    ..This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing...
  6. pmc The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast
    José García-Martínez
    Universitat de Valencia, Valencia, Spain
    Transcription 3:39-44. 2012
    ....
  7. ncbi request reprint Functional analysis of 12 ORFs from Saccharomyces cerevisiae chromosome II
    S Rodriguez-Navarro
    Departament de Bioquimica i Biologia Molecular, Facultat de Ciencies Biologiques, Universitat de Valencia, Spain
    Yeast 15:913-9. 1999
    ..No effects were detected in any of the haploid deletion mutants for the rest of the ORFs with respect to growth, gross morphology or mating...
  8. ncbi request reprint A genomic view of mRNA turnover in yeast
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, Dr Moliner 50, 46100 Burjassot, Spain
    C R Biol 334:647-54. 2011
    ....
  9. doi request reprint Genomics of mRNA turnover
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Biologicas, Dr Moliner 50 E46100 Burjassot, Spain
    Brief Funct Genomic Proteomic 6:282-91. 2007
    ..They will be described in detail and their potential drawbacks discussed. I will also discuss the integration of the data obtained to fully analyse the expression strategies used by yeast and other eukaryotic cells...
  10. ncbi request reprint DNA chips for yeast biotechnology. The case of wine yeasts
    José E Pérez-Ortín
    Departamento de Bioquímica y Biología Molecular and Servicio de Chips de DNA, Universitat de Valencia, Spain
    J Biotechnol 98:227-41. 2002
    ..During the past two years some groups have started this study and the first results have been published. We review here the current state of the knowledge of wine yeast and the capacity of DNA chip technology for its improvement...
  11. pmc Molecular characterization of a chromosomal rearrangement involved in the adaptive evolution of yeast strains
    José E Pérez-Ortín
    Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, Spain
    Genome Res 12:1533-9. 2002
    ..This is the first time that a gross chromosomal rearrangement is shown to be involved in the adaptive evolution of Saccharomyces cerevisiae...
  12. ncbi request reprint Genomics and gene transcription kinetics in yeast
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, C Dr Moliner 50, E46100 Burjassot, Spain
    Trends Genet 23:250-7. 2007
    ..Such experiments could provide a new picture of the transcriptional response, by enabling us to characterize the kinetic strategies that are used by different genes under given environmental conditions...
  13. ncbi request reprint Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms
    José García-Martínez
    Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, Burjassot, Spain
    Mol Cell 15:303-13. 2004
    ..These results indicate that, although TR is the main determinant of mRNA abundance in yeast, modulation of mRNA stability is a key factor for gene regulation...
  14. pmc A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding
    Ignacio Bermúdez
    Instituto de Biologia Molecular de Barcelona CSIC, Barcelona, Laboratorio de Chips de DNA SCSIE Universitat de València, Burjassot, Spain
    Nucleic Acids Res 38:e182. 2010
    ..Genome-wide analysis of psoralen-DNA PB can be, therefore, a useful approach to uncover a trait of the chromosome architecture not amenable to other techniques...
  15. pmc Chimeric genomes of natural hybrids of Saccharomyces cerevisiae and Saccharomyces kudriavzevii
    Carmela Belloch
    Instituto de Agroquimica y Tecnologia de los Alimentos, IATA CSIC, P O Box 73, E 46100 Burjassot, Spain
    Appl Environ Microbiol 75:2534-44. 2009
    ..As a result of the selective processes acting during fermentation, hybrid genomes maintained the S. cerevisiae genome but reduced the S. kudriavzevii fraction...
  16. ncbi request reprint Study of the first hours of microvinification by the use of osmotic stress-response genes as probes
    Roberto Perez-Torrado
    Departament de Bioquimica i Biologia Molecular, Facultat de Ciencies Biologiques, Universitat de Valencia, Burjassot, Spain
    Syst Appl Microbiol 25:153-61. 2002
    ..These results point out the importance of the control of these parameters and the yeast molecular response during the first hours of vinification for an accurate winemaking process...
  17. ncbi request reprint Arginase activity is a useful marker of nitrogen limitation during alcoholic fermentations
    Purificación Carrasco
    Department de Bioquimica i Biologia Molecular, Facultat de Ciencies Biologiques, Universitat de Valencia, Spain
    Syst Appl Microbiol 26:471-9. 2003
    ..The results suggest that ethanol produced during vinification or exogenously added up to 8% (v/v) concentration does not cause nitrogen starvation under the conditions tested because arginase activity is not increased...
  18. pmc Topoisomerase II regulates yeast genes with singular chromatin architectures
    Christoforos Nikolaou
    Molecular Biology Institute of Barcelona, CSIC, 08028 Barcelona, Spain, Department of Biology, University of Crete, 71409 Heraklion, Greece, Department of Genetics and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain, Centre for Genomic Regulation CRG, 08003 Barcelona, Spain and Department of Biochemistry and Molecular Biology and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain
    Nucleic Acids Res 41:9243-56. 2013
    ..These findings indicate that yeast topo II operates on singular chromatin architectures to activate or repress DNA transcription and that this activity produces functional responses to ensure chromatin stability. ..
  19. pmc Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress
    Elena Garre
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biológicas Universitat de València, Valencia, Spain
    PLoS ONE 8:e61240. 2013
    ..Altogether, our results indicate that the degradation of yeast RP unspliced transcripts by NMD increases during osmotic stress, and suggest that this might be another mechanism to control RP synthesis during the stress response...
  20. ncbi request reprint A genomic study of the inter-ORF distances in Saccharomyces cerevisiae
    Vicent Pelechano
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, C Dr Moliner 50, E46100 Burjassot, Spain
    Yeast 23:689-99. 2006
    ....
  21. ncbi request reprint Yeast HAT1 and HAT2 deletions have different life-span and transcriptome phenotypes
    Lorena E Rosaleny
    Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, Dr Moliner 50, E46100 Burjassot, Spain
    FEBS Lett 579:4063-8. 2005
    ..The hat1hat2 double mutant shows a transcriptional phenotype similar to that of the hat1 mutant but strongly enhanced. These results indicate that Hat2p could have additional functions in the cell to those of Hat1p...
  22. pmc Specific and global regulation of mRNA stability during osmotic stress in Saccharomyces cerevisiae
    Lorena Romero-Santacreu
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, E 46100 Burjassot, Spain
    RNA 15:1110-20. 2009
    ..Our results indicate that regulation of mRNA turnover contributes to coordinate gene expression upon osmotic stress, and that there are both specific and global controls of mRNA stability depending on the strength of the osmotic stress...
  23. doi request reprint External conditions inversely change the RNA polymerase II elongation rate and density in yeast
    Ana Miguel
    Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biologicas, Universitat de Valencia, C Dr Moliner 50, E46100 Burjassot, Spain
    Biochim Biophys Acta 1829:1248-55. 2013
    ..Moreover, we discovered that yeast cells control the transcription initiation rate by changing the total amount of available RNA pol II...
  24. pmc Common gene expression strategies revealed by genome-wide analysis in yeast
    José García-Martínez
    Sección de Chips de DNA SCSIE, Universitat de Valencia, Dr Moliner 50, E 46100, Burjassot, Spain
    Genome Biol 8:R222. 2007
    ..However, because mRNA is an intermediate step and the amounts of both mRNA and protein are controlled by their synthesis and degradation rates, the desired amount of protein can be achieved following different strategies...
  25. doi request reprint Genomic-wide methods to evaluate transcription rates in yeast
    José García-Martínez
    Facultad de Ciencias Biologicas, Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, Burjassot, Spain
    Methods Mol Biol 734:25-44. 2011
    ..These techniques allow the discrimination of the relative importance of TR and DR in gene regulation for the first time in a eukaryote...
  26. ncbi request reprint Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6
    Susana Rodriguez-Navarro
    Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, C Dr Moliner 50, E 46100, Burjassot, Spain
    Yeast 19:1261-76. 2002
    ..Whereas copy 1 is required for conditions in which B(6) is essential for growth, copies 2 and 3 seem more related with B(1) biosynthesis during the exponential phase...
  27. doi request reprint There is a steady-state transcriptome in exponentially growing yeast cells
    Vicent Pelechano
    Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universitat de Valencia, C Dr Moliner 50, 46100 Burjassot, Spain
    Yeast 27:413-22. 2010
    ..With this kinetic approach, we were also able to determine the relative influence of the transcription rate and the mRNA stability changes for the mRNA variation for those genes that deviate from the steady state...
  28. ncbi request reprint What do you mean by transcription rate?: the conceptual difference between nascent transcription rate and mRNA synthesis rate is essential for the proper understanding of transcriptomic analyses
    José E Pérez-Ortín
    Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, Burjassot, Spain
    Bioessays 35:1056-62. 2013
    ....
  29. ncbi request reprint SRC1: an intron-containing yeast gene involved in sister chromatid segregation
    Susana Rodriguez-Navarro
    Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, C Dr Moliner 50, E 46100 Burjassot, Spain
    Yeast 19:43-54. 2002
    ..Deletion of the gene induces a shortening of the anaphase and aggravates the phenotype of scc1 and esp1 conditional mutants, which suggests a direct role of the protein in sister chromatid separation...
  30. ncbi request reprint The transcriptional inhibitor thiolutin blocks mRNA degradation in yeast
    Vicent Pelechano
    Departamento de Bioquimica y Biologia Molecular, Universitat de Valencia, C Dr Moliner 50, E46100 Burjassot, Spain
    Yeast 25:85-92. 2008
    ..Moreover, the thiolutin-dependent inhibition of mRNA degradation has variable effects on different functional groups of genes, suggesting that they use various degradation pathways for their mRNAs...
  31. pmc The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes
    Lorena E Rosaleny
    Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, Valencia, Spain
    Genome Biol 8:R119. 2007
    ..This study is focused on the genome-wide binding of Saccharomyces cerevisiae histone acetyltransferases that are specific for Lys14 of histone H3...
  32. doi request reprint mRNAStab--a web application for mRNA stability analysis
    Andrei Alic
    Department of Informatics and Department of Biochemistry and Molecular Biology, Universitat de Valencia, 46100 Burjassot, Spain
    Bioinformatics 29:813-4. 2013
    ..It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments...