LABORATORY
OF
DNA CHIPS
 
 
 
 

Introduction

Personnel and contact addresses

Laboratory Equipment

Products and services

Publications and experimental data

Interesting links
 
 
 
 

 
 

Introduction

The advances in the sequencing projects of different genomes (completed for several organisms) has revitalized exploration in biological research. As a consequence of the knowledge of the genome sequences for different organisms, it has been inherent, among other aspects, the functional analysis of these genomes. DNA arrays provide a simple and natural vehicle for exploring the genome in a way that is both systematic and comprehensive, since that technique allows researchers to perform genome-scale experiments. According to the solid support used and the spotting density, different modalities of arrays can be distinguished. Here, we only will mention two modalities, such as Macroarrays  (spotting at low density on nylon membranes) and Microarrays (high spotting density on glass slides). This technology promises to monitor the whole genome on a simgle chip so that researchers can have a better picture of the interactions among thousands of genes simultaneously.

In our lab, integrated in the  Central Services for Research Support of the University of Valencia, we are developping the procedures to manufacture DNA macroarrays, spotting gene-specific PCR products on nylon membranes at a density of 75 samples/cm². DNA microarrays on glass slides, are also available. In addition  the commercialization of the yeast Chip (covering the whole genome), the lab also offers a spotting service, designing the chip according to the user's requirements. Besides the manufacturing of the chips, it will be also possible to analyze them, since we have the appropiate software.

In addition to the manufacturing the chips, a data base on yeast DNA Chips experiments will be constructed. This data base will contain all the possible data on transcription experimants at different conditions, and will be accessible on-line from this WEB page. This data base will be integrated in the CYGD (Comprehensive Yeast Genome Database) MIPS database.
 
 

 

Address:

Differential expression of wine yeast T73 vs. laboratory strain MYC730

      Hauser et al. Comp. Funct. Genom. 2:69-79 (2001) 

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  DNA chips for yeast biotechnology. The case of wine yeasts.
         Pérez-Ortín, J.E.; García-Martínez, J. and Alberola, T.  J. Biotech. 98:227-241 (2002) 
 

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  Structural characterization of chromosome I size variants from a natural yeast strain
        Carro, D.; García-Martínez, J.; Pérez-Ortín, J.E. and Piña, B. Yeast 20:171-183 (2003) 

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   Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery
Rodríguez-Navarro, et al. Cell 116:75-86 (2004) 
 

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  Saccharomyces cerevisiae glutaredoxin 5-deficient cells subjected to constitutive oxidizing conditions are affected in the expression of specific sets of genes

  Bellí, et al. J. Biol. Chem.  279:12386-12395  (2004) 
 
 

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  Genomic Run-On evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms

  García-Martínez, J; Aranda, A. and Pérez-Ortín, J.E.  Mol. Cell.  15:303-313  (2004) 

            mRNA data    TR data mRNA stability
 

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A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses

  Alberola, T.M; García-Martínez, J; Antúnez, O; Viladevall, L; Barceló, A; Ariño, J. and Pérez-Ortín, J.E.  Int. Microbiology 7:199-206  (2004) 
 

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  Yeast HAT1 and HAT2 deletions have different life-span and transcriptome phenotypes

  Rosaleny, L.E; Antúnez, O; Ruiz-Garcia, A.B; Pérez-Ortín, J.E. Tordera, V.  FEBS Letters 579:4063-4068  (2005) 

  The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes

  Rosaleny, L.E; Ruiz-Garcia, A.B; García-Martínez, J; Pérez-Ortín, J.E. Tordera, V.  Genome Biology 8: R119 (2007) 
 

                - elp3-ha
                - sas2-ha
                - sas3-ha
                - nut1-ha
                - hpa2-ha
                - gcn5-myc
                - RNApol III
                - k14h3-vs-h3ct
                - Dgcn5-k14h3
                - Dsas3-k14h3
 

  Specific Defects in Different Transcription Complexes Compensate for the Requirement of the Negative Cofactor 2 Repressor in Saccharomyces cerevisiae

       Lorena Peiró-Chova and Francisco Estruch. Genetics 176: 125-138 (2007) 

                 - DYDR1 vs wt
                - wt+rpb2t vs wt
                - DYDR1+rpb2t vs wt
                - DYDR1+rpb2t vsDYDR1
 

  RSC14-controlled expression of MNN6, MNN4 and MNN1 regulates mannosylphosphorylation of Saccharomyces cerevisiae cell wall mannoproteins

     Raúl Conde, Rosario Cueva and Germán Larriba. FEMS Yeast Research 7: 1248-1255  (2007)
 
 

  Genomics and transcription kinetics in yeast

     José E. Pérez-Ortín, Paula M. Alepuz and Joaquín Moreno. Trends in Genetics 23:250-257  (2007)
 

  Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation

Mendes-Ferreira, A; del Olmo, M; García-Martínez, J; Jiménez-Martí, E; Mendes-Faia, A; Pérez-Ortín, J.E. and Leao, C. Applied and Environmental Microbiology 73:3049-3060  (2007)
 

   Saccharomyces cerevisiae signature genes for predicting nitrogen deficiency during alcoholic fermentation

Mendes-Ferreira, A; del Olmo, M; García-Martínez, J; Jiménez-Martí, E; Leao, C; Mendes-Faia, A and Pérez-Ortín, J.E. Applied and Environmental Microbiology 73:5363-5369  (2007)

  Common gene expression estrategies revealed by genome-wide analysis in yeast

     García-Martinez, J; González-Candelas, F. and Pérez-Ortín, JE. Genome Biology  8:R222  (2007) 
 

  The transcriptional inhibitor thiolutine blocks mRNA degradation in yeast

   Pelechano, V. and Pérez-Ortín, JE. Yeast  25: 85-92  (2008) 
 

Genomics of mRNA turnover

  J.E. Pérez-Ortín. Briefings in functinal Genomics and Proteomics  6(4): 284-291  (2008) 
 
 

   Production of a cecropin A in transgenic rice plants has an impact on host gene expression

     Campo, S; Manrique, S; García-Martínez, J. and San Segundo, B. Plant Biotechnology Journal 6: 585-608 (2008) 
 
 

   Mitochondrial inheritance and fermentative: oxidative balanc in hybrids between Saccharomyces cerevisiae and Saccharomyces uvarum

    Solieri, L; Antúnez, O; Pérez-Ortín, JE; Barrio, E. and Giudici, P. Yeast  25: 485-500 (2008) 
 
 

   Comprehensive transcriptional analysis of the oxidative response in yeast

    Molina-Navarro, M.M; Castells-Roca, L; Bellí, G; García-Martínez, J; Marín-Navarro, J; Moreno, J; Pérez-Ortín, J.E. and Herrero, E. Journal of Biological Chemistry 283: 17918-17918 (2008) 
 

  The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression

  Grund, S.E; Fischer, T; Cabal, G.G; Antúnez, O; Pérez-Ortín, J.E. and Hurt, E. Journal of Cell Biology  (doi 10.1083 jcb. 200803098) (2008) 
 

                      Yeast databases:

SGD

YPD

CYGD (MIPS)

ExpressDB

Genome-Wide Expresion Page

Yeast Cell Cycle Analysis Project

Transcriptional Program of Sporulation in Budding Yeast

mRNA Abundance Home Page

          Yeast Microarray Global Viewer (yMGV)
 

Other links: