GENERAL GENOMICS SERVICE - GENE EXPRESSION UNIT

Introduction

One of the most surprising and incredible phenomena in biology is the accuracy with which the correct expression is coordinated for thousands of genes from an organism: each gene must be expressed at a suitable moment in time and place to ensure proper cellular function. In terms of establishing the function of the genes, knowing when, where and how they are expressed is essential for understanding the activity and biological role of the proteins encoded by these genes. Furthermore, changes in gene expression patterns may provide indications about regulating mechanisms and also cellular functions and metabolic routes. On the other hand, awareness of the regulation of the gene expression and gene interactions which are formed in each cellular type for full knowledge about the molecular causes of diverse complex diseases such as cancer, neuro-degenerative diseases and ageing processes.  Knowledge about the molecular causes of such pathologies would entail the development of new methods of diagnosis, and new therapeutic products used for treatment. Functional genomics and, specifically, microarray technology, enables the genes associated with physiological and pathological processes to be identified. Information deriving from such identification enables new early research systems to be developed and the genetic predisposition towards being affected by a disease to be assessed, as well as enabling new drugs to be developed that are able to combat illnesses which are difficult to cure at present. 

Large-scale gene expression analysis via the use of high-density microarray technology using oligonucleotides or additional DNAs enables biological problems to be tackled from a global standpoint, and has brought about a major revolution in the study of normal and pathological gene regulation in areas such as human, animal, plant and microbial biology.

Although the most important application of microarrays involves monitoring global gene expression,  they are also used in the study of gene regulation by analysing the joining of proteins to promoter sequences of genome genes as a whole (ChIP-chip microarrays), and in the study of delection or expansion of genomic regions (aCGH microarrays) - a very common type of alteration in cancer.
The Gene Expression Unit of the Genomics and Proteomics Service at the University of the Basque Country, UPV/EHU, has been set up in order to provide full back-up on both an experimental and intellectual level to researchers belonging to the Basque Network of Science, Technology and Innovation, to biocompanies from the milieu, and to public and private institutions throughout Spain and overseas, in activities related to the study of genes and genomes. To this end, it has qualified personnel at its disposal together with state-of-the-art, high-performance equipment and a recently-created laboratory that has been designed in accordance with the recommendations of laboratory good practices.

The Gene Expression Unit offers the following systems for comparative analysis of gene expression, in addition to other applications: 

  • Quantitative or real-time PCR, using the 7900HT Fast Real Time PCR system made by Applied Biosystems. Measurement of the gene expression using real-time or quantitative PCR (qPCR) is based on the detection of fluorescence by a fluorochrome reporter, whose signal increases proportionally to the amount of product generated in each PCR cycle. This technique permits more accurate quantitative analyses which are sensitive to nucleic acids. Two types of chemistry are used to detect the PCR product: specific fluorescent colouring for SYBR Green double-stranded DNA, or specific fluorescent probes known as TaqMan.
  • Microarray Platform made by Agilent Technologies, one of the most advanced microarray systems providing a high quality and very reproducible methodology. Agilent microarrays are made up of specific 60-mer oligonucleotides arranged on a matrix with high sensitivity, which enables low amounts of initial RNA to be used. Agilent at present offers a series of microarrays that haven been pre-designed for applications such as monitoring gene expression, ChIP-chip or CGH (aCGH) arrays, although it also enables tailor-made microarrays to be designed with the probes chosen by the customer for specific studies in the field being developed by their research.
  • RNA quality control analysis using the Agilent 2100 Bioanalyzer.