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Open Access Highly Accessed Research article

Whole genome analysis of p38 SAPK-mediated gene expression upon stress

Isabel Ferreiro1, Manel Joaquin1, Abul Islam2, Gonzalo Gomez-Lopez3, Montserrat Barragan1, Luís Lombardía4, Orlando Domínguez5, David G Pisano3, Nuria Lopez-Bigas2, Angel R Nebreda6* and Francesc Posas1*

Author affiliations

1 Cell Signaling Unit, Universitat Pompeu Fabra (UPF) Dr aiguader 88, Barcelona 08003, Spain

2 Research Unit on Biomedical Informatics. Departament de Ciències Experimentals i de la Salut (DCEXS), Universitat Pompeu Fabra (UPF) Dr aiguader 88, Barcelona 08003, Spain

3 Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

4 Molecular Diagnostics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

5 Genomics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

6 Signalling and Cell Cycle Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, Madrid 28029, Spain

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Citation and License

BMC Genomics 2010, 11:144  doi:10.1186/1471-2164-11-144

Published: 1 March 2010

Abstract

Background

Cells have the ability to respond and adapt to environmental changes through activation of stress-activated protein kinases (SAPKs). Although p38 SAPK signalling is known to participate in the regulation of gene expression little is known on the molecular mechanisms used by this SAPK to regulate stress-responsive genes and the overall set of genes regulated by p38 in response to different stimuli.

Results

Here, we report a whole genome expression analyses on mouse embryonic fibroblasts (MEFs) treated with three different p38 SAPK activating-stimuli, namely osmostress, the cytokine TNFα and the protein synthesis inhibitor anisomycin. We have found that the activation kinetics of p38α SAPK in response to these insults is different and also leads to a complex gene pattern response specific for a given stress with a restricted set of overlapping genes. In addition, we have analysed the contribution of p38α the major p38 family member present in MEFs, to the overall stress-induced transcriptional response by using both a chemical inhibitor (SB203580) and p38α deficient (p38α-/-) MEFs. We show here that p38 SAPK dependency ranged between 60% and 88% depending on the treatments and that there is a very good overlap between the inhibitor treatment and the ko cells. Furthermore, we have found that the dependency of SAPK varies depending on the time the cells are subjected to osmostress.

Conclusions

Our genome-wide transcriptional analyses shows a selective response to specific stimuli and a restricted common response of up to 20% of the stress up-regulated early genes that involves an important set of transcription factors, which might be critical for either cell adaptation or preparation for continuous extra-cellular changes. Interestingly, up to 85% of the up-regulated genes are under the transcriptional control of p38 SAPK. Thus, activation of p38 SAPK is critical to elicit the early gene expression program required for cell adaptation to stress.