Open Access Research

Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling

Mariona Nadal-Ribelles1, Núria Conde1, Oscar Flores2, Juan González-Vallinas3, Eduardo Eyras34, Modesto Orozco2, Eulàlia de Nadal1* and Francesc Posas1*

Author Affiliations

1 Cell Signaling Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), E-08003 Barcelona, Spain

2 Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine, Baldiri i Reixac 10, 08028 Barcelona, Spain

3 Computational Genomics, Universitat Pompeu Fabra, Dr Aiguader 88, E08003 Barcelona, Spain

4 Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, E08010 Barcelona, Spain

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Genome Biology 2012, 13:R106  doi:10.1186/gb-2012-13-11-r106

Published: 18 November 2012

Abstract

Background

Cells are subjected to dramatic changes of gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription upon osmostress in yeast.

Results

Genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1 showed that stress induced major changes in RNA Pol II localization, with a shift toward stress-responsive genes relative to housekeeping genes. RNA Pol II relocalization required Hog1, which was also localized to stress-responsive loci. In addition to RNA Pol II-bound genes, Hog1 also localized to RNA polymerase III-bound genes, pointing to a wider role for Hog1 in transcriptional control than initially expected. Interestingly, an increasing association of Hog1 with stress-responsive genes was strongly correlated with chromatin remodeling and increased gene expression. Remarkably, MNase-Seq analysis showed that although chromatin structure was not significantly altered at a genome-wide level in response to stress, there was pronounced chromatin remodeling for those genes that displayed Hog1 association.

Conclusion

Hog1 serves to bypass the general down-regulation of gene expression that occurs in response to osmostress, and does so both by targeting RNA Pol II machinery and by inducing chromatin remodeling at stress-responsive loci.