The role of the chromatin remodelling complex INO80 for the regulation of canonical chromatin structure at stress induced genes.
Abstract
The role of the chromatin remodelling complex INO80 for the regulation of canonical chromatin structure at stress induced genes. A large proportion of chromosomal DNA in eukaryotic cells is bound to nucleosomes. Replication, repair and transcription all require opening of the DNA-Histone contacts. Several types of protein complexes are involved in chromatin modification and nucleosome positioning during these activities to ensure homeostasis of chromatin structure. The chromatin status plays a vital role in the maintenance of proper control of transcription patterns. This is also important for ageing and senescent cells of many organisms having aberrant transcription due to loss of function of chromatin remodeling factors. Here we propose to further investigate the function of the highly conserved ATP-dependent remodeling complex INO80 which is providing a link between chromatin remodeling and control of transcription. In Saccharomyces cerevisiae, transcription of a number of genes, among them many stress protective genes, is influenced by INO80. Our current data set is conforming to a model suggesting a specific requirement of INO80 for efficient positioning or re-assembly of nucleosomes of the open reading frame and the promoter. How is INO80 recruited to target sites? The recruitment to sites of action is the key to its true biochemical role but remains poorly understood. Therefore, we propose to investigate the role of INO80 to chromatin in three parallel approaches. This includes (i) the genome-wide study of the effect of INO80 action on transcription and nucleosome pattern, (ii) the identification of components interacting with chromatin and the Pol II transcription machinery, and (iii) the study of the opposing functions of nucleosome eviction and INO80 dependent replenishment. To this end we will extract from our genome wide expression and nucleosome data the nucleosome dynamics and the associated genomic sequence environment. We will investigate all subunits of INO80 for a recruitment function. We will then approach an analysis of the types of contacts between INO80 and promoter chromatin and also to RNA Pol II. The latter is based on the cooperation of the RNA PolII associated nucleosome chaperone Spt6 with INO80. Finally we will investigate the antagonism of INO80 to nucleosome depleting factors such as RSC or SWI/SNF to gain insight in the dynamics during the transcription cycle. The suggested analysis addresses basic mechanisms of chromatin remodeling and gene regulation. The model system opens the possibility to approach the mechanism and timing of these processes in a highly resolved and efficient way even on a genome wide scale. Spatial and temporal resolution of the interaction of these INO80 with chromatin and the other involved factors during initiation will help to characterize the sequence and interdependence of events at stress activated promoters.
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Project staff
Christoph Schüller
Priv.-Doz. Dr. Christoph Schüller
christoph.schueller@boku.ac.at
Tel: +43 1 47654-35071, 94488
Project Leader
01.07.2012 - 31.03.2015