The role of Chd1 chromatin remodelers in the repression of pervasive transcription and dissecting the crosstalk between pervasive transcription, nucleosome positioning and turnover.

• Applicant: Dr. Tamás Fischer
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry ; Bioinformatics and Theoretical Biology ; Cell Biology
• Term: from 2015 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 284266649

The eukaryotic chromatin structure compacts and protects the genome but also limits the accessibility of the underlying DNA. Chromatin modifying activities can open the chromatin and provide regulated access to specific genomic loci. Chromatin characteristics, such as position, occupancy and turnover-rate of nucleosomes, establish an elaborate genomic indexing mechanism, which is responsible for defining functional units in the genome. Defects in this process lead to increased transcription outside of genetically defined transcription units, toxic accumulation of non-coding transcripts and genomic instability. However, how genomic indexing mechanisms accurately define transcription units and their transcripts is one of the fundamental questions in chromatin biology. The aims of this proposal are: (i) to understand the relationship between nucleosome position, turnover and repression of pervasive transcription; and (ii) to investigate the mechanism by which Chd1 maintains nucleosome arrays in gene coding regions with uniform, species-specific nucleosome distance. We will use various Schizosaccharomyces pombe (S. pombe) mutants that show increased cryptic promoter activity and determine the chromatin characteristics that are critical for repressing transcription initiation outside of the promoter regions. We plan to generate various Chd1 deletion and point mutants to dissect the crosstalk between nucleosome positioning, turnover and pervasive transcription and to further understand the role of Chd1 in these processes. Since the length of the linker DNA between nucleosomes varies widely between species, we will compare nucleosome arrays generated by Chd1-type enzymes from S.pombe (typical linker DNA length, 6 bp), Chaetomium thermophilum (typical linker DNA length, 26 bp) and various chimera proteins and test their effect on pervasive transcription and higher order chromatin structure. These studies will significantly increase our understanding of the eukaryotic genome-organization and the role of the chromatin in the definition of functional units in the genome. Disturbing this highly conserved structure leads to increased pervasive transcription activity and to genomic instability, which is a major cause of cancer development and aging. Increased understanding of the molecular mechanisms behind these processes may have important long-term therapeutic implications.

• DFG Programme: Research Grants