The role of Chd1 chromatin remodelers in the repression of pervasive transcription and dissecting the crosstalk between pervasive transcription, nucleosome positioning and turnover.
Biochemistry
Bioinformatics and Theoretical Biology
Cell Biology
Final Report Abstract
Objectives: • To understand the relationship between nucleosome position, turnover and repression of pervasive transcription in gene coding regions. • To investigate the mechanism by which Chd1 maintains nucleosome arrays in gene coding regions with uniform, species-specific nucleosome distances. Major Outcomes: • Our results strongly suggest that the presence of high-turnover nucleosomes is the minimum requirement to allow transcription initiation from cryptic promoter sequences. • We established a new highly sensitive and reproducible genome-wide nucleosome turnover assay, using ChIP-exo technology to allow the comparison of nucleosome turnover between mutants. • We were able to determine the effect of various histone modifications/chromatin remodelling enzymes on nucleosome turnover: We showed that several chromatin modifications that were previously suggested to affect nucleosome turnover, did not significantly change nucleosome turnover. Increases in nucleosome turnover were observed in strains lacking the Chd1 chromatin remodellers, Pob3 (member of the FACT complex) and Alp13 (member of Rpd3S HDAC complex). The level of nucleosome turnover correlates directly with the level of histone acetylation. Our study into the minimum requirement for transcription initiation led us to pursue some unplanned experiments. We found that double-strand breaks (DSBs) can also initiate pervasive transcription and these transcripts form hybrids with their template DNA strand. These RNA-DNA hybrids around the DSB have to be removed by RNase H enzymes to efficiently repair the DSB by the Homologous recombination (HR)-mediated DNA repair pathway.
Publications
- Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair, Cell 167 (4), 1001-1013 (2016)
Ohle, C., Tesorero, R., Schermann, G., Dobrev, N., Sinning, I., Fischer, T.
(See online at https://doi.org/10.1016/j.cell.2016.10.001)
