Biology subjects

Wilkes, C. D.

Publications and source records attributed to Wilkes, C. D..

3 recordsLinked to original sources

bioRxiv2022

Functional interplay between Mediator and RSC chromatin remodeling complex controls nucleosome-depleted region maintenance at promoters

Chromatin organization is crucial for the transcriptional regulation in eukaryotes. Mediator is an essential and conserved coactivator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. Here, we provide evidence in the yeast Saccharomyces cerevisiae that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. We determined the role of Mediator-RSC interaction in their recruitment, nucleosome occupancy and transcription on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and TSS-associated +1 nucleosome stability. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.

genomics↗

bioRxiv2022

A Quantitative Modelling Approach for DNA Repair on a Population Scale

Despite intensive research of DNA repair after UV in eukaryotes, a framework to quantitatively describe the dynamics in vivo is still lacking. We developed a new data-driven approach to analyse CPD repair kinetics over time in Saccharomyces cerevisiae. In contrast to other studies that consider sequencing signals as an average behaviour, we introduce a hidden axis representing independent cells where loci can transition from damaged to repaired. This permits the application of the Kolmogorov-Johnson-Mehl-Avrami model to find a region-specific and continuous representation of the entire temporal process. We correlated the parameters via a k-nearest neighbour approach to a variety of genomic features, including transcription rate and nucleosome density. The clearest link was found for the gene size, which has been unreported for budding yeast to our knowledge. The framework hence allows a comprehensive analysis of nuclear processes on a population scale. Author SummaryAs DNA encodes our very identity, it has been subject to a plethora of studies over the last century. The advent of new technologies that permit rapid sequencing of large DNA and RNA samples opened doors to before unknown mechanisms and interactions on a genomic scale. This led to an in-depth analysis of several nuclear processes, including transcription of genes and lesion repair. However, the applied protocols do mostly not allow a high temporal resolution. Quite the contrary, the experiments yield often only some few data signals over several hours. Missing dynamics between time points are chiefly ignored, implicitly assuming that they straightforwardly transition from one to another. Here, we show that such an understanding can be flawed. We use the repair process of UV-induced DNA damage as an example to present a quantitative analysis framework that permits the representation of the entire temporal process with only three parameters. We subsequently describe how they can be linked to other heterogeneous data sets. Consequently, we evaluate a correlation to the whole kinetic process rather than to a single time point. Although the approach is exemplified using DNA repair, it can be readily applied to any other mechanism and sequencing data that represents a state transition between two states, such as damaged and repaired.

bioinformatics↗

bioRxiv2021

Genome-wide distribution of Rad26 and Rad1-Rad10 reveals their relationship with Mediator and RNA polymerase II

Transcription is coupled with DNA repair, especially within nucleotide excision repair (NER). Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and NER via a direct contact with Rad2/XPG endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/CSB and that of Rad1-Rad10/XPF-ERCC1, addressing the question on a potential interplay of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae. Our genome-wide analyses show that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially on highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we revealed that Rad1-Rad10 and Rad26 colocalize with Mediator on intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we showed that Mediator stabilization on core promoters lead to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy is less impacted by Mediator and follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results reveal the interplay between Rad1-Rad10, Rad26, Mediator and Pol II, modulated by the binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in Mediator relationships with Rad2, Rad1-Rad10 and Rad26. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair, relevant for human diseases including cancer and XP/CS syndromes.

genomics↗