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DNA Demethylation-Induced DNA Repair in Chromatin Regulation

Research Project
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01.10.2018
 - 30.09.2022

The concerted action of transcription factors, chromatin organizers, histone and DNA modifiers and DNA metabolic processes creates structural and functional dynamics in chromatin, facilitating the differentiation of stable gene expression programs that define cell identities. While this is accepted, insight into how the different layers of genome regulation co-operate has remained poor. The discovery of active DNA demethylation, which can occur through a process of 5mC oxidation by TET proteins and replacement of the oxidized 5mC by TDG-dependent base excision repair (BER), has added another piece to the puzzle. We contributed to and followed up on this discovery to delineate the mode of action of TET-TDG-BER-mediated DNA demethylation and to investigate its biological function. This revealed that certain genomic loci undergo continuous DNA repair-mediated demethylation, providing a conceptual framework to link DNA demethylation with nucleosomal dynamics. DNA repair processes inherently have dynamic properties as they entail opening, editing and re-synthesizing DNA, events that involve signaling to chromatin. Indeed, transcriptional activation and cellular reprogramming have been associated with the formation of DNA single strand-breaks (SSBs) and the engagement of BER proteins (XRCC1, PAPR1), consistent with DNA SSB formation and repair contributing to the establishment and/or maintenance of a permissive chromatin state. Prompted by such observations, we investigated the hypothesis that DNA demethylation operates to target DNA SSBs to genomic sites where epigenetic plasticity is to be established or maintained. This project is a refined approach to address the following hypothesis. TET-TDG-BER mediated DNA demethylation plays an active role in regulating chromatin accessibility at enhancers and gene promoters. Changes in chromatin accessibility are achieved (i) by modulation of linker histone H1 association, whereby DNA repair activity associated with DNA demethylation (NPM1, NPM3, PARP) plays an active role and facilitates the establishment of enhancer-promoter loops, and (ii) by changes in histone modification, facilitated by TET-TDG dependent modulation of MLL and PRC2 activities. Research towards the following objectives is pursued to address this hypothesis Objective 1: Deciphering the role of nucleophosmin in TET-TDG-dependent regulation of chromatin accessibility. Objective 2: Deciphering the role of TET-TDG dependent DNA demethylation in the regulation of MLL and PRC2 histone methyltransferase complexes.

Funding

DNA Demethylation-Induced DNA Repair in Chromatin Regulation

SNF Schweizerischer Nationalfonds, 10.2018-03.2023 (54)
PI : Schär, Primo Leo.

Members (1)

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Primo Leo Schär

Principal Investigator