Novel roles of Neil DNA glycosylases in genome dynamics

Epigenetic marks are dynamic modifications on genomic DNA. Epigenetic regulation and DNA repair are fundamental biological processes important for development and health, as acknowledged by recent Nobel Prizes (2012, 2015). DNA glycosylases initiate repair of damaged DNA by removing modified DNA bases that can cause cell death, mutations and ultimately cancer. However, DNA glycosylases are also used in immunity and are required to actively remove epigenetic marks in DNA. Thus, DNA repair and epigenetics use of common proteins and are mechanistically linked. Although initially recognized for their role in mutation avoidance, we hypothesized that a major, if not the main, function of Neil DNA glycosylases and presumed aberrant oxidized DNA lies in their ability to regulate epigenetic marks in specific sequence contexts in genomic DNA. This is based on our unexpected findings that spontaneous mutation frequencies are not increased in mice models lacking Neil DNA glycosylases, but show distinct effects on gene expression in mouse organs, particularly in networks associated with neuro-inflammation, cognition and anxiety. Consistent with this, mouse models lacking Neil enzymes display distinct changes in cognition and anxiety, but do not spontaneously develop cancer. Thus DNA repair and epigenetics use common factors. This project have addressed how epigenetic marks and oxidized DNA bases processed by Neil DNA glycosylases cooperate to dynamically regulate mammalian gene expression, contributing to normal as well as dysfunctional cognitive and behavioral phenotypes and even neurodegeneration. Identifying the mechanistic links between epigenetics and oxidative DNA base modifications have uncovered important new layers of genome regulation, likely with impacts on human health. During the project, behavioral studies and ischemia studies for mouse models with catalytically inactive Neil DNA glycosylases have revealed new functions independent of catalytic activity. We have performed biochemical analyzes that define new substrates for Neil glycosylases important for cell function, including neuronal cells in brain.

Epigenetic regulation and DNA repair are fundamental biological processes that strongly influence human development and health. This project has determined how epigenetic marks and oxidized DNA bases cooperate to dynamically regulate mammalian gene expression and hence phenotype. The project has uncovered novel molecular mechanisms of genome regulation, thereby laying the foundation for (i) new diagnostic/research tools (i.e, new technology for single base resolution sequencing of oxidized bases), (ii) novel sequence signatures/motifs (including oxidized base modifications and epigenetic marks) and (iii) new drug targets.

Epigenetic regulation and DNA repair are fundamental biological processes important for development and health, as acknowledged by recent Nobel Prizes (2012, 2015). DNA glycosylases initiate base excision repair (BER) by eliminating modified bases that can cause cytotoxicity, mutations and ultimately cancer. However, DNA glycosylases are also used in innate and adaptive immunity and are required to actively remove epigenetic marks in DNA after oxidative modification of 5mC and 5hmC. Thus, DNA repair and epigenetics use of common proteins and are mechanistically linked. Although initially recognized for their role in mutation avoidance, we hypothesize that a major, if not the main, function of Neil DNA glycosylases and presumed “aberrant” oxidized pyrimidines lies in their ability to regulate epigenetic marks in specific sequence contexts. This is based on our unexpected findings that spontaneous mutation frequencies are not increased in Neil single, double or triple knockouts, whereas knockout of each of Neil1, 2 or 3 has distinct effects on gene expression in mouse organs, particularly in networks associated with neuro-inflammation, cognition and anxiety. Consistent with this, Neil knockout animals display distinct changes in cognition and anxiety, but do not spontaneously develop cancer. Thus DNA repair and epigenetics use common factors. This project will address how epigenetic marks and oxidized DNA bases processed by Neil DNA glycosylases cooperate to dynamically regulate mammalian gene expression, contributing to normal as well as dysfunctional cognitive and behavioral phenotypes and even neurodegeneration. Identifying the mechanistic links between epigenetics and oxidative DNA base modifications will uncover important new layers of genome regulation, likely with impacts on human health.