No one knows why we age, but it is clear that our ageing health and even our lifespan are profoundly affected by our environment. We study the molecular mechanisms of ageing, how the environment determines our metabolic state, how responses to the environment affect our genome and epigenome, and how all of these impact the ageing process.
We aim to discover underlying drivers of ageing health, and to determine how these could be moderated by our environment and our diet. Epigenetic and genetic resilience are clearly critical for maintaining health through life, though we do not understand why, and we are researching how changes in metabolite levels caused by environmental conditions affect the activity of epigenetic modifying factors and DNA processing enzymes.
The ability to adapt to changing environments is of critical for pathogens, and we have a major research programme on the mechanisms by which pathogens acquire beneficial mutations - beneficial for that pathogen that is. Unexpectedly, we have linked adaptation in fungal pathogens to the same mechanisms that cause ageing, suggesting that fungi have evolved to use to their benefit the very processes that drive irreversible decay in us.
The germinal center (GC) reaction drives the production of high-affinity antibodies by iterative cycles of B cell somatic hypermutation, selection, and proliferation. How GC B cells undergo rapid cell division while maintaining genome stability is poorly understood. Here, we show that the RNA binding proteins ZFP36L1 and ZFP36L2 act downstream of antigen sensing and protect GC B cells from replication stress by controlling a cell cycle-related posttranscriptional regulon. They safeguard the successful completion of mitosis by balancing CDK1 and p21-mediated regulation of cell-cycle progression. In their absence, GC B cells are prone to arrest in the G-M phase and die by apoptosis, resulting in curtailed GC responses. DNA replication forks stalled at active replication initiation zones, causing replication stress and increased activity of the ATR-CHK1 DNA damage response. Thus, RNA binding proteins guide posttranscriptional gene regulation and maintain a functional G-M checkpoint in GC B cells.
Replication fork collision with a DNA nick can generate a one-ended break, fostering genomic instability. The opposing fork's collision with the nick could form a second DNA end, enabling conservative repair by homologous recombination (HR). To study mechanisms of nickase-induced HR, we developed the Flp recombinase "step arrest" nickase in mammalian cells. A Flp-nick induces two-ended, BRCA2/RAD51-dependent short tract gene conversion (STGC), BRCA2/RAD51-independent long tract gene conversion, and discoordinated two-ended invasions. HR pathways induced by a replication-independent break and the Flp-nickase differ in their dependence on BRCA1, MRE11, and CtIP. To determine the origin of the second DNA end during Flp-nickase-induced STGC, we blocked the opposing fork using a Tus/Ter replication fork barrier (RFB). Flp-nickase-induced STGC remained robust and two ended. Thus, a single replication fork's collision with a Flp-nick triggers two-ended HR, possibly reflecting replicative bypass of lagging strand nicks. This response may limit genomic instability during replication of nicked DNA.
The fork protection complex (FPC), composed of Mrc1, Tof1, and Csm3, supports rapid and stable DNA replication. Here, we show that FPC activity also introduces DNA damage by increasing DNA topological stress during replication. Mrc1 action increases DNA topological stress during plasmid replication, while Mrc1 or Tof1 activity causes replication stress and DNA damage within topologically constrained regions. We show that the recruitment of Top1 to the fork by Tof1 suppresses the DNA damage generated in these loci. While FPC activity introduces some DNA damage due to increased topological stress, the FPC is also necessary to prevent DNA damage in long replicons across the genome, indicating that the FPC is required for complete and faithful genome duplication. We conclude that FPC regulation must balance ensuring full genome duplication through rapid replication with minimizing the consequential DNA topological stress-induced DNA damage caused by rapid replication through constrained regions.
Re-engineering of acetyl coenzyme A metabolism prevents senescence in budding yeast Hanane Hadj-Moussa, Megan Ulusan, Dorottya Horkai, Mohammed Kamran Afzal Mirza, Jonathan Houseley
TrAEL-seq captures DNA replication dynamics in mammalian cells Neesha Kara, Laura Biggins, Vera Grinkevich, Alex Whale, Paola Garran-Garcia, Jhanavi Srinivasan, Peter J. Rugg-Gunn, Simon Andrews, Aled Parry, Helen M. R. Robinson, Jonathan Houseley
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