Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair

Abstract

Repairing DNA double-strand breaks is crucial for maintaining genome integrity, which occurs primarily through homologous recombination (HR) in S. cerevisiae. Nucleosomes, composed of DNA wrapped around a histone octamer, present a natural barrier to end-resection to initiate HR, but the impact on the downstream HR steps of homology search, DNA strand invasion and repair synthesis remain to be determined. Displacement loops (D-loops) play a pivotal role in HR, yet the influence of chromatin dynamics on D-loop metabolism remains unclear. Using the physical D-loop capture (DLC) and D-loop extension (DLE) assays to track HR intermediates, we employed genetic analysis to reveal that H2B mono-ubiquitylation (H2Bubi) affects multiple steps during HR repair. We infer that H2Bubi modulates chromatin structure, not only promoting histone degradation for nascent D-loop formation but also stabilizing extended D-loops through nucleosome assembly. Furthermore, H2Bubi regulates DNA resection via Rad9 recruitment to suppress a feedback control mechanism that dampens D-loop formation and extension at hyper-resected ends. Through physical and genetic assays to determine repair outcomes, we demonstrate that H2Bubi plays a crucial role in preventing break-induced replication and thus promoting genomic stability. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/612919v1_ufig1.gif" ALT="Figure 1"> View larger version (74K): org.highwire.dtl.DTLVardef@48b9edorg.highwire.dtl.DTLVardef@a6b23forg.highwire.dtl.DTLVardef@707dorg.highwire.dtl.DTLVardef@d93e58_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIH2Bubi is epistatic to H2A.Z and INO80 in promoting homology search and D-loop formation C_LIO_LIH2Bubi stabilizes extended D-loop C_LIO_LIExcessive resection counteracts D-loop formation and extension C_LIO_LIH2Bubi promotes crossover events and limits the frequency of break-induced replication outcomes in HR repair C_LI