Histone H2B mono-ubiquitylation maintains genomic integrity at stalled replication forks

Abstract

Histone modifications play an important role in regulating access to DNA for transcription, DNA repair and DNA replication. A central player in these events is the mono-ubiquitylation of histone H2B (H2Bub1), which has been shown to regulate nucleosome dynamics. Previously, it was shown that H2Bub1 was important for nucleosome assembly onto nascent DNA at active replication forks. In the absence of H2Bub1, incomplete chromatin structures resulted in several replication defects. Here, we report new evidence, which shows that loss of H2Bub1 contributes to genomic instability in yeast. Specifically, we demonstrate that H2Bub1-deficient yeast accumulate mutations at a high frequency under conditions of replicative stress. This phenotype is due to an aberrant DNA Damage Tolerance (DDT) response upon fork stalling. We show that H2Bub1 normally functions to promote error-free translesion synthesis (TLS) mediated by DNA polymerase eta (Polη). Without H2Bub1, DNA polymerase zeta (Polζ) is responsible for a highly mutagenic alternative mechanism. While H2Bub1 does not appear to regulate other DDT pathways, error-free DDT mechanisms are employed by H2Bub1-deficient cells as another means for survival. However, in these instances, the anti-recombinase, Srs2, is essential to prevent the accumulation of toxic HR intermediates that arise in an unconstrained chromatin environment.

E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae

“…Bre1 is a conserved E3 ubiquitin ligase containing a C3HC4 zinc-finger RING domain at its C-terminus, which forms a complex with Lge1 and associates with the E2 ubiquitin-conjugating enzyme Rad6 to mediate histone H2B monoubiquitination (H2Bub1) on lysine 123 (H2BK123) in Saccharomyces cerevisiae ( Hwang et al, 2003 ; Robzyk et al, 2000 ; Wood et al, 2003 ). H2Bub1 is one of the histone posttranslational modifications that has been implicated in diverse cellular functions, including: transcription regulation ( Fleming et al, 2008 ; Minsky et al, 2008 ; Pavri et al, 2006 ; Sansó et al, 2012 ) that is mediated through cycles of ubiquitination and deubiquitination ( Henry et al, 2003 ; Osley, 2006 ) and by cross-talk effects on histone H3 methylation on residues K4 and K79 ( Briggs et al, 2002 ; Dover et al, 2002 ; Nakanishi et al, 2009 ; Ng et al, 2002 ; Sun and Allis, 2002 ); DNA replication progression ( Trujillo and Osley, 2012 ); modulation of nucleosome dynamics ( Chandrasekharan et al, 2009 ; Fierz et al, 2011 ); DNA double-strand breaks (DSBs) repair ( Chernikova et al, 2010 ; Moyal et al, 2011 ; Nakamura et al, 2011 ; Northam and Trujillo, 2016 ); DSB in meiosis ( Yamashita et al, 2004 ); maintenance of functional, transcriptionally active centromeric chromatin in fission yeast ( Sadeghi et al, 2014 ); methylation of kinetochore protein Dam1 ( Latham et al, 2011 ); apoptosis ( Walter et al, 2010 ); and cell size control ( Hwang et al, 2003 ; Jorgensen et al, 2002 ).…”

The DNA repair protein SHPRH is a nucleosome-stimulated ATPase and a nucleosome-E3 ubiquitin ligase

“…For instance, different histone ubiquitination marks have been shown to promote different repair mechanisms such as homologous recombination or non-homologous end joining. Given the implications of H2B monoubiquitination in DNA damage bypass after UV damage or MMS treatment [71, 72], it remains to be established whether, in addition to PCNA ubiquitylation, histone ubiquitylation by SHPRH might also contribute to the choice between different arms of the DNA damage tolerance pathways. Likewise, it would be interesting to test whether, despite their lack of obvious histone binding domains, RAD5- or RAD16-related proteins including HLTF, the yeast proteins increased recombination centers 20 (IRC20/YLR247C), or as hypothesized previously by Yu et al, ubiquitin ligase for SUMO conjugates protein 1 (ULS1/role in silencing protein 1 (RIS1); [73]) can ubiquitinate nucleosomes directly, or once they are primed by monoubiquitination.…”

Lsm12 mediates Pol·q deubiquitination to help Saccharomyces cerevisiae resist oxidative stress

“…In the budding yeast Saccharomyces cerevisiae , there are three major strategies to maintain genome stability: template switch (TS) (7), homologous recombination (HR) (8), and TLS (9). TS is an error-free damage branch of the DNA damage tolerance mechanism, which is regulated by the polyubiquitination of proliferating cell nuclear antigen (PCNA) catalyzed by the Ubc13 and Mms2 enzymes (7,10,11). HR mainly repairs DNA double-strand breaks and is regulated by Srs2 and Rad51 (11).…”

“…TS is an error-free damage branch of the DNA damage tolerance mechanism, which is regulated by the polyubiquitination of proliferating cell nuclear antigen (PCNA) catalyzed by the Ubc13 and Mms2 enzymes (7,10,11). HR mainly repairs DNA double-strand breaks and is regulated by Srs2 and Rad51 (11). Srs2 is a DNA helicase that can bind with SIZ1 -mediated sumoylated PCNA to prevent HR, and Rad51 is a recombinase that promotes HR (12).…”