Review
Crosstalk between ubiquitin and other post-translational modifications on chromatin during double-strand break repair

https://doi.org/10.1016/j.tcb.2014.01.005Get rights and content

Highlights

  • Ubiquitination is central to DNA double-strand break (DSB) signaling.

  • Other modifications, such as methylation, crosstalk with ubiquitination on chromatin.

  • Effector protein recruitment depends on coordination between specific modifications.

The cellular response to DNA double-stranded breaks (DSBs) involves a conserved mechanism of recruitment and activation of numerous proteins involved in this pathway. The events that trigger this response in mammalian cells involve several post-translational modifications, but the role of non-proteasomal ubiquitin signaling is particularly central to this pathway. Recent work has demonstrated that ubiquitination does not act alone, but in concert with other post-translational modifications, including phosphorylation, methylation, acetylation, ADP-ribosylation, and other ubiquitin-like modifiers, particularly SUMOylation. We review novel and exciting crosstalk mechanisms between ubiquitination and other post-translational modifications, many of which work synergistically with each other to activate signaling events and help recruit important DNA damage effector proteins, particularly BRCA1 (breast cancer 1, early onset) and 53BP1 (tumor protein p53 binding protein 1), to sites of DNA damage.

Section snippets

The DSB response in the chromatin context

A DSB in DNA represents a difficult problem for any cell, and its proper repair is important for cell survival and the prevention of oncogenic translocations. In eukaryotes, an elaborate signaling pathway takes place on chromatin near the break site that coordinates ordered recruitment of specific factors, promotes DNA repair and cell cycle arrest. This response to DSBs (herein referred to as the DSB response) relies heavily on post-translational modifications of both chromatin components

Ubiquitination and SUMOylation

Similarly to ubiquitination, SUMOylation is catalyzed by a cascade of enzymes initiated by E1 SUMO-activating enzymes (SAE1 and SAE2), a single E2 conjugating enzyme (UBC9, ubiquitin-conjugating enzyme E2I), and various E3 SUMO ligases, which are considered to be important for target selection [16]. Established examples of SUMOylation regulating ubiquitination pathways have been known for many years [17], and indirect evidence suggested a role for SUMOylation in the DSB response 18, 19.

Ubiquitination and acetylation

Histone acetylation plays an important role in the regulation of chromatin structure [30], and therefore it is not surprising that specific histone acetyltransferases (HATs) play key roles in the DSB response. One major HAT, TIP60 (Tat interactive protein 60 kD; also known as lysine acetyltransferase 5, KAT5), was originally found to be part of a multimeric complex, and this seminal study demonstrated a role for TIP60 in DNA repair [31]. The activity of TIP60 as a regulator of chromatin

Ubiquitination and phosphorylation

As mentioned in the previous section, acetylation promotes RNF8 recruitment by activating the ATM kinase, which suggests crosstalk between ubiquitination and phosphorylation events during the DSB response. Not surprisingly, other crosstalk mechanisms between ubiquitination and phosphorylation also exist. Phosphorylation of MDC1 by these kinases promotes the recruitment of RNF8, which causes a feedback loop that promotes further ATM activation via RNF8 and another DSB response-associated E3

Ubiquitination and methylation

Although histone methylation is canonically associated with transcriptional regulation, early studies revealed an evolutionarily conserved role for histone H4K20 methylation in recruiting 53BP1 to DNA damage sites [44]. 53BP1 binds to this methylation mark via its tandem Tudor domains [45]. Although there are conflicting reports on which histone methyltransferase (HMTase) is primarily responsible for this modification 45, 46, 47, it is likely that many distinct HMTases contribute to H4K20

Ubiquitination and ADP-ribosylation

It is accepted that ADP-ribosylation plays a role in the DSB response, among many other signaling pathways [54]. Activation of poly(ADP-ribose) polymerase (PARP) enzymes is an early event in the DSB response [54], and recent work has demonstrated that ADP-ribosylation promotes the recruitment of multiple chromatin-modifying enzymes to damage sites 55, 56, 57. The most prominent of these is the CHD4/NuRD (chromodomain helicase DNA binding protein 4/nucleosome remodeling deacetylase) complex,

Concluding remarks

The molecular mechanisms involved in protein recruitment and activation during the DSB response are noticeably complex. The crosstalk mechanisms described here reflect only a small portion of this complexity, and crosstalk mechanisms that involve other modifications most definitely exist. For example, recent work has suggested that protein neddylation is also important for promoting ubiquitination events at sites of damage [63]. This complexity and various crosstalk mechanisms likely arose due

Acknowledgments

We wish to thank Barry Sleckman and Andrea Bredemeyer for critical reading and feedback on this manuscript. We also wish to thank the numerous scientists who have contributed significantly to our understanding of ubiquitination and its role in the DNA damage response, and we apologize that we could not cite all pertinent papers due to space limitations. This work was supported by the National Institutes of Health (NIH) National Cancer Institute (K08 CA158133), the American Cancer Society

References (73)

  • J.H. Lee

    53BP1 promotes ATM activity through direct interactions with the MRN complex

    EMBO J.

    (2010)
  • S.L. Sanders

    Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage

    Cell

    (2004)
  • M.V. Botuyan

    Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair

    Cell

    (2006)
  • H. van Attikum et al.

    Crosstalk between histone modifications during the DNA damage response

    Trends Cell Biol.

    (2009)
  • S.F. Bunting

    53BP1 inhibits homologous recombination in Brca1-deficient cells by blocking resection of DNA breaks

    Cell

    (2010)
  • Q. Yan

    BBAP monoubiquitylates histone H4 at lysine 91 and selectively modulates the DNA damage response

    Mol. Cell

    (2009)
  • T. Kalisch

    New readers and interpretations of poly(ADP-ribosyl)ation

    Trends Biochem. Sci.

    (2012)
  • M. Li et al.

    Function of BRCA1 in the DNA damage response is mediated by ADP-ribosylation

    Cancer Cell

    (2013)
  • T. Ma

    RNF111-dependent neddylation activates DNA damage-induced ubiquitination

    Mol. Cell

    (2013)
  • J.J. Sims et al.

    Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80

    Mol. Cell

    (2009)
  • S. Panier

    Tandem protein interaction modules organize the ubiquitin-dependent response to DNA double-strand breaks

    Mol. Cell

    (2012)
  • M. Stucki

    MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-stranded breaks

    Cell

    (2005)
  • K. Luger

    Crystal structure of the nucleosome core particle at 2.8 A resolution

    Nature

    (1997)
  • B.M. Sirbu et al.

    DNA damage response: three levels of DNA repair regulation

    Cold Spring Harb. Perspect. Biol.

    (2013)
  • S. Matsuoka

    ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage

    Science

    (2007)
  • A. Celeste

    Genomic instability in mice lacking histone H2AX

    Science

    (2002)
  • H.C. Reinhardt et al.

    Phospho-Ser/Thr-binding domains: navigating the cell cycle and DNA damage response

    Nat. Rev. Mol. Cell Biol.

    (2013)
  • N.K. Kolas

    Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase

    Science

    (2007)
  • M. Gatti

    A novel ubiquitin mark at the N-terminal tail of histone H2As targeted by RNF168 ubiquitin ligase

    Cell Cycle

    (2012)
  • M.S. Huen

    BRCA1 and its toolbox for the maintenance of genome integrity

    Nat. Rev. Mol. Cell Biol.

    (2010)
  • S. Jentsch et al.

    Control of nuclear activities by substrate-selective and protein-group SUMOylation

    Annu. Rev. Genet.

    (2013)
  • A.M. Sriramachandran et al.

    SUMO-targeted ubiquitin ligases

    Biochim. Biophys. Acta

    (2013)
  • X. Zhao et al.

    A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization

    Proc. Natl. Acad. Sci. U.S.A.

    (2005)
  • A.M. Mabb

    PIASy mediates NEMO sumoylation and NF-kappaB activation in response to genotoxic stress

    Nat. Cell Biol.

    (2006)
  • Y. Galanty

    Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks

    Nature

    (2009)
  • J.R. Morris

    The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress

    Nature

    (2009)
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