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The heterochromatic barrier to DNA double strand break repair: how to get the entry visa.

Goodarzi AA, Jeggo PA - Int J Mol Sci (2012)

Bottom Line: Over recent decades, a deep understanding of pathways that repair DNA double strand breaks (DSB) has been gained from biochemical, structural, biophysical and cellular studies.Chromatin is broadly divided into open, transcriptionally active, euchromatin (EC) and highly compacted, transcriptionally inert, heterochromatin (HC), although these represent extremes of a spectrum.Moreover, DSBs within HC (HC-DSBs) are rapidly relocalized to the EC-HC interface.

View Article: PubMed Central - PubMed

Affiliation: Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.

ABSTRACT
Over recent decades, a deep understanding of pathways that repair DNA double strand breaks (DSB) has been gained from biochemical, structural, biophysical and cellular studies. DNA non-homologous end-joining (NHEJ) and homologous recombination (HR) represent the two major DSB repair pathways, and both processes are now well understood. Recent work has demonstrated that the chromatin environment at a DSB significantly impacts upon DSB repair and that, moreover, dramatic modifications arise in the chromatin surrounding a DSB. Chromatin is broadly divided into open, transcriptionally active, euchromatin (EC) and highly compacted, transcriptionally inert, heterochromatin (HC), although these represent extremes of a spectrum. The HC superstructure restricts both DSB repair and damage response signaling. Moreover, DSBs within HC (HC-DSBs) are rapidly relocalized to the EC-HC interface. The damage response protein kinase, ataxia telangiectasia mutated (ATM), is required for HC-DSB repair but is dispensable for the relocalization of HC-DSBs. It has been proposed that ATM signaling enhances HC relaxation in the DSB vicinity and that this is a prerequisite for HC-DSB repair. Hence, ATM is essential for repair of HC-DSBs. Here, we discuss how HC impacts upon the response to DSBs and how ATM overcomes the barrier that HC poses to repair.

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Related in: MedlinePlus

Ataxia telangiectasia mutated (ATM)-dependent heterochromatic DSB repair. (1) DSBs elicit ATM activation and IRIF formation, however repair processes within heterochromatin are inhibited by the compacted nucleosome configuration produced by KAP-1 dependent CHD3 activity; (2) Active ATM phosphorylates KAP-1 at S824, which interferes with the SUMOylation-dependent retention of CHD3 in chromatin; (3) In the absence of CHD3, the chromatin surrounding the DSB site relaxes, allowing (3A) non-homologous end-joining or (3B) if cells are in G2-phase, DNA end resection and homologous recombination mediated repair of the DSB; (4) Once the DSB is rejoined, ATM signaling is deactivated. Heterochromatic nucleosomes re-compact once KAP-1 is dephosphorylated and CHD3 activity is again retained.
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f2-ijms-13-11844: Ataxia telangiectasia mutated (ATM)-dependent heterochromatic DSB repair. (1) DSBs elicit ATM activation and IRIF formation, however repair processes within heterochromatin are inhibited by the compacted nucleosome configuration produced by KAP-1 dependent CHD3 activity; (2) Active ATM phosphorylates KAP-1 at S824, which interferes with the SUMOylation-dependent retention of CHD3 in chromatin; (3) In the absence of CHD3, the chromatin surrounding the DSB site relaxes, allowing (3A) non-homologous end-joining or (3B) if cells are in G2-phase, DNA end resection and homologous recombination mediated repair of the DSB; (4) Once the DSB is rejoined, ATM signaling is deactivated. Heterochromatic nucleosomes re-compact once KAP-1 is dephosphorylated and CHD3 activity is again retained.

Mentions: Notwithstanding this limitation, there is compelling mechanistic evidence for how pKAP-1 foci formation leads to localized HC relaxation. The C-terminal region of KAP-1 encompasses several lysines that have been shown to undergo SUMOylation with SUMO1 (of which K554, K779, K804 are the most prominent), potentially via an auto-SUMOylation mechanism involving KAP-1’s N-terminal RING finger [53]. The S824 phosphorylation site of KAP-1 lies in a structurally-disordered region at the extreme C-terminal region. SUMOylation of KAP-1 is known to mediate interactions with the multi-subunit nucleosome remodeling and deacetylase (NuRD) complex as well as with the histone methyltransferase, SETDB1. The interaction between SUMOylated KAP-1 and NuRD occurs via the ATP-dependent chromatin remodeling subunit, CHD3 (specifically isoform 1, CHD3.1) [53,54]. Unlike the second isoform of CHD3 (CHD3.2), CHD3.1 contains a SUMO-interacting motif (SIM) at its extreme C-terminus, which, as its name implies, interacts with SUMO1-modified KAP-1. One possible model is that phosphorylation at S824 on KAP-1 might inhibit SUMOylation at the nearby residues, K804/K779/K554. However, although a previous finding was supportive of such a model [55], we were unable to observe any change in KAP-1 SUMOylation from 0.5 h to 8 h following 10–80 Gy IR. We did, however, observe a reduction in the level of chromatin bound CHD3 in the vicinity of the DSB following irradiation, which was ATM and 53BP1 (and hence pKAP-1)-dependent [56]. The model, supported by biochemical interaction studies, suggests that phosphorylation at the disordered C-terminal region of KAP-1 produces a SIM-like domain within KAP-1, which can interfere with the KAP-1SUMO1:CHD3SIM interaction and causes CHD3 dispersal from the DSB site (Figure 2). This exquisitely dynamic mechanism is highly suited to confer rapid, reversible and highly localized HC relaxation in the vicinity of HC-DSBs. However, it is currently unclear whether the dispersal of CHD3 chromatin remodeling activity from HC-DSBs is sufficient to enable DSB-induced, ATM-dependent chromatin relaxation or whether additional factors are required.


The heterochromatic barrier to DNA double strand break repair: how to get the entry visa.

Goodarzi AA, Jeggo PA - Int J Mol Sci (2012)

Ataxia telangiectasia mutated (ATM)-dependent heterochromatic DSB repair. (1) DSBs elicit ATM activation and IRIF formation, however repair processes within heterochromatin are inhibited by the compacted nucleosome configuration produced by KAP-1 dependent CHD3 activity; (2) Active ATM phosphorylates KAP-1 at S824, which interferes with the SUMOylation-dependent retention of CHD3 in chromatin; (3) In the absence of CHD3, the chromatin surrounding the DSB site relaxes, allowing (3A) non-homologous end-joining or (3B) if cells are in G2-phase, DNA end resection and homologous recombination mediated repair of the DSB; (4) Once the DSB is rejoined, ATM signaling is deactivated. Heterochromatic nucleosomes re-compact once KAP-1 is dephosphorylated and CHD3 activity is again retained.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3472778&req=5

f2-ijms-13-11844: Ataxia telangiectasia mutated (ATM)-dependent heterochromatic DSB repair. (1) DSBs elicit ATM activation and IRIF formation, however repair processes within heterochromatin are inhibited by the compacted nucleosome configuration produced by KAP-1 dependent CHD3 activity; (2) Active ATM phosphorylates KAP-1 at S824, which interferes with the SUMOylation-dependent retention of CHD3 in chromatin; (3) In the absence of CHD3, the chromatin surrounding the DSB site relaxes, allowing (3A) non-homologous end-joining or (3B) if cells are in G2-phase, DNA end resection and homologous recombination mediated repair of the DSB; (4) Once the DSB is rejoined, ATM signaling is deactivated. Heterochromatic nucleosomes re-compact once KAP-1 is dephosphorylated and CHD3 activity is again retained.
Mentions: Notwithstanding this limitation, there is compelling mechanistic evidence for how pKAP-1 foci formation leads to localized HC relaxation. The C-terminal region of KAP-1 encompasses several lysines that have been shown to undergo SUMOylation with SUMO1 (of which K554, K779, K804 are the most prominent), potentially via an auto-SUMOylation mechanism involving KAP-1’s N-terminal RING finger [53]. The S824 phosphorylation site of KAP-1 lies in a structurally-disordered region at the extreme C-terminal region. SUMOylation of KAP-1 is known to mediate interactions with the multi-subunit nucleosome remodeling and deacetylase (NuRD) complex as well as with the histone methyltransferase, SETDB1. The interaction between SUMOylated KAP-1 and NuRD occurs via the ATP-dependent chromatin remodeling subunit, CHD3 (specifically isoform 1, CHD3.1) [53,54]. Unlike the second isoform of CHD3 (CHD3.2), CHD3.1 contains a SUMO-interacting motif (SIM) at its extreme C-terminus, which, as its name implies, interacts with SUMO1-modified KAP-1. One possible model is that phosphorylation at S824 on KAP-1 might inhibit SUMOylation at the nearby residues, K804/K779/K554. However, although a previous finding was supportive of such a model [55], we were unable to observe any change in KAP-1 SUMOylation from 0.5 h to 8 h following 10–80 Gy IR. We did, however, observe a reduction in the level of chromatin bound CHD3 in the vicinity of the DSB following irradiation, which was ATM and 53BP1 (and hence pKAP-1)-dependent [56]. The model, supported by biochemical interaction studies, suggests that phosphorylation at the disordered C-terminal region of KAP-1 produces a SIM-like domain within KAP-1, which can interfere with the KAP-1SUMO1:CHD3SIM interaction and causes CHD3 dispersal from the DSB site (Figure 2). This exquisitely dynamic mechanism is highly suited to confer rapid, reversible and highly localized HC relaxation in the vicinity of HC-DSBs. However, it is currently unclear whether the dispersal of CHD3 chromatin remodeling activity from HC-DSBs is sufficient to enable DSB-induced, ATM-dependent chromatin relaxation or whether additional factors are required.

Bottom Line: Over recent decades, a deep understanding of pathways that repair DNA double strand breaks (DSB) has been gained from biochemical, structural, biophysical and cellular studies.Chromatin is broadly divided into open, transcriptionally active, euchromatin (EC) and highly compacted, transcriptionally inert, heterochromatin (HC), although these represent extremes of a spectrum.Moreover, DSBs within HC (HC-DSBs) are rapidly relocalized to the EC-HC interface.

View Article: PubMed Central - PubMed

Affiliation: Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.

ABSTRACT
Over recent decades, a deep understanding of pathways that repair DNA double strand breaks (DSB) has been gained from biochemical, structural, biophysical and cellular studies. DNA non-homologous end-joining (NHEJ) and homologous recombination (HR) represent the two major DSB repair pathways, and both processes are now well understood. Recent work has demonstrated that the chromatin environment at a DSB significantly impacts upon DSB repair and that, moreover, dramatic modifications arise in the chromatin surrounding a DSB. Chromatin is broadly divided into open, transcriptionally active, euchromatin (EC) and highly compacted, transcriptionally inert, heterochromatin (HC), although these represent extremes of a spectrum. The HC superstructure restricts both DSB repair and damage response signaling. Moreover, DSBs within HC (HC-DSBs) are rapidly relocalized to the EC-HC interface. The damage response protein kinase, ataxia telangiectasia mutated (ATM), is required for HC-DSB repair but is dispensable for the relocalization of HC-DSBs. It has been proposed that ATM signaling enhances HC relaxation in the DSB vicinity and that this is a prerequisite for HC-DSB repair. Hence, ATM is essential for repair of HC-DSBs. Here, we discuss how HC impacts upon the response to DSBs and how ATM overcomes the barrier that HC poses to repair.

Show MeSH
Related in: MedlinePlus