Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch

Lehmann, Laura C.; Bacic, Luka; Hewitt, Graeme; Brackmann, Klaus; Sabantsev, Anton; Gaullier, Guillaume; Pytharopoulou, Sofia; Degliesposti, Gianluca; Okkenhaug, Hanneke; Tan, Song; Costa, Alessandro; Skehel, J. Mark; Boulton, Simon J.; Deindl, Sebastian

doi:10.1016/j.celrep.2020.108529

Cited by 29 publications

(30 citation statements)

References 92 publications

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“…The ATPase domain is highly dynamic along the entire trajectory (Figure 3 The states with an open, loosely bound ATPase domain also feature an interaction with the nucleosome acidic patch (Figure 4B, 4E, Movie M2). This observation is consistent with our earlier discovery of an interaction between the linker region of ALC1 and the acidic patch, and the role of this interaction in regulating ALC1 (Lehmann et al, 2020). Moreover, the density attributed to the macro domain is visible in all these states.…”

Section: Analysis Of Heterogeneity In the Cryo-em Data Reveals Additional Functional States Of Alc1supporting

confidence: 92%

“…Notably, our map does not show density for either the macro domain of ALC1 or PAR chains on the nucleosome, most likely due to their extreme conformational flexibility in the active state. However, the average map from a consensus 3D refinement of all 43 698 particles displays clear density for an interaction between ALC1 and the nucleosome acidic patch (Figure 3A), confirming at the structural level and in the context of ALC1 fl our previous finding that the acidic patch is important for remodeling by ALC1 (Lehmann et al, 2020). Moreover, this map also features density that we assign to the macro domain (Figure 3A) based on the following rationale: this density makes contact with the ATPase motor, in agreement with the previously reported ATPase motor-macro domain interaction (Lehmann et al, 2017;Singh et al, 2017).…”

Section: Cryo-em Structure Of the Complex Between A Parylated Nucleosome And Alc1 In Its Active Statesupporting

confidence: 81%

“…To investigate the role of the H4 tail and acidic patch interactions, we constructed two different FRET-labeled end-positioned nucleosomes in addition to WT: a nucleosome with acidic patch mutations (APM nucleosome; alanine substitutions of H2A E61A, E64A, D90A and E92A) and a nucleosome with tail-less (globular) H4 histones (gH4 nucleosome; with a deletion of H4 residues 1-19). Additionally, we used ALC1 fl with the two substitutions R611A and S612A within the regulatory linker segment (ALC1 fl R611A/S612A) to disrupt the acidic patch interaction on the part of ALC1, as previously (Lehmann et al, 2020).…”

Section: Nucleosome Remodeling By Alc1 Depends On Its Interactions With the Acidic Patch And The H4 Tailmentioning

confidence: 99%

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Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

Bacic

Gaullier

Sabantsev

et al. 2021

Preprint

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The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and reveal that ALC1 preferentially slides nucleosomes away from DNA breaks.

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Section: Analysis Of Heterogeneity In the Cryo-em Data Reveals Additional Functional States Of Alc1supporting

confidence: 92%

Section: Cryo-em Structure Of the Complex Between A Parylated Nucleosome And Alc1 In Its Active Statesupporting

confidence: 81%

Section: Nucleosome Remodeling By Alc1 Depends On Its Interactions With the Acidic Patch And The H4 Tailmentioning

confidence: 99%

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Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

Bacic

Gaullier

Sabantsev

et al. 2021

Preprint

Self Cite

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“…Moreover, the direction of sliding by ISWI is impacted by an asymmetry between the two acidic patches [ 121 ]. Interestingly, the ALC1/CHD1L remodeler strongly depends on the binding of its linker segment to the proximal acidic patch for tethering and efficient coupling of ATP hydrolysis to nucleosome remodeling [ 122 ].…”

Section: Shared and Specific Regulatory Principles And Features Governing The Sophisticated Conversations Between Nucleosomes And Remodelmentioning

confidence: 99%

Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer

Clapier

2021

IJMS

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The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions—in particular, the regulation of gene expression—and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.

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“…In fact, in cells with engineered PARPi resistance through restoration of the HR pathway ALC1 deficiency has been proposed to reinstate PARPi sensitivity [172]. The structure of ALC1 in complex with a nucleosome was recently published revealing ALC1 regulation by both an acidic patch on nucleosomes and its macro domain binding to PAR chains at sites of DNA damage [173]. Given the emerging evidence of the role of ALC1 in PARylation dependent chromatin relaxation and PARPi resistance, it has been proposed as a possible target for combination therapies.…”

Section: Other Interaction Partners Of Parp1mentioning

confidence: 99%

PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling

Beek

McClay

Patel

et al. 2021

IJMS

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Poly (ADP-ribose) polymerases (PARP) 1-3 are well-known multi-domain enzymes, catalysing the covalent modification of proteins, DNA, and themselves. They attach mono- or poly-ADP-ribose to targets using NAD+ as a substrate. Poly-ADP-ribosylation (PARylation) is central to the important functions of PARP enzymes in the DNA damage response and nucleosome remodelling. Activation of PARP happens through DNA binding via zinc fingers and/or the WGR domain. Modulation of their activity using PARP inhibitors occupying the NAD+ binding site has proven successful in cancer therapies. For decades, studies set out to elucidate their full-length molecular structure and activation mechanism. In the last five years, significant advances have progressed the structural and functional understanding of PARP1-3, such as understanding allosteric activation via inter-domain contacts, how PARP senses damaged DNA in the crowded nucleus, and the complementary role of histone PARylation factor 1 in modulating the active site of PARP. Here, we review these advances together with the versatility of PARP domains involved in DNA binding, the targets and shape of PARylation and the role of PARPs in nucleosome remodelling.

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Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch

Cited by 29 publications

References 92 publications

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer

PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling

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