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PARylation converts PARP-1 from a chromatin architectural protein to a histone chaperone. (A and B) Representative binding curves and stoichiometry measurements of AM-PARP-1 to LE-Tri (•, solid lines) and NLE-Tri (▲, dashed lines). (C) Binding curves for PARP-1 and AM-PARP-1 to histones. H2AH2B-PARP-1 (•, solid line), H3-H4-PARP-1 (■, dashed line), H2A-H2B-AMPARP-1 (♢, solid line), and H3-H4-AM-PARP-1 (▿, dashed line) are shown. (D) Endogenous PARylated PARP-1 coimmunoprecipitates soluble histones. U2OS cells were treated with H 2 O 2 in combination with PJ34 or gallotannin as indicated. PAR antibodies (P) or control IgG (I) were used in immunoprecipitation (IP) assays from soluble lysates. Bound proteins were detected by immunoblotting with a mixture of PARP-1 and PAR antibodies (Top) and H2B and H4 antibodies (Middle and Bottom). (E) AM-PARP-1 does not disassemble nucleosomes. Labeled Nuc165 with PARP-1 and 30Nick DNA was incubated with increasing amounts of NAD +. Samples were analyzed by native PAGE and visualized by gel FRET between H2B (cyanine 5 633/670) and H4 (Alexa488 488/520). Lane 2 contains nucleosomes alone; lane 3 contains nucleosomes with PARP-1 and 30Nick DNA; and lanes 4-8 contain nucleosomes with PARP-1, 30Nick DNA, and 0.1, 1, 10, 20, and 40 μM NAD + , respectively. FRET between histones H2B and H4 is observed in all lanes, indicating that nucleosomes remain intact throughout.
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Poly-ADP-ribosylation (PARylation) is an abundant posttranslational modification in eukaryotes. The responsible enzyme, poly [ADP-ribose] polymerase 1 (PARP-1), binds to chromatin and shapes its architecture. It is activated by DNA damage and other triggers, and catalyzes the addition of long chains of poly-ADP ribose (PAR) mainly to i...
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... Imperial Stain that AM-PARP-1 ( Fig. S3A) loses its ability to shift NLE-Tri but maintains residual interactions with LE-Tri ( Fig. 1 B and C); nei- ther array is visibly compacted by AM-PARP-1 (Fig. S1F). HI-FI FRET measurements reveal that automodification of PARP-1 does not significantly weaken its interaction with free DNA or LE-Tri ( Fig. 2A and Table 1). Indeed, AM-PARP-1 binds all sub- strates with free DNA ends [i.e., DNA, Nuc207 (Fig. S2C), LE-Tri] with comparable affinities (Table 1). In contrast, AM-PARP-1 affinity for NLE-Tri is reduced by a factor of 20 (∼100 nM; Fig. 2A). The number of AM-PARP-1 molecules bound to either trinucleosome remains unaffected by ...
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... interactions with LE-Tri ( Fig. 1 B and C); nei- ther array is visibly compacted by AM-PARP-1 (Fig. S1F). HI-FI FRET measurements reveal that automodification of PARP-1 does not significantly weaken its interaction with free DNA or LE-Tri ( Fig. 2A and Table 1). Indeed, AM-PARP-1 binds all sub- strates with free DNA ends [i.e., DNA, Nuc207 (Fig. S2C), LE-Tri] with comparable affinities (Table 1). In contrast, AM-PARP-1 affinity for NLE-Tri is reduced by a factor of 20 (∼100 nM; Fig. 2A). The number of AM-PARP-1 molecules bound to either trinucleosome remains unaffected by automodification (Fig. ...
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... that automodification of PARP-1 does not significantly weaken its interaction with free DNA or LE-Tri ( Fig. 2A and Table 1). Indeed, AM-PARP-1 binds all sub- strates with free DNA ends [i.e., DNA, Nuc207 (Fig. S2C), LE-Tri] with comparable affinities (Table 1). In contrast, AM-PARP-1 affinity for NLE-Tri is reduced by a factor of 20 (∼100 nM; Fig. 2A). The number of AM-PARP-1 molecules bound to either trinucleosome remains unaffected by automodification (Fig. ...
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... and Table 1). Indeed, AM-PARP-1 binds all sub- strates with free DNA ends [i.e., DNA, Nuc207 (Fig. S2C), LE-Tri] with comparable affinities (Table 1). In contrast, AM-PARP-1 affinity for NLE-Tri is reduced by a factor of 20 (∼100 nM; Fig. 2A). The number of AM-PARP-1 molecules bound to either trinucleosome remains unaffected by automodification (Fig. ...
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... Binds Histones with High Affinity. PAR chains are neg- atively charged and chemically represent a "third type of nucleic acid." We therefore quantified whether PARP-1 binds non- nucleosomal histones in a PAR-dependent manner. Unmodified PARP-1 interacts only weakly (>500 nM) with either H2A-H2B or H3-H4 histone complex ( Fig. 2C and Table 1). In striking contrast, AM-PARP-1 ( Fig. S3B) binds free nonnucleosomal H2A-H2B and H3-H4 complexes with high affinity (∼2-16 nM; Fig. 2C and Table 1). Importantly, the measured affinities of AM-PARP-1 for histones are similar to those obtained for clas- sical histone chaperones under similar conditions [e.g., nucleo- some ...
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... We therefore quantified whether PARP-1 binds non- nucleosomal histones in a PAR-dependent manner. Unmodified PARP-1 interacts only weakly (>500 nM) with either H2A-H2B or H3-H4 histone complex ( Fig. 2C and Table 1). In striking contrast, AM-PARP-1 ( Fig. S3B) binds free nonnucleosomal H2A-H2B and H3-H4 complexes with high affinity (∼2-16 nM; Fig. 2C and Table 1). Importantly, the measured affinities of AM-PARP-1 for histones are similar to those obtained for clas- sical histone chaperones under similar conditions [e.g., nucleo- some assembly protein 1 (Nap1) ...
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... verify the relevance of histone binding by AM-PARP-1 in cells, we performed immunoprecipitation with anti-PAR anti- bodies, utilizing soluble lysates from cells exposed to oxidative stress using hydrogen peroxide (Fig. 2D). PARP-1 is activated by H 2 O 2 treatment, and the PAR modification can be stabilized by a PAR inhibitor, gallotannin (Fig. 2D, lane 4). Basal levels of H2B and H4 are coimmunoprecipitated with anti-PAR anti- bodies in the absence of H 2 O 2 , or when cells were treated with the combination of H 2 O 2 and PJ34 hydrochloride hydrate ...
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... verify the relevance of histone binding by AM-PARP-1 in cells, we performed immunoprecipitation with anti-PAR anti- bodies, utilizing soluble lysates from cells exposed to oxidative stress using hydrogen peroxide (Fig. 2D). PARP-1 is activated by H 2 O 2 treatment, and the PAR modification can be stabilized by a PAR inhibitor, gallotannin (Fig. 2D, lane 4). Basal levels of H2B and H4 are coimmunoprecipitated with anti-PAR anti- bodies in the absence of H 2 O 2 , or when cells were treated with the combination of H 2 O 2 and PJ34 hydrochloride hydrate (PJ34), a potent PARP-1 inhibitor (Fig. 2D, compare lanes 5 and 10). H 2 O 2 treatment alone results in increased coimmunopreci- pitation ...
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... by H 2 O 2 treatment, and the PAR modification can be stabilized by a PAR inhibitor, gallotannin (Fig. 2D, lane 4). Basal levels of H2B and H4 are coimmunoprecipitated with anti-PAR anti- bodies in the absence of H 2 O 2 , or when cells were treated with the combination of H 2 O 2 and PJ34 hydrochloride hydrate (PJ34), a potent PARP-1 inhibitor (Fig. 2D, compare lanes 5 and 10). H 2 O 2 treatment alone results in increased coimmunopreci- pitation of H2B and H4 (Fig. 2D, lane 8). This effect is magnified when PARG is inhibited (Fig. 2D, lane 12). We do not detect any PARylated histones under these conditions, consistent with results from others (8). We conclude that automodification of ...
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... Basal levels of H2B and H4 are coimmunoprecipitated with anti-PAR anti- bodies in the absence of H 2 O 2 , or when cells were treated with the combination of H 2 O 2 and PJ34 hydrochloride hydrate (PJ34), a potent PARP-1 inhibitor (Fig. 2D, compare lanes 5 and 10). H 2 O 2 treatment alone results in increased coimmunopreci- pitation of H2B and H4 (Fig. 2D, lane 8). This effect is magnified when PARG is inhibited (Fig. 2D, lane 12). We do not detect any PARylated histones under these conditions, consistent with results from others (8). We conclude that automodification of PARP-1 enhances its interaction with soluble histones in ...
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... bodies in the absence of H 2 O 2 , or when cells were treated with the combination of H 2 O 2 and PJ34 hydrochloride hydrate (PJ34), a potent PARP-1 inhibitor (Fig. 2D, compare lanes 5 and 10). H 2 O 2 treatment alone results in increased coimmunopreci- pitation of H2B and H4 (Fig. 2D, lane 8). This effect is magnified when PARG is inhibited (Fig. 2D, lane 12). We do not detect any PARylated histones under these conditions, consistent with results from others (8). We conclude that automodification of PARP-1 enhances its interaction with soluble histones in ...
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... of 30Nick DNA and increasing amounts of NAD + . Under these conditions, PARP-1 modifies itself in an NAD + dose-dependent fashion, without PARylating nucleosomal histones (Fig. S3 C and D). Nucleosomes were flu- orescently labeled on histones H4 and H2B; thus, their integrity in the presence of PARP-1 and NAD + can be assayed by in-gel FRET (Fig. 2E). In agreement with the effects of PARylation on PARP-1 interactions with Nuc207 (Table 1), increasing amounts of NAD + decrease the ability of PARP-1 to shift nucleosomes (also reported in ref. 28). However, the nucleosome band remains Table 1. PARP-1 affinities measured by HI-FI FRET 27.8 ± 5.6 0.95 5 23.4 ± 4.8* 0.98 2 3 3 . 2 ± ...
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... We therefore tested whether AM-PARP-1 promotes nucleosome assembly under conditions of histone imbalance. We developed an assay in which an over- abundance of histone H2A-H2B (or H3-H4) complex over DNA precludes nucleosome assembly. In the absence of a histone chaperone, no nucleosomes are formed and the entire sample remains in the well (Fig. 3D, lane 2). Bona fide histone chaperones (e.g., Nap1), are able to rescue aggregated chromatin in this assay [rescue of aggregated chromatin (RAC) assay], as observed by the appearance of nucleosomes with fluorescent markers on H4 and H2B (Fig. 3E, lanes 18-20). This assay allows for a more direct readout of the appearance of canonical ...
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... RAC assay. It is possible that at higher concentrations, AM-PARP-1 binds to the nucleosomes it assembles (Fig. 1C, lanes 16-19), resulting in an apparent loss of nucleosomes on native PAGE. Alternatively, excess AM-PARP-1 may disassemble partially assembled nucleosomes, even though it has no effect when presented with fully assembled nucleosomes (Fig. ...
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... and used for immunoprecipitation with IgG or poly [ADP-ribose] (PAR) antibody overnight. Protein G Dyna beads (Life Tech- nologies) were added for additional 1-h incubation and washed, and bound proteins were eluted by boiling in SDS sample buffer. Eluates were analyzed by SDS/PAGE and immunoblotting with the antibodies indicated in Fig. ...
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Citations
... (3) The enzymatic action of Poly(ADP)-ribose glycohydrolase (PARG) cleaves pADPr, restoring PARP-1's binding affinity to mono-methylated active histone marks. This proposed hypothesis is consistent with existing research conducted across various model organisms, including mice, Drosophila, and Humans (Tulin and Spradling, 2003;Krishnakumar and Kraus, 2010;Ji and Tulin, 2010;Liu and Kraus, 2017;Tulin et al., 2002;Muthurajan et al., 2014). Notably, previous studies have consistently demonstrated that PARP-1 predominantly associates with highly expressed genes and plays a crucial role in mediating nucleosome dynamics and assembly. ...
PARP-1 is central to transcriptional regulation under both normal and stress conditions, with the governing mechanisms yet to be fully understood. Our biochemical and ChIP-seq-based analyses showed that PARP-1 binds specifically to active histone marks, particularly H4K20me1. We found that H4K20me1 plays a critical role in facilitating PARP-1 binding and the regulation of PARP-1-dependent loci during both development and heat shock stress. Here, we report that the sole H4K20 mono-methylase, pr-set7 , and parp-1 Drosophila mutants undergo developmental arrest. RNA-seq analysis showed an absolute correlation between PR-SET7- and PARP-1-dependent loci expression, confirming co-regulation during developmental phases. PARP-1 and PR-SET7 are both essential for activating hsp70 and other heat shock genes during heat stress, with a notable increase of H4K20me1 at their gene body. Mutating pr-set7 disrupts monomethylation of H4K20 along heat shock loci and abolish PARP-1 binding there. These data strongly suggest that H4 monomethylation is a key triggering point in PARP-1 dependent processes in chromatin.
... In the DNA damage repair process, short-term binding of PARP 1 to DNA free ends occurs and PARP 1 activation attracts repair proteins which initiate DNA repair pathway to a specific point, where PARP 1 molecule turned to a mechanical obstacle for repair machinery. Heavily auto-PARylated PARP 1 molecules dissociate from DNAbinding sites (Muthurajan et al., 2014), thus enabling repair proteins to localize in the site of DNA damage and complete damage repair (Hopkins et al., 2019). When the loosened state of chromatin is required for the free access to DNA in relatively prolonged processes (e.g. ...
Bleomycin-induced lung pathology in rodents is a well recognized animal model widely used for evaluation of new therapeutic approaches in treatment of lung inflammation and fibrotic diseases. It is documented that poly(ADP-ribose)polymerase 1 activity has a significant role in development of inflammatory processes in the heart, liver and brain. Herein, we used biochemical and immunochemical methods for estimation of poly(ADP-ribose)polymerase 1 (PARP 1) activity, NAD+ and poly(ADP-ribose)glycohydrolase (PARG) protein content in rat lung nuclei during the inflammatory phase in a bleomycin-induced one-hit rat model. To evaluate the influence of bleomycin – induced alterations in DNA structure on regulation of poly(ADP-ribose)polymerase 1 activation pathways, we isolated DNA from nuclei of lung tissues in the phase of acute lung inflammation induced by bleomycin, and DNA melting profiles were investigated. In the present study we investigated whether naturally occurring water-soluble polyphenol tannic acid with widely accepted anti-fibrotic and anti-inflammatory effects can influence poly(ADP-ribose)polymerase 1 activity, NAD+ and poly(ADP-ribose)glycohydrolase protein content in nuclear fraction isolated from rat lung tissues in a bleomycin-induced acute lung injury model. It was demonstrated that NAD+ level and poly(ADP-ribose)glycohydrolase protein content decreased in rat lung nuclei during the inflammatory phase in the bleomycin-induced acute lung injury model. Treatment of rats with tannic acid enhanced the effects displayed by bleomycin in lung nuclei, thus indicating synergistic interaction with the drug in the field covering PARP 1 activity, poly(ADP-ribose)glycohydrolase (PARG) protein and NAD+ content in lung nuclei. We observed PARP 1 inhibition in nuclei of lung tissue during the inflammatory phase in the bleomycin-induced acute lung injury rat model, which could be coupled with the drop of NAD+ level in nuclei. In the present study we highlighted that bleomycin (BLM) can induce DNA destabilization in lung nuclei. It was proposed that bleomycin-induced modulations in DNA structure could hamper PARP 1 binding with DNA and down-regulate the enzyme activating pathway in lung nuclei. The role of poly(ADP-ribose)glycohydrolase depletion in lung nuclei and sequential accumulation of poly(ADP-ribose)polymers in lung cells, which triggers their destruction and tissues damage, was proposed. It is suggested that in the light of synergistic interaction between bleomycin and tannic acid (TA) the anti-inflammatory role of tannic acid should be repurposed.
... The high-density deposition of PAR generates a transient repair compartment that concentrates repair proteins and activates signaling factors ( 78 , 79 ). PARP-1 automodification also causes its release from DNA ( 80 ) and promotes chroma tin relaxa tion, a crucial process for downstream repair e v ents (81)(82)(83). ...
Poly(ADP-ribosylation) (PARylation) by poly(ADP-ribose) polymerases (PARPs) is a highly regulated process that consists of the covalent addition of polymers of ADP-ribose (PAR) through post-translational modifications of substrate proteins or non-covalent interactions with PAR via PAR binding domains and motifs, thereby reprogramming their functions. This modification is particularly known for its central role in the maintenance of genomic stability. However, how genomic integrity is controlled by an intricate interplay of covalent PARylation and non-covalent PAR binding remains largely unknown. Of importance, PARylation has caught recent attention for providing a mechanistic basis of synthetic lethality involving PARP inhibitors (PARPi), most notably in homologous recombination (HR)-deficient breast and ovarian tumors. The molecular mechanisms responsible for the anti-cancer effect of PARPi are thought to implicate both catalytic inhibition and trapping of PARP enzymes on DNA. However, the relative contribution of each on tumor-specific cytotoxicity is still unclear. It is paramount to understand these PAR-dependent mechanisms, given that resistance to PARPi is a challenge in the clinic. Deciphering the complex interplay between covalent PARylation and non-covalent PAR binding and defining how PARP trapping and non-trapping events contribute to PARPi anti-tumour activity is essential for developing improved therapeutic strategies. With this perspective, we review the current understanding of PARylation biology in the context of the DNA damage response (DDR) and the mechanisms underlying PARPi activity and resistance.
... 58,59 PARP1 is also a nucleosome-binding nucleoprotein involved in a variety of nuclear processes, including modulation of chromatin structure/accessibility and transcription. 45,48,60 Given that PARP1 is rapidly recruited and activated by DNA double-strand breaks (DSBs), it is surprising that PARP1-mediated METTL3 transcription is inhibited upon irradiation. The phenomenon of radiation-attenuated m 6 A modification of total mRNA in a dose-dependent manner indicates that, upon IR-induced DNA damage, the dynamics of PARP1 binding to METTL3 promoter region chromatin could be altered, which affected the transcriptional activity of the target gene. ...
Chromatin remodelling and m6A modification are two critical layers in controlling gene expression and DNA damage signaling in most eukaryotic bioprocesses. Here, we report that PARP1 controls the chromatin accessibility of METTL3 to regulate its transcription and subsequent m6A methylation of poly(A)+RNA in response to DNA damage induced by radiation. The transcription factors NFIC and TBP are dependent on PARP1 to access the METTL3 promoter to activate METTL3 transcription. Upon irradiation or PARP1 inhibitor treatment, PARP1 disassociated from METTL3 promoter chromatin, which resulted in attenuated accessibility of NFIC and TBP and consequently suppressed METTL3 expression and RNA m6A methylation. LPAR5 mRNA was identified as a target of METTL3, and m6A methylation was located at A1881. The level of m6A methylation of LPAR5 significantly decreased along with METTL3 depression in cells after irradiation or PARP1 inhibition. Mutation of the LPAR5 A1881 locus in its 3'UTR results in loss of m6A methylation and consequently decreased stability of LPAR5 mRNA. METTL3-targeted small-molecule inhibitors depress murine xenograft tumor growth and exhibit a synergistic effect with radiotherapy in vivo. These findings advance our comprehensive understanding of PARP-related biological roles, which may have implications for developing valuable therapeutic strategies for PARP1 inhibitors in oncology.
... Given C/EBPb roles in satellite cells, the myocyte, and its interactions with MYOD [41][42][43], there is potential for C/EBPb PARylation in muscle tissue. Additional mechanisms of both PARP1 and catalytic PAR control are also not discounted and exert influence over 3D chromatin organization [44,45]. However, it should be noted that PARP2 which also contributes to PAR accumulation, has demonstrated roles in myogenesis and skeletal muscle structure [46]. ...
The ADP-ribosyltransferase, PARP1 enzymatically generates and applies the post-translational modification, ADP-Ribose (ADPR). PARP1 roles in genome maintenance are well described, but recent work highlights roles in many fundamental processes including cellular identity and energy homeostasis. Herein, we show in both mouse and human skeletal muscle cells that PARP1-mediated PARylation is a regulator of the myogenic program and the muscle transcriptional response to steroid hormones. Chemical PARP1 modulation impacts the expression of major myocellular proteins, including troponins, key in dictating muscle contractile force. Whilst PARP1 in absence of DNA damage is often assumed to be basally inactive, we show PARylation to be acutely sensitive to extracellular glucose concentrations and the steroid hormone class, glucocorticoids which exert considerable authority over muscle tissue mass. Specifically, we find during myogenesis, a transient and significant rise in PAR. This early-stage differentiation event, if blocked with PARP1 inhibition, reduced the abundance of important muscle proteins in the fully differentiated myotubes. This suggests that PAR targets during early-stage differentiation are central to the proper development of the muscle contractile unit. We also show that reduced PARP1 in myoblasts impacts a variety of metabolic pathways in line with the recorded actions of glucocorticoids. Currently, as both regulators of myogenesis and muscle mass loss, glucocorticoids represent a clinical conundrum. Our work goes on to identify that PARP1 influences transcriptional activation by glucocorticoids of a subset of genes critical to human skeletal muscle pathology. These genes may therefore signify a regulatory battery of targets through which selective glucocorticoid modulation could be achieved. Collectively, our data provide clear links between PARP1-mediated PARylation and skeletal muscle homeostatic mechanisms crucial to tissue mass maintenance and endocrine response.
... Towards DNA duplexes, the strongest affinity of PARP1 is observed in the presence of blunt ends or a 5 -phosphorylated single-strand break in DNA [160][161][162]. During the interaction with nucleosome particles, PARP1 shows consistent selectivity: initial complexes are formed by one PARP1 molecule located near blunt ends or near linker regions of nucleosomal DNA; after the binding of other molecules, PARP1 has additionally been found to be located near the entry-exit site [163][164][165][166]. It has been shown that PARP1 binding to an end of nucleosomal dsDNA leads to a significant increase in the distance between adjacent gyres of the duplex and this process is not accompanied by a loss of histones and is reversible after PARylation [167]. ...
... This principle applies to both histones and PARP1 itself [172,176] (Figure 4). Indeed, PARylation enhances the dissociation of PARP1 from DSB sites [65,165]. A research article about kinetics of PARP1 accumulation on and dissociation from the NCP in the presence of H2A.X leads to a conclusion that the presence of an alternative histone variant can promote either association or a final release of PARP1 after self PARylation during DNA repair [65]. ...
... As for PARP1 itself, it is reported that as the length of PAR increases, so does the affinity of this protein for this polymer [209]. It is noteworthy that the affinity of the PARP1for PAR is the same range as the affinity of unmodified PARP1 for the NCP [65,163,165,210]. Therefore, during the interaction of PARP1 with damaged nucleosomal DNA, activation and subsequent selfmodification of PARP1 should lead to an inevitable breakup of the PARP1-NCP complex owing to competitive interactions [176,210]. ...
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
... The induction of PARP-1 activity by DNA breaks locally and transiently relaxes chromatin, reducing the affinity of PARP-1 for nucleosomes and facilitating the recruitment of DNA repair factors that must operate in those sites [16,27]. The same mechanism is required for PARP-mediated regulation of transcription [17,28,29]. In this context, PARP-1 contributes to the long-term chromatin relaxation required for sustained transcription. ...
Simple Summary
PARP-1 and poly(ADP-ribosyl)ation control gene expression, DNA repair pathways, and genomic stability in multiple ways, such as affecting chromatin remodelling. This review article summarises how PARP-1 activity directly modifies histone proteins and the enzymes involved in DNA/histone epigenetic modifications to mould chromatin structure during transcription and DNA damage response. Understanding the role of poly(ADP-ribosyl)ation in the epigenetic regulation of chromatin organisation will help clarify resistance mechanisms to PARP inhibitors and highlight the clinical relevance of a combinatory approach based on epigenetic drugs.
Abstract
The regulation of chromatin state and histone protein eviction have been proven essential during transcription and DNA repair. Poly(ADP-ribose) (PAR) polymerase 1 (PARP-1) and poly(ADP-ribosyl)ation (PARylation) are crucial mediators of these processes by affecting DNA/histone epigenetic events. DNA methylation/hydroxymethylation patterns and histone modifications are established by mutual coordination between all epigenetic modifiers. This review will focus on histones and DNA/histone epigenetic machinery that are direct targets of PARP-1 activity by covalent and non-covalent PARylation. The effects of these modifications on the activity/recruitment of epigenetic enzymes at DNA damage sites or gene regulatory regions will be outlined. Furthermore, based on the achievements made to the present, we will discuss the potential application of epigenetic-based therapy as a novel strategy for boosting the success of PARP inhibitors, improving cell sensitivity or overcoming drug resistance.
... 3,13,14 In addition to its role in DNA repair, highly abundant PARP1 also regulates chromatin architecture and transcription. [15][16][17] Un-PARylated PARP1 binds chromatin with high affinity and compacts it into higher order structures to block transcription in vitro. 15,17,18 In addition, genomic studies have identified PARP1 at promoters of actively transcribed genes. ...
... [15][16][17] Un-PARylated PARP1 binds chromatin with high affinity and compacts it into higher order structures to block transcription in vitro. 15,17,18 In addition, genomic studies have identified PARP1 at promoters of actively transcribed genes. 19,20 The enzymatic activity of PARP1/2 is inhibited by a class of pharmacological agents known as PARP inhibitors (PARPi), which are NAD + analogs that bind the catalytic site of PARPs to block cellular PARylation, which causes accumulation of SSBs. ...
... 63 Previous studies with purified protein have shown that un-PARylated PARP1 associates with intact chromatin lacking free ends. 8,15,16,64 Genome-wide approaches have captured steady-state snapshots of its genomic interactions. 19,20,65 In vitro single-molecule experiments suggest that PARP1 decorates DNA and compacts it by stabilizing crossover points. ...
PARP1 contributes to genome architecture and DNA damage repair through its dynamic association with chromatin. PARP1 and PARP2 (PARP1/2) recognize damaged DNA and recruit the DNA repair machinery. Using single molecule microscopy in live cells, we monitored the movement of PARP1/2 on undamaged and damaged chromatin. We identify two classes of freely diffusing PARP1/2 and two classes of bound PARP1/2. The majority (> 60%) of PARP1/2 diffuse freely in both undamaged and damaged nuclei and in the presence of inhibitors of PARP1/2 used for cancer therapy (PARPi). Laser induced DNA damage results in a small fraction of slowly diffusing PARP1 and PARP2 to become transiently bound. Treatment of cells with PARPi in the presence of DNA damage causes subtle changes in the dynamics of bound PARP1/2, but not the high levels of PARP1/2 trapping seen previously. Our results imply that next-generation PARPi could specifically target the small fraction of DNA-bound PARP1/2.
... It is known that the binding of PARP1 to DNA activates the enzyme, and ini the NAD+-induced PARylation of nearby proteins and PARP1 itself [31][32][33][34][35]. The P lation of PARP1 leads to the dissociation of the PARP1-nucleosome complexes an ...
... It is known that the binding of PARP1 to DNA activates the enzyme, and initiates the NAD+-induced PARylation of nearby proteins and PARP1 itself [31][32][33][34][35]. The PARylation of PARP1 leads to the dissociation of the PARP1-nucleosome complexes and the almost complete restoration of the native structure of the released nucleosomes [29], despite the possible PARylation of histones [33], which strongly depends on the presence of HPF1 (histone PARylation factor 1) [24,36]. ...
Inhibitors (PARPi) of poly(ADP-ribose-)polymerase-1 (PARP1) are used in antitumor therapy; their cytotoxicity correlates with the efficiency of PARP1 trapping in cell chromatin. Previous studies have demonstrated the PARPi-induced trapping of PARP1 on DNA, although details of the mechanism remain controversial. Here, the interactions of PARP1-nucleosome complexes with PARPi, olaparib (Ola), talazoparib (Tala), and veliparib (Veli) were studied. PARPi trap PARP1 on nucleosomes without affecting the structure of PARP1-nucleosome complexes. The efficiency of PARP1 trapping on nucleosomes increases in the order of Tala>Ola>>Veli, recapitulating the relative trapping efficiencies of PARPi in cells, but different from the relative potency of PARPi to inhibit the catalytic activity of PARP1. The efficiency of PARP1 trapping on nucleosomes correlates with the level of inhibition of auto-PARylation, which otherwise promotes the dissociation of PARP1-nucleosome complexes. The trapping efficiencies of Tala and Ola (but not Veli) are additionally modulated by the enhanced PARP1 binding to nucleosomes. The dissociation of PARP1-nucleosome complexes occurs without a loss of histones and leads to the restoration of the intact structure of nucleosomal DNA. The data suggest that the chromatin structure can considerably affect the efficiency of the PARPi action.
... PARP-1 plays a dual role of chromatin 'architectural protein' through its specific binding to nucleosomes and that of a histone 'chaperone' without affecting core histones or assembly of nucleosomes through its intrinsic enzymatic activity (Kim et al. 2004;Kraus 2008;Muthurajan et al. 2014;Ummarino et al. 2021). Indeed, its abundance to the tune of 106 molecules/cell accords it the status Fig. 7 a, b Epigenetic underpinnings of PARP-1 and SIRTs involvement in regulating long-term memory acquisition during varied learning paradigms. ...
The redox coenzymes viz., oxidized β-nicotinamide adenine dinucleotide (NAD⁺) and flavin adenine dinucleotide (FAD) by way of generation of optimal reducing power and cellular energy currency (ATP), control a staggering array of metabolic reactions. The prominent cellular contenders for NAD⁺ utilization, inter alia, are sirtuins (SIRTs) and poly(ADP-ribose) polymerase (PARP-1), which have been significantly implicated in ischemic stroke (IS) pathogenesis. NAD⁺ and FAD are also two crucial epigenetic enzyme-required metabolites mediating histone deacetylation and poly(ADP-ribosyl)ation through SIRTs and PARP-1 respectively, and demethylation through FAD-mediated lysine specific demethylase activity. These enzymes and post-translational modifications impinge on the components of neurovascular unit, primarily neurons, and elicit diverse functional upshots in an ischemic brain. These could be circumstantially linked with attendant cognitive deficits and behavioral outcomes in post-stroke epoch. Parsing out the contribution of NAD⁺/FAD-synthesizing and utilizing enzymes towards epigenetic remodeling in IS setting, together with their cognitive and behavioral associations, combined with possible therapeutic implications will form the crux of this review.
Graphical Abstract
