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Article ; Online: Withdrawal notice to "Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC)".

Prasad, Rajendra / Horton, Julie K / Wilson, Samuel H

2022 Volume 114, Page(s) 103322

Language	English
Publishing date	2022-03-23
Publishing country	Netherlands
Document type	Published Erratum
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2022.103322
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Article ; Online: Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC).

Prasad, Rajendra / Horton, Julie K / Wilson, Samuel H

DNA repair

2020 Volume 90, Page(s) 102850

MeSH term(s)	DNA/chemistry ; DNA/metabolism ; DNA Adducts ; DNA Damage ; DNA Repair ; Humans ; Poly (ADP-Ribose) Polymerase-1/chemistry ; Poly (ADP-Ribose) Polymerase-1/metabolism
Chemical Substances	DNA Adducts ; DNA (9007-49-2) ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30)
Language	English
Publishing date	2020-04-28
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2020.102850
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Article ; Online: WITHDRAWN: Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC).

Prasad, Rajendra / Horton, Julie K / Wilson, Samuel H

DNA repair

2020 Volume 89, Page(s) 102824

MeSH term(s)	Animals ; Cross-Linking Reagents ; DNA/chemistry ; DNA/metabolism ; DNA Damage ; DNA Repair ; Humans ; Mutagenicity Tests ; Poly (ADP-Ribose) Polymerase-1/chemistry ; Poly (ADP-Ribose) Polymerase-1/metabolism
Chemical Substances	Cross-Linking Reagents ; DNA (9007-49-2) ; PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30)
Language	English
Publishing date	2020-02-17
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2020.102824
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Article ; Online: Temporal recruitment of base excision DNA repair factors in living cells in response to different micro-irradiation DNA damage protocols.

Zhao, Ming-Lang / Stefanick, Donna F / Nadalutti, Cristina A / Beard, William A / Wilson, Samuel H / Horton, Julie K

DNA repair

2023 Volume 126, Page(s) 103486

Abstract: Laser micro-irradiation across the nucleus rapidly generates localized chromatin-associated DNA lesions permitting analysis of repair protein recruitment in living cells. Recruitment of three fluorescently-tagged base excision repair factors [DNA ... ...

Abstract	Laser micro-irradiation across the nucleus rapidly generates localized chromatin-associated DNA lesions permitting analysis of repair protein recruitment in living cells. Recruitment of three fluorescently-tagged base excision repair factors [DNA polymerase β (pol β), XRCC1 and PARP1], known to interact with one another, was compared in gene-deleted mouse embryonic fibroblasts and in those expressing the endogenous factor. A low energy micro-irradiation (LEMI) forming direct single-strand breaks and a moderate energy (MEMI) protocol that additionally creates oxidized bases were compared. Quantitative characterization of repair factor recruitment and sensitivity to clinical PARP inhibitors (PARPi) was dependent on the micro-irradiation protocol. PARP1 recruitment was biphasic and generally occurred prior to pol β and XRCC1. After LEMI, but not after MEMI, pol β and XRCC1 recruitment was abolished by the PARPi veliparib. Consistent with this, pol β and XRCC1 recruitment following LEMI was considerably slower in PARP1-deficient cells. Surprisingly, the recruitment half-times and amplitudes for pol β were less affected by PARPi than were XRCC1 after MEMI suggesting there is a XRCC1-independent component for pol β recruitment. After LEMI, but not MEMI, pol β dissociation was more rapid than that of XRCC1. Unexpectedly, PARP1 dissociation was slowed in the absence of XRCC1 as well with a PARPi after LEMI but not MEMI, suggesting that XRCC1 facilitates PARP1 dissociation from specific DNA lesions. XRCC1-deficient cells showed pronounced hypersensitivity to the PARPi talazoparib correlating with its known cytotoxic PARP1 trapping activity. In contrast to DNA methylating agents, PARPi only minimally sensitized pol β and XRCC1-deficient cells to oxidative DNA damage suggesting differential binding of PARP1 to alternate repair intermediates. In summary, pol β, XRCC1, and PARP1 display recruitment kinetics that exhibit correlated and unique properties that depend on the DNA lesion and PARP activity revealing that there are multiple avenues utilized in the repair of chromatin-associated DNA.
MeSH term(s)	Animals ; Mice ; Fibroblasts/metabolism ; DNA Repair ; DNA Damage ; X-ray Repair Cross Complementing Protein 1/metabolism ; Poly (ADP-Ribose) Polymerase-1/metabolism ; DNA/metabolism ; Poly(ADP-ribose) Polymerases/metabolism ; Chromatin ; Poly(ADP-ribose) Polymerase Inhibitors
Chemical Substances	X-ray Repair Cross Complementing Protein 1 ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; DNA (9007-49-2) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; Chromatin ; Poly(ADP-ribose) Polymerase Inhibitors
Language	English
Publishing date	2023-03-22
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2023.103486
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Article ; Online: Histone H3 Lysine 56 Acetylation Enhances AP Endonuclease 1-Mediated Repair of AP Sites in Nucleosome Core Particles.

Rodriguez, Yesenia / Horton, Julie K / Wilson, Samuel H

Biochemistry

2019 Volume 58, Issue 35, Page(s) 3646–3655

Abstract: Deciphering factors modulating DNA repair in chromatin is of great interest because nucleosomal positioning influences mutation rates. H3K56 acetylation (Ac) is implicated in chromatin landscape regulation, impacting genomic stability, yet the effect of ... ...

Abstract	Deciphering factors modulating DNA repair in chromatin is of great interest because nucleosomal positioning influences mutation rates. H3K56 acetylation (Ac) is implicated in chromatin landscape regulation, impacting genomic stability, yet the effect of H3K56Ac on DNA base excision repair (BER) remains unclear. We determined whether H3K56Ac plays a role in regulating AP site incision by AP endonuclease 1 (APE1), an early step in BER. Our
MeSH term(s)	Acetylation ; Animals ; Binding Sites/genetics ; DNA Repair/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/physiology ; Escherichia coli ; Genomic Instability ; Histone Acetyltransferases/metabolism ; Histones/chemistry ; Histones/metabolism ; Humans ; Lysine/metabolism ; Methanosarcina barkeri ; Mice ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Protein Binding ; Protein Processing, Post-Translational/physiology ; Sirtuins/genetics ; Sirtuins/metabolism ; Xenopus laevis
Chemical Substances	Histones ; Nucleosomes ; Histone Acetyltransferases (EC 2.3.1.48) ; Sirt6 protein, mouse (EC 2.4.2.31) ; Sirtuins (EC 3.5.1.-) ; APEX1 protein, human (EC 4.2.99.18) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2019-08-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.9b00433
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Article ; Online: The Utility of Functional Data Analyses to Reveal Between-Limbs Asymmetries in Those With a History of Anterior Cruciate Ligament Reconstruction.

White, McKenzie S / Horton, William Z / Burland, Julie P / Seeley, Matthew K / Lepley, Lindsey K

Journal of athletic training

2021 Volume 56, Issue 3, Page(s) 272–279

Abstract: Context: Researchers have traditionally used motion capture to quantify discrete data points (peak values) during hop testing. However, these analyses restrict the evaluation to a single time point (ie, certain percentage of stance) and provide only a ... ...

Abstract	Context: Researchers have traditionally used motion capture to quantify discrete data points (peak values) during hop testing. However, these analyses restrict the evaluation to a single time point (ie, certain percentage of stance) and provide only a narrow view of movement. Applying more comprehensive analyses may help investigators identify important characteristics that are masked by discrete analyses often used to screen patients for activity. Objective: To examine the utility of functional data analyses to reveal asymmetries that are undetectable using discrete (ie, single time point) evaluations in participants with a history of anterior cruciate ligament reconstruction (ACLR) who achieved clinical hop symmetry. Design: Cross-sectional study. Setting: Laboratory. Patients or other participants: Fifteen participants with unilateral ACLR (age = 21 ± 3 years, time from surgery = 4 ± 3 years) and 15 control participants without ACLR (age = 23 ± 2 years). Intervention(s): Lower extremity biomechanics during the triple-hop-for-distance task for the ACLR and contralateral limbs of patients and a representative limb of control participants were measured. Main outcome measure(s): Peak sagittal-plane joint power, joint work, and power profiles were determined. Results: Using discrete analyses, we identified lower peak knee power and work in the ACLR limb compared with the contralateral and control limbs (P < .05) but were unable to demonstrate differences at the ankle or hip. Using functional data analyses, we observed asymmetries at the ankle, knee, and hip between the ACLR and contralateral or control limbs throughout stance (P < .05), and it was revealed that these asymmetries stemmed from knee power deficits that were prominent during early loading. Conclusions: Despite achieving hop-distance symmetry, the ACLR knees absorbed less power. Although this information was revealed using discrete analyses, underlying asymmetries at the ankle and hip were masked. Using functional data analyses, we found interlimb asymmetries at the ankle, knee, and hip. Importantly, we found that functional data analyses more fully elucidated the extent and source of asymmetries, which can be used by clinicians and researchers alike to aid in clinical decision making.
Language	English
Publishing date	2021-02-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2070051-9
ISSN	1938-162X ; 1062-6050
ISSN (online)	1938-162X
ISSN	1062-6050
DOI	10.4085/1062-6050-0081.20
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Article ; Online: Lysines in the lyase active site of DNA polymerase β destabilize nonspecific DNA binding, facilitating searching and DNA gap recognition.

Howard, Michael J / Horton, Julie K / Zhao, Ming-Lang / Wilson, Samuel H

The Journal of biological chemistry

2020 Volume 295, Issue 34, Page(s) 12181–12187

Abstract: DNA polymerase (pol) β catalyzes two reactions at DNA gaps generated during base excision repair, gap-filling DNA synthesis and lyase-dependent 5´-end deoxyribose phosphate removal. The lyase domain of pol β has been proposed to function in DNA gap ... ...

Abstract	DNA polymerase (pol) β catalyzes two reactions at DNA gaps generated during base excision repair, gap-filling DNA synthesis and lyase-dependent 5´-end deoxyribose phosphate removal. The lyase domain of pol β has been proposed to function in DNA gap recognition and to facilitate DNA scanning during substrate search. However, the mechanisms and molecular interactions used by pol β for substrate search and recognition are not clear. To provide insight into this process, a comparison was made of the DNA binding affinities of WT pol β, pol λ, and pol μ, and several variants of pol β, for 1-nt-gap-containing and undamaged DNA. Surprisingly, this analysis revealed that mutation of three lysine residues in the lyase active site of pol β, 35, 68, and 72, to alanine (pol β KΔ3A) increased the binding affinity for nonspecific DNA ∼11-fold compared with that of the WT. WT pol μ, lacking homologous lysines, displayed nonspecific DNA binding behavior similar to that of pol β KΔ3A, in line with previous data demonstrating both enzymes were deficient in processive searching. In fluorescent microscopy experiments using mouse fibroblasts deficient in PARP-1, the ability of pol β KΔ3A to localize to sites of laser-induced DNA damage was strongly decreased compared with that of WT pol β. These data suggest that the three lysines in the lyase active site destabilize pol β when bound to DNA nonspecifically, promoting DNA scanning and providing binding specificity for gapped DNA.
MeSH term(s)	Animals ; Catalytic Domain ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Damage ; DNA Polymerase beta/chemistry ; DNA Polymerase beta/genetics ; DNA Polymerase beta/metabolism ; Enzyme Stability/genetics ; Humans ; Mice ; Protein Binding
Chemical Substances	DNA (9007-49-2) ; DNA Polymerase beta (EC 2.7.7.7) ; POLB protein, human (EC 2.7.7.7)
Language	English
Publishing date	2020-07-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA120.013547
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Article ; Online: Monitoring DNA polymerase β mitochondrial localization and dynamics.

Horton, Julie K / Janoshazi, Agnes K / Nadalutti, Cristina A / Zhao, Ming-Lang / Stefanick, Donna F / Wilson, Samuel H

DNA repair

2022 Volume 116, Page(s) 103357

Abstract: Mouse fibroblasts lacking (null) DNA polymerase β (pol β) were transfected with fluorescently tagged pol β and stained with biomarkers to allow visualization within living cells by confocal microscopy. Transient transfection resulted in varying pol β ... ...

Abstract	Mouse fibroblasts lacking (null) DNA polymerase β (pol β) were transfected with fluorescently tagged pol β and stained with biomarkers to allow visualization within living cells by confocal microscopy. Transient transfection resulted in varying pol β expression levels. Separating cells into three groups based on pol β fluorescence intensity and morphological distribution, permitted analysis of the concentration dependence and spatial distribution of cytoplasmic pol β. Colocalization between pol β and mitochondria was pol β concentration dependent. A decrease in overlap with nucleoids containing mitochondrial DNA (mtDNA) was observed at the highest pol β intensity where pol β exhibits a tubular appearance, suggesting the ability to load elevated levels of pol β into mitochondria readily available for relocation to damaged mtDNA. The dynamics of pol β and mitochondrial nucleoids were followed by confocal recording of time series images. Two populations of mitochondrial nucleoids were observed, with and without pol β. Micro-irradiation, known to form DNA single-strand breaks, in a line across nucleus and cytoplasm of pol β stably transfected cells enhanced apparent localization of pol β with mitochondria in the perinuclear region of the cytoplasm near the nuclear membrane. Exposure of pol β expressing cells to H
MeSH term(s)	Animals ; DNA Damage ; DNA Polymerase beta/metabolism ; DNA Repair ; DNA Replication ; DNA, Mitochondrial/metabolism ; Hydrogen Peroxide/pharmacology ; Mice
Chemical Substances	DNA, Mitochondrial ; Hydrogen Peroxide (BBX060AN9V) ; DNA Polymerase beta (EC 2.7.7.7)
Language	English
Publishing date	2022-06-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2022.103357
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Article ; Online: Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism.

Beard, William A / Horton, Julie K / Prasad, Rajendra / Wilson, Samuel H

Annual review of biochemistry

2019 Volume 88, Page(s) 137–162

Abstract: Genomic DNA is susceptible to endogenous and environmental stresses that modify DNA structure and its coding potential. Correspondingly, cells have evolved intricate DNA repair systems to deter changes to their genetic material. Base excision DNA repair ... ...

Abstract	Genomic DNA is susceptible to endogenous and environmental stresses that modify DNA structure and its coding potential. Correspondingly, cells have evolved intricate DNA repair systems to deter changes to their genetic material. Base excision DNA repair involves a number of enzymes and protein cofactors that hasten repair of damaged DNA bases. Recent advances have identified macromolecular complexes that assemble at the DNA lesion and mediate repair. The repair of base lesions generally requires five enzymatic activities: glycosylase, endonuclease, lyase, polymerase, and ligase. The protein cofactors and mechanisms for coordinating the sequential enzymatic steps of repair are being revealed through a range of experimental approaches. We discuss the enzymes and protein cofactors involved in eukaryotic base excision repair, emphasizing the challenge of integrating findings from multiple methodologies. The results provide an opportunity to assimilate biochemical findings with cell-based assays to uncover new insights into this deceptively complex repair pathway.
MeSH term(s)	DNA/chemistry ; DNA/metabolism ; DNA/ultrastructure ; DNA Damage ; DNA Glycosylases/chemistry ; DNA Glycosylases/metabolism ; DNA Glycosylases/ultrastructure ; DNA Repair ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; DNA-Directed DNA Polymerase/ultrastructure ; Endonucleases/chemistry ; Endonucleases/metabolism ; Endonucleases/ultrastructure ; Eukaryota/genetics ; Eukaryota/metabolism ; Eukaryotic Cells/cytology ; Eukaryotic Cells/enzymology ; Genome ; Genomic Instability ; Humans ; Ligases/chemistry ; Ligases/metabolism ; Ligases/ultrastructure ; Lyases/chemistry ; Lyases/metabolism ; Lyases/ultrastructure ; Models, Molecular ; Mutagenesis ; Nucleic Acid Conformation ; Protein Conformation
Chemical Substances	DNA (9007-49-2) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Endonucleases (EC 3.1.-) ; DNA Glycosylases (EC 3.2.2.-) ; Lyases (EC 4.-) ; Ligases (EC 6.-)
Language	English
Publishing date	2019-06-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	207924-0
ISSN	1545-4509 ; 0066-4154
ISSN (online)	1545-4509
ISSN	0066-4154
DOI	10.1146/annurev-biochem-013118-111315
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Article: Histone H3 Lysine 56 Acetylation Enhances AP Endonuclease 1-Mediated Repair of AP Sites in Nucleosome Core Particles

Rodriguez, Yesenia / Horton, Julie K / Wilson, Samuel H

Biochemistry. 2019 Aug. 13, v. 58, no. 35

2019

Abstract	Deciphering factors modulating DNA repair in chromatin is of great interest because nucleosomal positioning influences mutation rates. H3K56 acetylation (Ac) is implicated in chromatin landscape regulation, impacting genomic stability, yet the effect of H3K56Ac on DNA base excision repair (BER) remains unclear. We determined whether H3K56Ac plays a role in regulating AP site incision by AP endonuclease 1 (APE1), an early step in BER. Our in vitro studies of acetylated, well-positioned nucleosome core particles (H3K56Ac-601-NCPs) demonstrate APE1 strand incision is enhanced compared with that of unacetylated WT-601-NCPs. The high-mobility group box 1 protein enhances APE1 activity in WT-601-NCPs, but this effect is not observed in H3K56Ac-601-NCPs. Therefore, our results suggest APE1 activity on NCPs can be modulated by H3K56Ac.
Keywords	DNA repair ; acetylation ; genomics ; histones ; in vitro studies ; lysine ; mutation rate ; nucleobases ; nucleosomes ; particles
Language	English
Dates of publication	2019-0813
Size	p. 3646-3655.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-light
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.9b00433
Database	NAL-Catalogue (AGRICOLA)

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