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Study of Interaction of the PARP Family DNA-Dependent Proteins with Nucleosomes Containing DNA Intermediates of the Initial Stages of BER Process

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Abstract

Reaction of (ADP-ribosyl)ation catalyzed by DNA-dependent proteins of the poly(ADP-ribose)polymerase (PARP) family, PARP1, PARP2, and PARP3, comprises the cellular response to DNA damage. These proteins are involved in the base excision repair (BER) process. Despite the extensive research, it remains unknown how PARPs are involved in the regulation of the BER process and how the roles are distributed between the DNA-dependent members of the PARP family. Here, we investigated the interaction of the PARP’s family DNA-dependent proteins with nucleosome core particles containing DNA intermediates of the initial stages of BER. To do that, the nucleosomes containing damage in the vicinity of one of the DNA duplex blunt ends were reconstituted based on the Widom’s Clone 603 DNA sequence. Dissociation constants of the PARP complexes with nucleosomes bearing DNA contained uracil (Native), apurine/apyrimidine site (AP site), or a single-nucleotide gap with 5′-dRp fragment (Gap) were determined. It was shown that the affinity of the proteins for the nucleosomes increased in the row: PARP3<<PARP2<PARP1; whereas the affinity of each protein for the certain damage type increased in the row: Native = AP site < Gap for PARP1 and PARP2, Gap<<<Native = AP site for PARP3. The interaction regions of each PARP protein with nucleosome were also determined by sodium borohydride cross-linking and footprinting assay. Based on the obtained and published data, the involvement pattern of the PARP1, PARP2, and PARP3 into the interaction with nucleosome particles containing DNA intermediates of the BER process was discussed.

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Abbreviations

AP site:

apurine/apyrimidine site

AP cluster:

cluster of AP sites

APE1:

apurinic/apyrimidinic endonuclease 1

BER:

base excision repair

DNase I:

deoxyribonuclease I

Gap:

DNA duplex containing 5′-dRp-fragment

NCP:

nucleosome or nucleosome core particle

PARP:

poly(ADP-ribose)polymerase

PARylation:

poly(ADP-ribosyl)ation

UDG:

uracil-DNA glycosylase

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Funding

This work was financially supported by the Russian Foundation for Basic Research (grant no. 20-04-00674) and Russian Government funded budget project of ICBFM SB RAS no. 121031300041-4.

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    Authors and Affiliations

    1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

      Alexander A. Ukraintsev, Ekaterina A. Belousova, Mikhail M. Kutuzov & Olga I. Lavrik

    2. Novosibirsk State University, 630090, Novosibirsk, Russia

      Olga I. Lavrik

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    1. Alexander A. Ukraintsev
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    Correspondence to Olga I. Lavrik.

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    Ukraintsev, A.A., Belousova, E.A., Kutuzov, M.M. et al. Study of Interaction of the PARP Family DNA-Dependent Proteins with Nucleosomes Containing DNA Intermediates of the Initial Stages of BER Process. Biochemistry Moscow 87, 331–345 (2022). https://doi.org/10.1134/S0006297922040034

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