Mechanisms of Nucleosome Reorganization by PARP1

Marie-France Langelier,John M. Pascal,Md. Sohail Akhtar,Elena Y. Kotova,Alexey V. Feofanov,Dmitry K. Nilov,Natalya V. Maluchenko,Sergey V. Pushkarev,Mikhail P. Kirpichnikov,Nadezhda S. Gerasimova,Vasily M. Studitsky

doi:10.3390/ijms222212127

Abstract

Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair, chromatin organization and transcription. During transcription initiation, PARP1 interacts with gene promoters where it binds to nucleosomes, replaces linker histone H1 and participates in gene regulation. However, the mechanisms of PARP1-nucleosome interaction remain unknown. Here, using spFRET microscopy, molecular dynamics and biochemical approaches we identified several different PARP1-nucleosome complexes and two types of PARP1 binding to mononucleosomes: at DNA ends and end-independent. Two or three molecules of PARP1 can bind to a nucleosome depending on the presence of linker DNA and can induce reorganization of the entire nucleosome that is independent of catalytic activity of PARP1. Nucleosome reorganization depends upon binding of PARP1 to nucleosomal DNA, likely near the binding site of linker histone H1. The data suggest that PARP1 can induce the formation of an alternative nucleosome state that is likely involved in gene regulation and DNA repair.

Highlights

Poly(ADP-ribose) polymerase 1 (PARP1) is an abundant nuclear enzyme (1–2 million molecules per cell) and a nucleosome-binding protein localized in cell nuclei and involved in a variety of cellular processes including DNA repair, chromatin organization and transcription [1,2,3,4].PARP1 has distinct catalytic activity-dependent and independent functions duringDNA transactions [5,6]
We have shown that catalytic activity-independent binding of two or three PARP1 molecules to a core nucleosome or a nucleosome with a linker, respectively, is required to induce complete nucleosome reorganization in vitro
We have shown previously that PARP1 can introduce structural changes in the DNA of nucleosomes containing a double-stranded break exposed at the end of a 20 bp DNA region adjacent to the core nucleosome [21]

Summary

Introduction

PARP1 is an abundant nuclear enzyme (1–2 million molecules per cell) and a nucleosome-binding protein localized in cell nuclei and involved in a variety of cellular processes including DNA repair, chromatin organization and transcription [1,2,3,4].PARP1 has distinct catalytic activity-dependent and independent functions duringDNA transactions [5,6]. There are two types of catalytic activity-dependent functions of PARP1. Upon binding to DNA lesions, PARP1 becomes catalytically active, acting as a DNA damage sensor enzyme, which hydrolyzes NAD+ and forms long and branched chains of negatively charged polyADP-ribose (PAR) on a variety of nuclear proteins, including histones and PARP1 itself [7]. In this case, an interaction between the DNA-binding domain of PARP1 and DNA ends results inactivation of PARP1 [8,9,10].

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Conclusion