DNA Damage Repair in the Context of Plant Chromatin

Abstract

The integrity of DNA molecules is constantly challenged. All organisms have developed mechanisms to detect and repair multiple types of DNA lesions. The basic principles of DNA damage repair (DDR) in prokaryotes and unicellular and multicellular eukaryotes are similar, but the association of DNA with nucleosomes in eukaryotic chromatin requires mechanisms that allow access of repair enzymes to the lesions. This is achieved by chromatin-remodeling factors, and their necessity for efficient DDR has recently been demonstrated for several organisms and repair pathways. Plants share many features of chromatin organization and DNA repair with fungi and animals, but they differ in other, important details, which are both interesting and relevant for our understanding of genome stability and genetic diversity. In this Update, we compare the knowledge of the role of chromatin and chromatin-modifying factors during DDR in plants with equivalent systems in yeast and humans. We emphasize plant-specific elements and discuss possible implications.A DNA molecule in a eukaryotic chromosome has a diameter of 2 nm but a length in the range of centimeters. Being 10 7 times longer than it is wide would make it highly sensitive to breakage if it were not organized in compact and dynamic chromatin, with nucleosomes as basic units followed by multiple higher order levels of organization. Within this packaging, replication and transcription constitute an endogenous mechanical strain, while exposure of cells to physical or chemical hazard creates a wide range of DNA damage induced by external factors, including photoproducts, pyrimidine dimers, interstrand crosslinking, and single and double-strand breaks (DSBs). All organisms possess mechanisms that repair DNA molecules. DNA damage repair (DDR) systems for the various types of damage are overlapping as well as complementary, and their prevalence depends on the organism, the stage of the cell cycle, the site and the amount of damage, and the availability of intact templates. A coarse categorization distinguishes nucleotide excision repair, base excision repair, nonhomologous end joining (NHEJ), and homologous recombination (HR). Many schematic models for these DDR pathways describe the action and interaction of several repair components, but they are usually misleading in one aspect: DNA strands are illustrated as straight lines, neglecting the emerging role of chromatin for the location and the fate of DNA lesions. More realistically, we should envisage DNA lesions in the chromatin context like the leakage or burst of an in-ground pipe. Recognizing the defect, localizing it, excavating the broken parts, cleaning the ends, reconnecting them, and restoring the original state are mirrored in the subsequent steps of DDR: signaling, labeling, accessing, resecting, religating, and reassembling. Chromatin is expected to especially affect the access, resection, and restoration of the original arrangement, and several factors that can dissolve higher order structures, slide, evict, or exchange ...

Compartmentalization of DNA Damage Response between Heterochromatin and Euchromatin Is Mediated by Distinct H2A Histone Variants

“…DNA double-strand break (DSB) repair depends on the ataxia telangiectasia mutated (ATM) kinase that phosphorylates the conserved C-terminal SQ motif present in the histone variant H2A.X [1][2][3][4][5][6][7]. In constitutive heterochromatin of mammals, DSB repair is delayed and relies on phosphorylation of the proteins HP1 and KAP1 by ATM [2,[8][9][10][11][12][13][14].…”

“…Kinetics of gH2A.X and gH2A.W.7 in Response to DNA Damage In response to DNA damage in metazoa and plants, gH2A.X decorates sites of DSBs as discrete gH2A.X foci, which are widely used to monitor DSB formation and repair [4,6,29,30]. In order to study the location and dynamics of H2A.X and H2A.W.7 phosphorylation during DDR, we used phospho-specific antibodies ( Figures S2A-S2C) to analyze and quantify the distribution of gH2A.W.7 and gH2A.X after bleomycin treatment using immunofluorescence.…”

Distinct roles of the histone chaperones NAP1 and NRP and the chromatin‐remodeling factor INO80 in somatic homologous recombination in Arabidopsis thaliana

“…Repair of DSBs occurs within the context of the complex structure of chromatin. The ATP‐dependent chromatin‐remodeling factor AtINO80 and the histone chaperones AtNAP1 and NRP are among the few chromatin regulators so far identified to be required in plant somatic HR (Fritsch et al ., ; Gao et al ., ; Dona and Mittelsten Scheid, ; Zhang et al ., ; Zhou et al ., ). A positive role of INO80 in HR has also been reported in yeast (Morrison et al ., ; Kawashima et al ., ) and mammalian cells (Wu et al ., ; Alatwi and Downs, ), and more recently NAP1 has also been reported to positively regulate HR in mammalian cells (Machida et al ., ).…”

“…A DNA lesion is repaired by HR using an intact/undamaged homologous DNA sequence as a template; such a sequence can be found within a repeat region, a sister chromatid or a homologous chromosome (Schuermann et al, 2005;Heyer et al, 2010). Although its precise role remains a matter for debate, phosphorylation of H2A.X (c-H2A.X) constitutes one of the earliest events occurring at DSB sites, preceding nucleosome dissociation and recruitment of ATP-dependent chromatin remodeling complexes (Morrison et al, 2004;van Attikum et al, 2004;Tsukuda et al, 2005;Bennett et al, 2013;Dona and Mittelsten Scheid, 2015). INOSITOL AUXOTROPHY 80 (INO80) is an ATP-dependent chromatin-remodeling factor initially demonstrated to be a positive regulator of HR in Arabidopsis , yeast (Morrison et al, 2004;Kawashima et al, 2007) and mammalian cells (Wu et al, 2007).…”

Chromatin and Epigenetics

“…The Update by Donà and Mittelsten Scheid (2015) on chromatin and DNA-damage repair (DDR) provides an excellent start into the topic, as it exemplifies the problem of how essential repair machinery gets to a site that is buried under a compact structure, with minimal disturbance. A nucleosome can be shifted, evicted, or exchanged, its composition can be altered, and its subunits can be covalently modified.…”