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Special Issue "Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry, Molecular Biology and Biophysics".

Deadline for manuscript submissions: closed (31 July 2012)

Special Issue Editor

Guest Editor
Prof. Raymond Waters

Cancer Genetics Building, Cardiff University Medical School, Heath Park, Cardiff, CF14 4XN, UK
Phone: +44 2920 687 336

Special Issue Information

Dear Colleagues,

The issue will focus on how nucleotide excision repair (NER) operates in cellular chromatin. This topic is receiving increasing focus, yet we are only beginning understand the ways by which the functionality of the NER core components can be maximised in various epigenetic environments. We will discuss how the cell modifies epigenetic states to facilitate efficient NER and how it restores these states to their pre-damaged status; an essential facet to maintain the epigenetic code and correct transcriptional regulation .
We will consider results accrued employing model genes and those obtained by examining entire genomes.
Thus the issue will summarize our current understanding, and it will consider how new approaches are enabling, and which will enable, major advances.

Prof. Raymond Waters
Guest Editor

Keywords

  • DNA damage and repair
  • Chromatin
  • Nucleotide Excision Repair
  • Epigenetics

Published Papers (7 papers)

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Review

Open AccessReview E2F1 and p53 Transcription Factors as Accessory Factors for Nucleotide Excision Repair
Int. J. Mol. Sci. 2012, 13(10), 13554-13568; doi:10.3390/ijms131013554
Received: 17 August 2012 / Revised: 10 October 2012 / Accepted: 15 October 2012 / Published: 19 October 2012
Cited by 5 | PDF Full-text (551 KB) | HTML Full-text | XML Full-text
Abstract
Many of the biochemical details of nucleotide excision repair (NER) have been established using purified proteins and DNA substrates. In cells however, DNA is tightly packaged around histones and other chromatin-associated proteins, which can be an obstacle to efficient repair. Several cooperating [...] Read more.
Many of the biochemical details of nucleotide excision repair (NER) have been established using purified proteins and DNA substrates. In cells however, DNA is tightly packaged around histones and other chromatin-associated proteins, which can be an obstacle to efficient repair. Several cooperating mechanisms enhance the efficiency of NER by altering chromatin structure. Interestingly, many of the players involved in modifying chromatin at sites of DNA damage were originally identified as regulators of transcription. These include ATP-dependent chromatin remodelers, histone modifying enzymes and several transcription factors. The p53 and E2F1 transcription factors are well known for their abilities to regulate gene expression in response to DNA damage. This review will highlight the underappreciated, transcription-independent functions of p53 and E2F1 in modifying chromatin structure in response to DNA damage to promote global NER. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Open AccessReview Implication of Posttranslational Histone Modifications in Nucleotide Excision Repair
Int. J. Mol. Sci. 2012, 13(10), 12461-12486; doi:10.3390/ijms131012461
Received: 21 August 2012 / Revised: 17 September 2012 / Accepted: 20 September 2012 / Published: 28 September 2012
Cited by 7 | PDF Full-text (1085 KB) | HTML Full-text | XML Full-text
Abstract
Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER) is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism [...] Read more.
Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER) is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism of NER is relatively well known, how cells detect and repair lesions in diverse chromatin environments is still under intensive research. As with all DNA-related processes, the NER machinery must deal with the presence of organized chromatin and the physical obstacles it presents. A huge catalogue of posttranslational histone modifications has been documented. Although a comprehensive understanding of most of these modifications is still lacking, they are believed to be important regulatory elements for many biological processes, including DNA replication and repair, transcription and cell cycle control. Some of these modifications, including acetylation, methylation, phosphorylation and ubiquitination on the four core histones (H2A, H2B, H3 and H4) or the histone H2A variant H2AX, have been found to be implicated in different stages of the NER process. This review will summarize our recent understanding in this area. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Open AccessReview The Emerging Roles of ATP-Dependent Chromatin Remodeling Enzymes in Nucleotide Excision Repair
Int. J. Mol. Sci. 2012, 13(9), 11954-11973; doi:10.3390/ijms130911954
Received: 2 August 2012 / Revised: 30 August 2012 / Accepted: 31 August 2012 / Published: 20 September 2012
Cited by 16 | PDF Full-text (484 KB) | HTML Full-text | XML Full-text
Abstract
DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon [...] Read more.
DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs) are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER) in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Open AccessReview The Heterochromatic Barrier to DNA Double Strand Break Repair: How to Get the Entry Visa
Int. J. Mol. Sci. 2012, 13(9), 11844-11860; doi:10.3390/ijms130911844
Received: 17 August 2012 / Revised: 13 September 2012 / Accepted: 14 September 2012 / Published: 19 September 2012
Cited by 37 | PDF Full-text (1444 KB) | HTML Full-text | XML Full-text
Abstract
Over recent decades, a deep understanding of pathways that repair DNA double strand breaks (DSB) has been gained from biochemical, structural, biophysical and cellular studies. DNA non-homologous end-joining (NHEJ) and homologous recombination (HR) represent the two major DSB repair pathways, and both [...] Read more.
Over recent decades, a deep understanding of pathways that repair DNA double strand breaks (DSB) has been gained from biochemical, structural, biophysical and cellular studies. DNA non-homologous end-joining (NHEJ) and homologous recombination (HR) represent the two major DSB repair pathways, and both processes are now well understood. Recent work has demonstrated that the chromatin environment at a DSB significantly impacts upon DSB repair and that, moreover, dramatic modifications arise in the chromatin surrounding a DSB. Chromatin is broadly divided into open, transcriptionally active, euchromatin (EC) and highly compacted, transcriptionally inert, heterochromatin (HC), although these represent extremes of a spectrum. The HC superstructure restricts both DSB repair and damage response signaling. Moreover, DSBs within HC (HC-DSBs) are rapidly relocalized to the EC-HC interface. The damage response protein kinase, ataxia telangiectasia mutated (ATM), is required for HC-DSB repair but is dispensable for the relocalization of HC-DSBs. It has been proposed that ATM signaling enhances HC relaxation in the DSB vicinity and that this is a prerequisite for HC-DSB repair. Hence, ATM is essential for repair of HC-DSBs. Here, we discuss how HC impacts upon the response to DSBs and how ATM overcomes the barrier that HC poses to repair. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Open AccessReview Chromatin Dynamics during Nucleotide Excision Repair: Histones on the Move
Int. J. Mol. Sci. 2012, 13(9), 11895-11911; doi:10.3390/ijms130911895
Received: 21 August 2012 / Revised: 6 September 2012 / Accepted: 7 September 2012 / Published: 19 September 2012
Cited by 11 | PDF Full-text (2318 KB) | HTML Full-text | XML Full-text
Abstract
It has been a long-standing question how DNA damage repair proceeds in a nuclear environment where DNA is packaged into chromatin. Several decades of analysis combining in vitro and in vivo studies in various model organisms ranging from yeast to human have [...] Read more.
It has been a long-standing question how DNA damage repair proceeds in a nuclear environment where DNA is packaged into chromatin. Several decades of analysis combining in vitro and in vivo studies in various model organisms ranging from yeast to human have markedly increased our understanding of the mechanisms underlying chromatin disorganization upon damage detection and re-assembly after repair. Here, we review the methods that have been developed over the years to delineate chromatin alterations in response to DNA damage by focusing on the well-characterized Nucleotide Excision Repair (NER) pathway. We also highlight how these methods have provided key mechanistic insight into histone dynamics coupled to repair in mammals, raising new issues about the maintenance of chromatin integrity. In particular, we discuss how NER factors and central players in chromatin dynamics such as histone modifiers, nucleosome remodeling factors, and histone chaperones function to mobilize histones during repair. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Open AccessReview Is DNA Damage Response Ready for Action Anywhere?
Int. J. Mol. Sci. 2012, 13(9), 11569-11583; doi:10.3390/ijms130911569
Received: 31 July 2012 / Revised: 6 September 2012 / Accepted: 7 September 2012 / Published: 14 September 2012
Cited by 3 | PDF Full-text (1259 KB) | HTML Full-text | XML Full-text
Abstract
Organisms are continuously exposed to DNA damaging agents, consequently, cells have developed an intricate system known as the DNA damage response (DDR) in order to detect and repair DNA lesions. This response has to be rapid and accurate in order to keep [...] Read more.
Organisms are continuously exposed to DNA damaging agents, consequently, cells have developed an intricate system known as the DNA damage response (DDR) in order to detect and repair DNA lesions. This response has to be rapid and accurate in order to keep genome integrity. It has been observed that the condensation state of chromatin hinders a proper DDR. However, the condensation state of chromatin is not the only barrier to DDR. In this review, we have collected data regarding the presence of DDR factors on micronuclear DNA lesions that indicate that micronuclei are almost incapable of generating an effective DDR because of defects in their nuclear envelope. Finally, considering the recent observations about the reincorporation of micronuclei to the main bulk of chromosomes, we suggest that, under certain circumstances, micronuclei carrying DNA damage might be a source of chromosome instability. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Figures

Open AccessReview Nucleotide Excision Repair in Cellular Chromatin: Studies with Yeast from Nucleotide to Gene to Genome
Int. J. Mol. Sci. 2012, 13(9), 11141-11164; doi:10.3390/ijms130911141
Received: 20 July 2012 / Revised: 22 August 2012 / Accepted: 24 August 2012 / Published: 7 September 2012
Cited by 4 | PDF Full-text (1808 KB) | HTML Full-text | XML Full-text
Abstract
Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER) in Saccharomyces cerevisiae. We have focused on how GGNER relates to histone acetylation for its functioning and we have identified the histone [...] Read more.
Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER) in Saccharomyces cerevisiae. We have focused on how GGNER relates to histone acetylation for its functioning and we have identified the histone acetyl tranferase Gcn5 and acetylation at lysines 9/14 of histone H3 as a major factor in enabling efficient repair. We consider results employing primarily MFA2 as a model gene, but also those with URA3 located at subtelomeric sequences. In the latter case we also see a role for acetylation at histone H4. We then go on to outline the development of a high resolution genome-wide approach that enables one to examine correlations between histone modifications and the nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers throughout entire genomes. This is an approach that will enable rapid advances in understanding the complexities of how compacted chromatin in chromosomes is processed to access DNA damage and then returned to its pre-damaged status to maintain epigenetic codes. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)

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