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Nucleotide excision repair in cellular chromatin: studies with yeast from nucleotide to gene to genome.

Waters R, Evans K, Bennett M, Yu S, Reed S - Int J Mol Sci (2012)

Bottom Line: Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER) in Saccharomyces cerevisiae.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK; E-Mails: evansKE3@cardiff.ac.uk (K.E.); bennettMR1@cardiff.ac.uk (M.B.); yuS@cardiff.ac.uk (S.Y.); reedSH1@cardiff.ac.uk (S.R.).

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 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.

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Model for UV induced chromatin remodeling during GG-NER. Top panel: In the absence of UV, basal levels of histone acetyl transferase occupancy is observed, histone H3 tails remain unacetylated and chromatin is repressed. Lower Panel: Following UV the DNA translocase (1) and E3 ligase (2) activities of Rad16 in the GG-NER complex promote increased histone acetyl transferase occupancy (3) and histone H3 acetylation (4) that drives chromatin remodeling (5). Failure of the GG-NER complex to slide nucleosomes may prevent transcription factor binding explaining the continued repression of MFA2 transcription (6) despite chromatin remodeling. GG-NER dependent chromatin remodeling promotes efficient lesion removal [7].
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f14-ijms-13-11141: Model for UV induced chromatin remodeling during GG-NER. Top panel: In the absence of UV, basal levels of histone acetyl transferase occupancy is observed, histone H3 tails remain unacetylated and chromatin is repressed. Lower Panel: Following UV the DNA translocase (1) and E3 ligase (2) activities of Rad16 in the GG-NER complex promote increased histone acetyl transferase occupancy (3) and histone H3 acetylation (4) that drives chromatin remodeling (5). Failure of the GG-NER complex to slide nucleosomes may prevent transcription factor binding explaining the continued repression of MFA2 transcription (6) despite chromatin remodeling. GG-NER dependent chromatin remodeling promotes efficient lesion removal [7].

Mentions: These data have shed some considerable insight in how GG-NER operates on repressed chromatin and they have led us to propose the model shown in Figure 14. In wild type cells in the absence of UV damage (Figure 14 upper panel), only basal levels of Gcn5 occupancy at the promoter region of MFA2 are observed, consequently the histone H3 acetylation status is maintained at a low level, and chromatin remains in a closed configuration preventing gene transcription from MFA2. Following UV irradiation (Figure 14 lower panel), Rad7 and Rad16 dependent increased occupancy of the histone acetyl transferase Gcn5 (Figure 14(3)) results in elevated levels of histone H3 acetylation (Figure 14(4)). This promotes an open chromatin structure at MFA2 (Figure 14(5)). Our results show that this is achieved via the dual action of the DNA translocase (Figure 14(1)) and E3 ligase (Figure 14(2)) activities associated with the ATPase and RING domains of the Rad16 component of the GG-NER complex. We recently showed that the GG-NER complex exhibits DNA translocase activity associated with the ATPase domain of Rad16 [33]. This activity generates superhelical torsion in DNA necessary for excision of DNA damage during GG-NER in vitro. In the same study we also reported that the GG-NER complex is not able to slide nucleosomes in an in vitro assay, unlike many SWI/SNF chromatin remodelling complexes. Given these results, we hypothesise that the DNA translocase activity of the GG-NER complex specifically modifies chromatin structure to facilitate access of the Gcn5 histone acetyl transferase, which subsequently promotes an open chromatin structure necessary for efficient GG-NER via increased histone H3 acetylation in the region. We reported previously that during GG-NER at MFA2, the gene remains repressed. We suggest that failure of the GG-NER complex to slide nucleosomes at the promoter of MFA2 in response to UV prevents access to critical transcription initiation sites such as the TATA box, which precludes the sequence specific binding of key transcription initiation factors. In this way, the GG-NER complex can promote specific changes in chromatin structure required for efficient GG-NER (Figure 14(7)), while at the same time preventing unregulated gene transcription (Figure 14(6)). Our results also reveal the importance of the RING domain of Rad16 in promoting chromatin remodelling necessary for efficient GG-NER. This suggests that the E3 ubiquitin ligase activity of the GG-NER complex also plays a role in chromatin remodelling necessary for repair.


Nucleotide excision repair in cellular chromatin: studies with yeast from nucleotide to gene to genome.

Waters R, Evans K, Bennett M, Yu S, Reed S - Int J Mol Sci (2012)

Model for UV induced chromatin remodeling during GG-NER. Top panel: In the absence of UV, basal levels of histone acetyl transferase occupancy is observed, histone H3 tails remain unacetylated and chromatin is repressed. Lower Panel: Following UV the DNA translocase (1) and E3 ligase (2) activities of Rad16 in the GG-NER complex promote increased histone acetyl transferase occupancy (3) and histone H3 acetylation (4) that drives chromatin remodeling (5). Failure of the GG-NER complex to slide nucleosomes may prevent transcription factor binding explaining the continued repression of MFA2 transcription (6) despite chromatin remodeling. GG-NER dependent chromatin remodeling promotes efficient lesion removal [7].
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3472735&req=5

f14-ijms-13-11141: Model for UV induced chromatin remodeling during GG-NER. Top panel: In the absence of UV, basal levels of histone acetyl transferase occupancy is observed, histone H3 tails remain unacetylated and chromatin is repressed. Lower Panel: Following UV the DNA translocase (1) and E3 ligase (2) activities of Rad16 in the GG-NER complex promote increased histone acetyl transferase occupancy (3) and histone H3 acetylation (4) that drives chromatin remodeling (5). Failure of the GG-NER complex to slide nucleosomes may prevent transcription factor binding explaining the continued repression of MFA2 transcription (6) despite chromatin remodeling. GG-NER dependent chromatin remodeling promotes efficient lesion removal [7].
Mentions: These data have shed some considerable insight in how GG-NER operates on repressed chromatin and they have led us to propose the model shown in Figure 14. In wild type cells in the absence of UV damage (Figure 14 upper panel), only basal levels of Gcn5 occupancy at the promoter region of MFA2 are observed, consequently the histone H3 acetylation status is maintained at a low level, and chromatin remains in a closed configuration preventing gene transcription from MFA2. Following UV irradiation (Figure 14 lower panel), Rad7 and Rad16 dependent increased occupancy of the histone acetyl transferase Gcn5 (Figure 14(3)) results in elevated levels of histone H3 acetylation (Figure 14(4)). This promotes an open chromatin structure at MFA2 (Figure 14(5)). Our results show that this is achieved via the dual action of the DNA translocase (Figure 14(1)) and E3 ligase (Figure 14(2)) activities associated with the ATPase and RING domains of the Rad16 component of the GG-NER complex. We recently showed that the GG-NER complex exhibits DNA translocase activity associated with the ATPase domain of Rad16 [33]. This activity generates superhelical torsion in DNA necessary for excision of DNA damage during GG-NER in vitro. In the same study we also reported that the GG-NER complex is not able to slide nucleosomes in an in vitro assay, unlike many SWI/SNF chromatin remodelling complexes. Given these results, we hypothesise that the DNA translocase activity of the GG-NER complex specifically modifies chromatin structure to facilitate access of the Gcn5 histone acetyl transferase, which subsequently promotes an open chromatin structure necessary for efficient GG-NER via increased histone H3 acetylation in the region. We reported previously that during GG-NER at MFA2, the gene remains repressed. We suggest that failure of the GG-NER complex to slide nucleosomes at the promoter of MFA2 in response to UV prevents access to critical transcription initiation sites such as the TATA box, which precludes the sequence specific binding of key transcription initiation factors. In this way, the GG-NER complex can promote specific changes in chromatin structure required for efficient GG-NER (Figure 14(7)), while at the same time preventing unregulated gene transcription (Figure 14(6)). Our results also reveal the importance of the RING domain of Rad16 in promoting chromatin remodelling necessary for efficient GG-NER. This suggests that the E3 ubiquitin ligase activity of the GG-NER complex also plays a role in chromatin remodelling necessary for repair.

Bottom Line: Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER) in Saccharomyces cerevisiae.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK; E-Mails: evansKE3@cardiff.ac.uk (K.E.); bennettMR1@cardiff.ac.uk (M.B.); yuS@cardiff.ac.uk (S.Y.); reedSH1@cardiff.ac.uk (S.R.).

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 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.

Show MeSH
Related in: MedlinePlus