Research communication copper-1,10-phenanthroline induces internucleosomal DNA fragmentation in HepG2 cells, resulting from direct oxidation by the hydroxyl radical

Tsang, Suk Ying; Tam, Shuk Ching; Bremner, I.; Burkitt, Mark J.

doi:10.1042/bj3170013

Cited by 101 publications

(59 citation statements)

References 28 publications

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“…3A) and nucleosome mapping using an alternative method based on DNA digestion by a chemical agent (phenanthroline) in human Raji B-cells (Supplemental Fig. 3C; Tsang et al 1996). In both cases, we confirmed a correlation between nucleosome depletion and CGI length; we also sequenced sonicated genomic DNA that showed only very little sequencing bias in the promoters containing the largest CpG content (Supplemental Fig.…”

Section: Gc Content and Cgis Define Nucleosome Depletion Patterns At supporting

confidence: 57%

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CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

et al. 2012

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One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties that correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion and show that CpG content and CGI width correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals.[Supplemental material is available for this article.]How the transcriptional machinery accesses gene promoters is a central question for understanding gene regulation. Because eukaryotic genomes are highly compacted, most of the DNA is not easily accessible to transcription factors, to the notable exception of promoters that tend to be more open chromatin structures. In recent years, with the development of genome-wide approaches, several studies in various organisms have described that nucleosomes are at least partially dependent on the primary sequence for their positioning (Kaplan et al. 2009). In yeast and Drosophila, for example, AT-rich stretches at promoters exclude nucleosomes both in vivo and in vitro, although the correlation of both data sets has been discussed in the literature, as opposed to GC-rich regions, often found in gene bodies, which favor nucleosome occupancy (Kaplan et al. 2009(Kaplan et al. , 2010Zhang et al. 2009;Pugh 2010). In contrast, most mammalian promoters are enriched for GC-rich areas-also called CpG islands (CGIs)-whereas TATA boxes only appear in a minority of genes (Sandelin et al. 2007). CGIs are defined as large genomic areas of over-enriched CpG dinucleotides estimated to amount to between 20,000 and 30,000 in various mammalian genomes lacking counterparts in cold blooded organisms or other eukaryotes (Illingworth and Bird 2009;Sharif et al. 2010). Although recent works suggest a link between nucleosome depletion at promoters and the presence of CGIs, a direct correlation was never established (Li et al. 2011;Valouev et al. 2011). Furthermore, it remains to be determined whether nucleosome depletion is a cause or a consequence of promoter transcription because in vitro experimental approaches describe apparently contradictory results (Ramirez-Carrozzi et al. 2009;Valouev et al. 2011).In this study, we report that GC content and CGIs are major promoter elements in mammals able to govern open chromatin conformation and support paused transcription genome-wide. First, we define t...

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Section: Gc Content and Cgis Define Nucleosome Depletion Patterns At supporting

confidence: 57%

“…The sequencing procedure was conducted using at least 1 ng of starting material and run on a Genome Analyzer II (Illumina). The in vivo phenanthroline digestion of nucleosomes was adapted from Tsang et al (1996) and is described in the Supplemental Methods together with the computational processing and analysis pipeline.…”

Section: Chip-seq and Mnase-seqmentioning

confidence: 99%

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

et al. 2012

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“…Extracellular addition of hydrogen peroxide could induce apoptosis and necrosis, and Z-DEVD-CH 2 F inhibited hydrogen peroxide-induced cell death (data not shown), indicating that hydrogen peroxide can induce cell death. Tsang et al reported that hydroxyl radical can induce internucleosomal DNA fragmentation even at 48C and proposed that hydroxyl radical directly aected DNA to induce DNA fragmentation (Tsang et al, 1996). It is still possible that direct oxidation of DNA by hydroxyl radical might synergistically work with the caspase 3-like protease to induce DNA fragmentation.…”

Section: Discussionmentioning

confidence: 99%

Regulation of reactive oxygen species-induced apoptosis and necrosis by caspase 3-like proteases

et al. 1998

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Reactive oxygen species (ROS) and caspases have been implicated as potential mediators of cell death. However, their mechanistic relationship remains to be elucidated. Here we investigated the roles of caspases in apoptosis and necrosis induced by ROS, generated by the mixture of xanthine and xanthine oxidase (X/XO). A low concentration of XO (0.025 U/ml) induced DNA fragmentation with little cellular membrane damage 3 h after treatment, suggesting the induction of apoptosis. The same treatment induced membrane blebbing, a morphological change typical of apoptosis, 15 min after treatment. A high concentration of XO (0.1 U/ml) damaged cell membranes with little concomitance of DNA fragmention, suggesting the induction of necrosis. ROS also activated caspase 3-like proteases and caspase 3 itself together with the release of cytochrome c which might be the cause of caspase activation. Apoptosis induced by low concentrations of XO and necrosis induced by high concentrations of XO was inhibited by Z-DEVD-CH 2 F, an irreversible inhibitor of caspase 3. However, rapid induction of membrane blebbing was not inhibited by Z-DEVD-CH 2 F. These results suggest that both apoptosis and necrosis could be induced by ROS through the activation of caspase 3-like protease; however, caspase 3 activation is not needed for ROSinduced membrane blebbing.

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“…It is noteworthy that nucleic acid oxidation occurs widely in vulnerable neuronal populations in AD (6) and oxidative damage can directly cause DNA fragmentation (7). Therefore, DNA damage possibly resulting from oxidative stress involves vulnerable neurons in AD beyond the distribution of amyloid deposition or neurofibrillary tangles, which may be related to neuronal cell death occurring independently of the classical AD pathology (3).…”

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confidence: 99%

Avoidance of Apoptosis in Alzheimer's Disease

Nunomura

2000

JAD

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Internucleosomal DNA fragmentation, which is a well-known feature of apoptosis but not an absolute criterion for identifying apoptosis (1), has often been observed in the brain tissue of Alzheimer's disease (AD). However, classical apoptotic morphology such as nuclear condensation, membrane blebbing and apoptotic bodies are seldom seen in AD brain. In this issue of Journal of Alzheimer's Disease, Velez-Pardo et al. have reported the DNA fragmentation using terminal dUTP labeling (TUNEL) in postmortem brains of familial AD with presenilin-1 [E280A] mutation. Importantly, no classical apoptotic morphology has been observed also in the brains of presenilin-1 familial AD. Furthermore, Velez-Pardo et al. have shown that there is no obvious correlation between DNA fragmentation and the severity of amyloid deposition as well as between DNA fragmentation and the severity of neurofibrillary tangle formation.An apoptotic pathway only takes several hours or at most a few days for completion. In the development of the lateral motor column of the chick embryo, 8,000 cells out of 20,000 cells die, i.e. loss of 40% of the population occurs within 3 days (2). The fact that only 5% of the population in the lateral motor column is undergoing apoptosis at any particular time in this period (2) indicates that apoptotic pathway requires about 10 hours for completion. In a striking contrast with the physiologically programmed cell death, loss of 40% of the population occurs (3,000 neurons

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Research communication copper-1,10-phenanthroline induces internucleosomal DNA fragmentation in HepG2 cells, resulting from direct oxidation by the hydroxyl radical

Cited by 101 publications

References 28 publications

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

Regulation of reactive oxygen species-induced apoptosis and necrosis by caspase 3-like proteases

Avoidance of Apoptosis in Alzheimer's Disease

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