The genome-wide sequence preference of ionising radiation-induced cleavage in human DNA

Hardie, Megan E.; Gautam, Shweta D.; Murray, Vincent

doi:10.1007/s11033-019-04815-6

Cited by 6 publications

(22 citation statements)

References 84 publications

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“…The J clone [60] contains a number of consecutive G nucleotides with different lengths. Purified human genomic DNA was utilised for the genome-wide studies [62].…”

Section: Methodsmentioning

confidence: 99%

“…The IR-induced DNA damage was generated by γ-irradiation from a sealed caesium-137 source that irradiated at a rate of 5.02 Gy/min at ambient atmosphere and temperature [60][61][62]. Experimental details of the three technique have been previously published for the LA/PS assay [60], the end-labelling technique [61] and the short-read Illumina next-generation genome-wide sequencing technique [62]. Purified DNA was utilised as the target for these three IR-induced DNA damage studies [60][61][62].…”

Section: Methodsmentioning

confidence: 99%

“…Experimental details of the three technique have been previously published for the LA/PS assay [60], the end-labelling technique [61] and the short-read Illumina next-generation genome-wide sequencing technique [62]. Purified DNA was utilised as the target for these three IR-induced DNA damage studies [60][61][62].…”

Section: Methodsmentioning

confidence: 99%

“…There are three techniques that have recently examined the DNA sequence preference of IR-induced DNA damage at nucleotide resolution using cutting-edge technology: the linear amplification/polymerase stop (LA/PS) assay [60], the end-labelling procedure [61], and Illumina next-generation genome-wide sequencing [62], as seen in Figure 1.…”

Section: Techniques To Determine the Sequence Preference Of Ir-inducementioning

confidence: 99%

“…The Illumina next-generation genome-wide sequencing technique mainly detects DSBs. A recent study with the human genome found that C nucleotides were the main site of IR-induced DNA damage [62].…”

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confidence: 99%

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Comparison of Different Methods to Determine the DNA Sequence Preference of Ionising Radiation-Induced DNA Damage

Murray

Hardie

Gautam

2019

Genes

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Ionising radiation (IR) is known to induce a wide variety of lesions in DNA. In this review, we compared three different techniques that examined the DNA sequence preference of IR-induced DNA damage at nucleotide resolution. These three techniques were: the linear amplification/polymerase stop assay, the end-labelling procedure, and Illumina next-generation genome-wide sequencing. The DNA sequence preference of IR-induced DNA damage was compared in purified DNA sequences including human genomic DNA. It was found that the DNA sequence preference of IR-induced DNA damage identified by the end-labelling procedure (that mainly detected single-strand breaks) and Illumina next-generation genome-wide sequencing (that mainly detected double-strand breaks) was at C nucleotides, while the linear amplification/polymerase stop assay (that mainly detected base damage) was at G nucleotides. A consensus sequence at the IR-induced DNA damage was found to be 5 -AGGC*C for the end-labelling technique, 5 -GGC*MH (where * is the cleavage site, M is A or C, H is any nucleotide except G) for the genome-wide technique, and 5 -GG* for the linear amplification/polymerase stop procedure. These three different approaches are important because they provide a deeper insight into the mechanism of action of IR-induced DNA damage.The hydroxyl radical can cause both SSBs and DSBs via reaction with the deoxyribose sugar of DNA [15,33,34]. IR also induces DNA damage to the bases in DNA. The purine bases are damaged to a greater extent than the pyrimidines [28,35,36]. The major purine lesions induced by IR are: 8-oxo-7,8-dihydroguanine (8-oxoG), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy-G), 8-oxo-7,8-dihydro-2 -deoxyadenosine (8-oxoA) and 4,6-diamino-5-formamidopyrimidine (Fapy-A). The major pyrimidine lesions are the thymine glycols that are the cis-and trans-diasteromers of 5,6-dihydroxy-5,6-dihydrothymine (Thy-Gly) [37,38].Apurinic/apyrimidinic (also known as abasic) sites are also produced by IR and can be identified by a number of enzymes [39][40][41][42][43][44][45][46]. These apurinic/apyrimidinic-specific enzymes can be used to detect the level of modified bases after IR treatment [33,34,47].The IR-induced damage site can be several nucleotides from the initial lesion [48,49]. A transfer process can occur whereby an electron loss centre (hole) can move along the DNA until it reaches a site with the lowest ionisation energy which is usually the guanine base [50,51]. In DNA with GG and GGG sequences, the hole is located at the 5 -G in a run of consecutive guanine nucleotides [52][53][54][55][56][57][58][59].It has been estimated that over 100 oxidatively generated DNA lesions and modifications are induced by IR [12]. A number of these lesions can be formed along the radiation track and thus can contribute to the complexity of IR-induced DNA damage. Techniques to Determine the Sequence Preference of IR-Induced DNA DamageThere are three techniques that have recently examined the DNA sequence preference of IR-induced DNA damage at nucleo...

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“…The J clone [60] contains a number of consecutive G nucleotides with different lengths. Purified human genomic DNA was utilised for the genome-wide studies [62].…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Techniques To Determine the Sequence Preference Of Ir-inducementioning

confidence: 99%

mentioning

confidence: 99%

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Comparison of Different Methods to Determine the DNA Sequence Preference of Ionising Radiation-Induced DNA Damage

Murray

Hardie

Gautam

2019

Genes

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The sequence preference of gamma radiation mutagenesis using a novel in vitro model

et al. 2021

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Detection and quantification of γ-H2AX using a dissociation enhanced lanthanide fluorescence immunoassay

Noubissi

McBride

Leppert

et al. 2021

Sci Rep

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Phosphorylation of the histone protein H2AX to form γ-H2AX foci directly represents DNA double-strand break formation. Traditional γ-H2AX detection involves counting individual foci within individual nuclei. The novelty of this work is the application of a time-resolved fluorescence assay using dissociation-enhanced lanthanide fluorescence immunoassay for quantitative measurements of γ-H2AX. For comparison, standard fluorescence detection was employed and analyzed either by bulk fluorescent measurements or by direct foci counting using BioTek Spot Count algorithm and Gen 5 software. Etoposide induced DNA damage in A549 carcinoma cells was compared across all test platforms. Time resolved fluorescence detection of europium as a chelated complex enabled quantitative measurement of γ-H2AX foci with nanomolar resolution. Comparative bulk fluorescent signals achieved only micromolar sensitivity. Lanthanide based immunodetection of γ-H2AX offers superior detection and a user-friendly workflow. These approaches have the potential to improve screening of compounds that either enhance DNA damage or protect against its deleterious effects.

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The genome-wide sequence preference of ionising radiation-induced cleavage in human DNA

Cited by 6 publications

References 84 publications

Comparison of Different Methods to Determine the DNA Sequence Preference of Ionising Radiation-Induced DNA Damage

Comparison of Different Methods to Determine the DNA Sequence Preference of Ionising Radiation-Induced DNA Damage

The sequence preference of gamma radiation mutagenesis using a novel in vitro model

Detection and quantification of γ-H2AX using a dissociation enhanced lanthanide fluorescence immunoassay

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