An in vitro method for detecting genetic toxicity based on inhibition of RNA synthesis by DNA lesions
© The Author(s) 2015
Received: 28 April 2015
Accepted: 9 July 2015
Published: 1 August 2015
A wide variety of DNA lesions such as ultraviolet light-induced photoproducts and chemically induced bulky adducts and crosslinks (intrastrand and interstrand) interfere with replication and lead to mutations and cell death. In the human body, these damages may cause cancer, inborn diseases, and aging. So far, mutation-related actions of DNA polymerases during replication have been intensively studied. However, DNA lesions also block RNA synthesis, making the detection of their effects on transcription equally important for chemical safety assessment. Previously, we established an in vivo method for detecting DNA damage induced by ultraviolet light and/or chemicals via inhibition of RNA polymerase by visualizing transcription.
Here, we present an in vitro method for detecting the effects of chemically induced DNA lesions using in vitro transcription with T7 RNA polymerase and real-time reverse transcription polymerase chain reaction (PCR) based on inhibition of in vitro RNA synthesis. Conventional PCR and real-time reverse transcription PCR without in vitro transcription can detect DNA lesions such as complicated cisplatin DNA adducts but not UV-induced lesions. We found that only this combination of in vitro transcription and real-time reverse transcription PCR can detect both cisplatin- and UV-induced DNA lesions that interfere with transcription.
We anticipate that this method will be useful for estimating the potential transcriptional toxicity of chemicals in terminally differentiated cells engaged in active transcription and translation but not in replication.
KeywordsDNA lesion Inhibition of RNA synthesis Genetic toxicity assay
Genomic DNA is continuously damaged by various exogenous and endogenous agents [1, 2]. The induced DNA lesions interfere with replication, leading to mutations and cell death, and have been associated with cancer, inborn diseases, and aging. In addition, DNA lesions interfere with transcription, inhibiting elongation by RNA polymerase and leading to reduced transcription and/or mutations of the transcript [3, 4]. Therefore, DNA lesions can induce cytotoxicity by inhibiting replication and/or transcription.
Under laboratory conditions, cell lines are maintained in an environment favorable to growth, DNA repair, prevention of apoptosis, and other aspects of cellular metabolism [3, 5–7]. As cancer and stem cells divide rapidly and constantly, proper experimental conditions for such cell lines are focused on replication. However, most cells within the human body are not exposed to such experimental conditions and are terminally differentiated, and post-mitotic cells engage in active transcription and translation but not in replication. Hence, transcription is assumed to be as important as replication for estimating the genetic toxicity of DNA lesions in human organs.
Inhibition of transcription can be effected by RNA polymerase stalling due to DNA lesions or RNA polymerase II inhibitors such as alpha-amanitin from the death cap [8, 9] and actinomycin D from Streptomyces bacteria, which intercalate into DNA and activate an inducer of apoptosis in many cell lines [10, 11].
All known organisms have repair systems to remove DNA lesions and maintain genomic integrity. When RNA polymerase II encounters DNA damage that blocks transcription during the elongation phase, transcription-coupled repair (TCR) immediately counteracts the interference. Previous studies have demonstrated TCR responses to bulky and helix-distorting lesions such as ultraviolet light (UV)-induced photolesions, e.g., cyclobutane pyrimidine dimers (CPD) [12, 13] and 6–4 photoproducts (6–4 pp) , cisplatin intrastrand crosslinks , and benzopyrene adducts .
Assessment of the biological risk and toxicity of newly synthesized chemicals is hampered by the large number of substances and the complexities of living cells. Current methods for detecting toxic substances are based on the DNA damage response in replication and cell proliferation. For example, the micronucleus assay that detects small nuclei is a well-established method for monitoring genetic toxicity of test substances in the environment , and the comet assay (single-cell gel electrophoresis) is a simple and sensitive method for measuring chemically induced DNA damage [18, 19]. Despite the availability of numerous assays to detect genotoxic chemicals, there was no simple method to estimate their effects on transcription until recently.
In our previous work, we established a method for detecting the effects of chemically induced DNA damage on transcription using the nucleotide analog 5-bromouridine and a anti-5-bromouridine antibody and/or the nucleotide analog 5-ethynyluridine  and a click chemistry reaction [21, 22] without radioisotopes . Our method is based on a model for transcription-coupled nucleotide excision repair (NER) triggered by blocked transcription at DNA lesions [24, 25]. The method employs common human cells without genetic modifications and terminally differentiated PC12 cells that actively undergo transcription but not replication, and it can detect a wide range of DNA lesions within 8 h of exposure to UV and/or chemicals, e.g., camptothecin, etoposide, 4-nitroquinoline 1-oxide (4NQO), mitomycin, and cisplatin.
Here we present an in vitro assay for detecting the effects of chemically induced DNA lesions using in vitro transcription and real-time reverse transcription polymerase chain reaction (PCR). The method is based on the inhibition of in vitro RNA synthesis for chemically treated DNA templates and allows evaluation of the potential effects of chemicals on transcription in terminally differentiated human cells.
Materials and methods
Enzymes and chemicals
T7 RNA polymerase (T7 RNAP) and reverse transcriptase were purchased from TOYOBO (Osaka, Japan). RNase inhibitor was from Wako (Osaka, Japan), restriction enzymes were from New England Biolabs (Ipswich, MA, USA), Fast SYBR Green Master Mix was from Life Technologies (Carlsbad, CA, USA), and cisplatin was from Sigma-Aldrich (St. Louis, MO, USA).
Plasmid (pBluescript II SK (−) containing the T7 promoter; Stratagene, La Jolla, CA, USA) DNA templates were purified using the QIAGEN Midi Kit (QIAGEN, Hilden, Germany). For UV irradiation of DNA templates, UV-light (254 nm, 450 J/m2) was used. For cisplatin treatment, DNA templates were incubated with cisplatin (drug/nucleotide ratio = 0.005) at 37 °C overnight.
Polymerase chain reaction (PCR)
For PCR, UV-irradiated or cisplatin-treated DNA samples were used with primers 2140–2159 (5′-tatcagcaataaaccagcca-3′) and 2440–2421 (5′-gcggccaacttacttctgac-3′) and EmeraldAmp PCR Master Mix (TaKaRa, Otsu, Shiga, Japan) according to the manufacturer’s instructions. PCR products were analyzed by 1 % agarose gel electrophoresis.
In vitro transcription
For in vitro transcription, 50-μL reactions containing 100 ng DNA template, 4 mM NTP mixture (ATP, CTP, GTP, and UTP), and 5 units thermo T7 RNAP in buffer (40 mM Tris–HCl, pH 8.0, 50 mM NaCl, 8 mM MgCl2, 5 mM dithiothreitol, 20 units RNase inhibitor) were incubated at 37 °C for 1 h. RNA transcripts were purified using an RNeasy Mini Kit (QIAGEN) with RNase-Free DNase (QIAGEN) according to the manufacturer’s instructions. Transcription products were analyzed by 1 % agarose gel electrophoresis.
Reverse transcription (RT)-PCR
cDNAs were generated from purified RNA samples using primer 2440–2421 (5′-gcggccaacttacttctgac-3′) and ReverTra Ace reverse transcriptase (TOYOBO) according to the manufacturer’s instructions.
Real-time quantitative PCR (qPCR)
Real-time quantitative PCR (qPCR) was performed on a StepOne System (Life Technologies) using Fast SYBR Green Master Mix (Life Technologies) with primers 2140–2159 (5′-tatcagcaataaaccagcca-3′) and 2440–2421 (5′-gcggccaacttacttctgac-3′) to ensure the appearance of a single product peak (301 bp) from mock mixtures in the melting curve analysis. Each reaction was run in triplicate, and the data were plotted as ∆Rn versus cycle number.
Results and discussion
In conclusion, conventional PCR and qPCR in the absence of T7 RNAP transcription can detect chemically induced DNA lesions such as cisplatin DNA adducts but not UV-induced lesions. Only the combination of T7 RNAP transcription and qPCR can detect both cisplatin- and UV-induced DNA lesions that interfere with transcription. Therefore, our results support the idea analysis of transcription products can be used to detect damage in DNA templates, consistent with the model of TCR [7, 25]. Our new method might reveal DNA lesions that cannot be detected by conventional replication-based methods and should facilitate research on DNA damage responses.
- 6-4 pp:
Cyclobutane pyrimidine dimer
Nucleotide excision repair
Polymerase chain reaction
Real-time quantitative PCR
- T7 RNAP:
T7 RNA polymerase
We would like to thank Editage (www.editage.jp) for English language editing. This work was supported by a Grant-in-Aid for Scientific Research (B) 25281018 from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.
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