Role of LET and chromatin structure on chromosomal inversion in CHO10B2 cells
© Cartwright et al.; licensee BioMed Central Ltd. 2014
Received: 9 October 2013
Accepted: 21 January 2014
Published: 28 January 2014
In this study we evaluated the effect of linear energy transfer (LET) and chromatin structure on the induction of chromosomal inversion. High LET radiation causes more complex DNA damage than low LET radiation; this “dirty” damage is more difficult to repair and may result in an increase in inversion formation. CHO10B2 cells synchronized in either G1 or M phase were exposed 0, 1, or 2 Gy of 5 mm Al and Cu filters at 200 kVp and 20 mA X-rays or 500 MeV/nucleon of initial energy and 200 keV/μ m Fe ion radiation. In order to increase the sensitivity of prior techniques used to study inversions, we modified the more traditional Giemsa plus fluorescence technique so that cells were only allowed to incorporate BrdU for a single cycle verses 2 cycles. The BrdU incorporated DNA strand was labeled using a BrdU antibody and an Alexa Fluor 488 probe. This modified technique allowed us to observe inversions smaller than 0.6 megabases (Mb).
In this study we have shown that high LET radiation induces significantly more inversions in G1 cells than in M phase cells. Additionally, we have shown that the sizes of the induced inversions not only differ between Fe ion and X-rays, but also between G1 and M phase cells exposed to Fe ions.
We have effectively shown that both radiation quality and chromosome structure interact to alter not only the number of inversions induced, but also the size of the inversions.
KeywordsInversions DNA damage DNA repair Cytogenetics
Chromosome inversions, along with several other symmetrical rearrangements, are commonly thought to cause a rearrangement of the chromosome without resulting in the loss of genomic information. There are two types of inversions; pericentric inversions, involving the centromere, and paracentric inversions, located on a single arm of the chromatid. Since pericentric inversions involve the centromere they can be detected by simple karyotyping with Giemsa staining if the breaks occur asymmetrically across the centromere [1, 2]. Paracentric inversions, however, do not cause a visual structural change in the chromosome, thus causing them to be extremely difficult to evaluate without using classical Giemsa banding or current mBAND techniques. Both of these techniques are limited by the size of detectable inversions. Additionally, mBAND is extremely costly and limited in the range of which it can stain [1, 3–6]. It has been shown that high linear transfer energy (LET) radiation, such as charged particle radiation, creates more complex DNA damage than X-ray and gamma radiation. This complex damage lends itself to an increase in chromosomal aberrations, including chromosome inversion [3, 7–9]. Chromosome inversions are a potentially important chromosomal aberration because the cell undergoes genetic recombination and loses no genomic material; this damage can be passed on to a daughter cell leading to a potential mutation. Chromosomal inversion may have played a key role in the evolution of the primate genome. There have been a total of 1,576 putative regions of inverted orientation identified, covering more than 154 Mb of DNA . Of these inversions, it is believed that the pericentric inversions have played the largest role in speciation and evolution . Additionally, it has been observed that radiation-associated papillary thyroid cancer can be caused by a rearrangement of the RET gene due to an inversion. It was shown that the common RET/PTC1 rearrangement is an inversion on chromosome 10 where RET and H4 are juxtaposed. These two genes, which are 30 Mb apart and roughly separated by 1–3 μm, were brought together by a single track of X-ray radiation . Finally, it has been shown that inversions can cause genomic instability by causing a fragile site in the DNA that could lead to future DSBs or translocation . This leads us to believe that despite the fact little to no DNA information is lost, chromosomal inversions have the possibility to cause potential mutagenesis of the irradiated cells, whether this is through direct rearrangement of regulatory elements or through the creation of fragile sites.
In 2013 the Bailey et al. utilized a directionally orientated single stranded probe to identify radiation induced inversion on human chromosome 3 and 10, this stain allowed for visualization of inversions as small as 1 Mb . In our study we altered the modified Giemsa plus Fluorescence (FPG) approached utilized by Bedford’s group by only incorporating BrdU for a single cycle and labeling the BrdU incorporated DNA strand with a BrdU antibody and an Alexa Fluor 488 probe . By utilizing this modified staining protocol we were able to observe extremely small inversions, as small as 0.6 Mb, over all 21 chromosomes of the CHO10B2 genome. This increase in sensitivity allows us to better understand the extent of the induced inversion in irradiated cells. In this study we have shown that both the quality of the radiation and the cell cycle are involved in not only the number of inversions formed, but also the size of these inversions.
Validation of BrdU staining protocol
This table outlines the predicted and observed values for a chromosome to contain at 1 SCE within a chromosome, at least 2 SCE within a chromosome, or 2 SCE events within 15 megabases
Average’Number’of’ SCE’per’21’ Chromosomes
Average’Number’of’ Chromosomes’with’1’ SCE’
Number’of’ Chromosomes’with’ at’least’2’SCE’
Number’of’ Chromosomes’with’2’ SCE’within’15’Mb
Effect of radiation quality and cell cycle on Induction of chromosomal inversion
Analysis of inverted fragment sizes
It can be seen in our study that both the LET of the radiation and chromatin structure play a role not only in the induction of chromosomal inversion, but also in the size of the induced inversions. Our modified staining protocol has allowed inversions to be observed on a level not seen in previous studies. To account for inversions observed at 0 Gy we used Poisson Distribution to show that these inversions were actually two SCE events occurring on a single chromatid within a close distance to one another. The small differences between our calculated false inversions and the observed inversions at 0 Gy can be attributed to naturally occurring true inversions, which is an extremely rare event. Our data strongly correlates with prior observations, with the exception of one prior study. In this paper, it was noted that radiation induced interstitial exchanges were formed primarily by true SCE events . Based on our observation of micro inversions, aberrations that were undetectable in this earlier study, and results from several other studies we believe that the majority of radiation-induced inversions are in fact true inversions and not caused by 2 SCE events. These findings highlight the importance of these micro inversions and additionally support the idea that ionizing radiation can produce inversions.
In conclusion, this study has effectively shown that the size and number of induced inversions are affected by both the LET of the radiation and the chromatin structure of the DNA. It appears that high LET radiation, Fe ions, create inversions whose size and number are directly dependent on chromatin structure, this observation was not seen in cells exposed to low LET X-rays. Additionally, we were able to show that high LET radiation was more effective at inducing inversions than the low LET radiation. Finally, the staining protocol utilized in this study was able to observe inversions smaller than previously reported, and by having this ability to observe these micro inversions allowed us to accurately record the number of induced inversions and avoid the background level of false inversions [3–5, 15].
We have been able to observe chromosomal inversions in a finer detail then prior papers have been able to achieve. We modified a traditional Giemsa staining approach by utilizing a fluorescent probe to identify inversions as small as 0.6 Mb. Using this approach we were able to see changes in not only the overall number of radiation induced inversion, but also a change in the size of the induced inversions. In this study we have shown that the cell cycle only effects the number and size of induced inversions if the cells were exposed to high LET radiation. It was seen that both G1 and M phase cells exposed to Fe ions had more and smaller inversions than X-ray exposed cells. Additionally, there was a difference between G1 and M phase Fe ion exposed cells, unlike X-ray exposed cells. Exposure to Fe ions produced more inversions in G1 cells, however the overall size is larger than M phase exposed cells.
Material and methods
Chinese Hamster Ovary 10B2 (CHO10B2) cells were kindly supplied from Dr. Joel Bedford at Colorado State University (Fort Collins, CO). Cells were cultured in MEM-alpha (Gibco, Indianapolis, IN) supplemented with 10% fetal bovine serum (FBS, Sigma, St Louis, MO) and 1% antibiotics and antimycotics (Gibco), and they were maintained at 37°C in a humidified atmosphere of 5% CO2 in air. The CHO10B2 cells where cultured for 1 cycle, 12 hours, with 1 μM BrdU (Sigma) to ensure uniform incorporation into the newly synthesized DNA and then harvested either in the G1 or M phase of the cell cycle by mitotic shake off [17–19]. CHO10B2 cells were chosen due to they short division time and the ability to effectively synchronize the cell population into either G1 or M phase.
Cells were synchronized into either G1 or M phase via a classic mitotic shake-off procedure and only cells with a mitotic index of 90% or higher were used [20–22]. For collection of G1 synchronized cells, the collected mitotic cells were incubated for 2 hours at 37°C to allow for the cells to proceed from M phase to G1. For collection of M phase synchronized cells the mitotic cells were collected immediately prior to irradiation and transferred into pre-warmed T25 flasks and irradiated.
Cells were irradiated with X-rays using a TITAN X-ray generator (Shimadzu, Tokyo, Japan) using 5 mm Al and Cu filters at 200 kVp and 20 mA. The dose rate was approximately 1 Gy/min for X-ray. Cells were also irradiated using accelerated iron-ions at HIMAC (Heavy Ion Medical Accelerator in Chiba), the National Institute of Radiological Sciences in Chiba, Japan, which have 500 MeV/nucleon of initial energy and 200 keV/μm of LET.
Metaphase chromosome preparation
Cells were sub-cultured immediately after irradiation and 0.1 μg/ml of colcemid was added to the flask of cells for 18 hours. The cells were harvested during the first post-irradiated metaphase. Cells were trypsinized and then suspended in 6 ml of a 75 mM KCl solution warmed to 37°C and placed in a 37°C water bath for 20 minutes. Carnoy’s solution (3:1 methanol to acetic acid) was added to the samples according to the standard protocol. The fixed cells were dropped onto slides. These were set aside and allowed to dry until the Carnoy’s solution had evaporated, roughly 4–5 minutes .
Chromosomes where denatured for 3 minutes in an 80°Celsius 70% formamide in 2× saline-sodium citrate (SSC) solution than washed in 2× SSC for 10 minutes . The chromosomes where stained with 1/1000 anti-BrdU antibody (BD Biosciences, San Jose, CA) for 2 hours and than a secondary Alexa Fluor 488 (Invitrogen, Washington, D.C.) antibody was applied for 2 hours. The chromosomes where counter stained with Prolong Gold Antifade with 4,6-diamidino-2-phenylindole (DAPI) (Invitrogen).
Olympus BX51 fluorescence microscope (Olympus, Tokyo, Japan) equipped with Q-imaging Aqua cooled CCD camera (Q-imaging, Surrey, BC, Canada) was used for image capture. DAPI and anti-BrdU signals where merged using ImageJ software (National Institute of Health, Maryland, USA).
Measurements of inversions
The size of the inversions was determined using the image analysis software Volocity (PerkinElmer, Waltham, MA). Using Volocity we measured the pixel intensity of each inversion and the total pixel intensity of all 21 chromosomes in each cell. To determine the size of the inversion we compared the total pixel intensity to the CHO genome size, roughly 2.45 gigabases. This allowed us to determine the number of basepairs per pixel for each metaphase spread.
Statistical comparison of mean values was performed using a two tailed t-test. Differences with a P-value of <0.05 were considered to indicate a statistically significant result. Error bars indicate the standard error of the means. Confidence interval values were calculated by Prism 5™ software (GraphPad, La Jolla, CA, USA). Induction rates were considered statistically similar if the slope fell within the 95% confidence interval of compared slope.
Classification of aberrations
Inversions where categorized into two groups, inversions and micro inversions. All interstitial exchanges were classified as inversions; these include both true and false inversions. The total inversions where further categorized by size. Any inversion that was smaller than the width of a chromatid was considered a micro inversion, all other inversions remained categorized as an inversion. As discussed later in the paper, induced micro inversions can be considered with confidence to be true inversions.
We would like to thank the Dr. Akiko M. Ueno Radiation Biology Research Fund, the Dr. John H. Venable Memorial Scholarship, the Technology Fee Stipend Student Experimental Learning Fund in College of Veterinary Medicine and Biosciences in Colorado State University and International Open Laboratory and HIMAC of National Institute of Radiological Sciences for helping support our research and making this project a possibility.
- de la Chapelle A, Schroder J, Stenstrand K, Fellman J, Herva R, Saarni M, Anttolainen I, Tallila I, Tervila L, Husa L, et al: Pericentric inversions of human chromosomes 9 and 10. Am J Hum Genet. 1974, 26: 746-766.PubMed CentralPubMedGoogle Scholar
- Davisson MT, Poorman PA, Roderick TH, Moses MJ: A pericentric inversion in the mouse. Cytogenet Cell Genet. 1981, 30: 70-76. 10.1159/000131593.View ArticlePubMedGoogle Scholar
- Hada M, Cucinotta FA, Gonda SR, Wu H: mBAND analysis of chromosomal aberrations in human epithelial cells exposed to low- and high-LET radiation. Radiat Res. 2007, 168: 98-105. 10.1667/RR0759.1.View ArticlePubMedGoogle Scholar
- Holmquist G, Gray M, Porter T, Jordan J: Characterization of Giemsa dark- and light-band DNA. Cell. 1982, 31: 121-129. 10.1016/0092-8674(82)90411-1.View ArticlePubMedGoogle Scholar
- Hande MP, Azizova TV, Geard CR, Burak LE, Mitchell CR, Khokhryakov VF, Vasilenko EK, Brenner DJ: Past exposure to densely ionizing radiation leaves a unique permanent signature in the genome. Am J Hum Genet. 2003, 72: 1162-1170. 10.1086/375041.PubMed CentralView ArticlePubMedGoogle Scholar
- Mitchell CR, Azizova TV, Hande MP, Burak LE, Tsakok JM, Khokhryakov VF, Geard CR, Brenner DJ: Stable intrachromosomal biomarkers of past exposure to densely ionizing radiation in several chromosomes of exposed individuals. Radiat Res. 2004, 162: 257-263. 10.1667/RR3231.View ArticlePubMedGoogle Scholar
- Ward JF: The complexity of DNA damage: relevance to biological consequences. Int J Radiat Biol. 1994, 66: 427-432. 10.1080/09553009414551401.View ArticlePubMedGoogle Scholar
- Hada M, Georgakilas AG: Formation of clustered DNA damage after high-LET irradiation: a review. J Radiat Res. 2008, 49: 203-210. 10.1269/jrr.07123.View ArticlePubMedGoogle Scholar
- Pastwa E, Neumann RD, Mezhevaya K, Winters TA: Repair of radiation-induced DNA double-strand breaks is dependent upon radiation quality and the structural complexity of double-strand breaks. Radiat Res. 2003, 159: 251-261. 10.1667/0033-7587(2003)159[0251:RORIDD]2.0.CO;2.View ArticlePubMedGoogle Scholar
- Feuk L, MacDonald JR, Tang T, Carson AR, Li M, Rao G, Khaja R, Scherer SW: Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLoS Genet. 2005, 1: e56-10.1371/journal.pgen.0010056.PubMed CentralView ArticlePubMedGoogle Scholar
- Nickerson E, Nelson DL: Molecular definition of pericentric inversion breakpoints occurring during the evolution of humans and chimpanzees. Genomics. 1998, 50: 368-372. 10.1006/geno.1998.5332.View ArticlePubMedGoogle Scholar
- Nikiforova MN, Stringer JR, Blough R, Medvedovic M, Fagin JA, Nikiforov YE: Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells. Science. 2000, 290: 138-141. 10.1126/science.290.5489.138.View ArticlePubMedGoogle Scholar
- de Kok YJ, Merkx GF, van der Maarel SM, Huber I, Malcolm S, Ropers HH, Cremers FP: A duplication/paracentric inversion associated with familial X-linked deafness (DFN3) suggests the presence of a regulatory element more than 400 kb upstream of the POU3F4 gene. Hum Mol Genet. 1995, 4: 2145-2150. 10.1093/hmg/4.11.2145.View ArticlePubMedGoogle Scholar
- Ray FA, Zimmerman E, Robinson B, Cornforth MN, Bedford JS, Goodwin EH, Bailey SM: Directional genomic hybridization for chromosomal inversion discovery and detection. Chromosome Res. 2013, 21: 165-174. 10.1007/s10577-013-9345-0.PubMed CentralView ArticlePubMedGoogle Scholar
- Muhlmann-Diaz MC, Bedford JS: Comparison of gamma-ray-induced chromosome ring and inversion frequencies. Radiat Res. 1995, 143: 175-180. 10.2307/3579154.View ArticlePubMedGoogle Scholar
- Wojcik A, Opalka B, Obe G: Analysis of inversions and sister chromatid exchanges in chromosome 3 of human lymphocytes exposed to X-rays. Mutagenesis. 1999, 14: 633-638. 10.1093/mutage/14.6.633.View ArticlePubMedGoogle Scholar
- Bailey SM, Bedford JS: Studies on chromosome aberration induction: what can they tell us about DNA repair?. DNA Repair (Amst). 2006, 5: 1171-1181. 10.1016/j.dnarep.2006.05.033.View ArticleGoogle Scholar
- Wolff S, Bodycote J, Painter RB: Sister chromatid exchanges induced in Chinese hamster cells by UV irradiation of different stages of the cell cycle: the necessity for cells to pass through S. Mutat Res. 1974, 25: 73-81. 10.1016/0027-5107(74)90220-6.View ArticlePubMedGoogle Scholar
- Littlefield LG, Colyer SP, Joiner EE, DuFrain RJ: Sister chromatid exchanges in human lymphocytes exposed to ionizing radiation during G0. Radiat Res. 1979, 78: 514-521. 10.2307/3574976.View ArticlePubMedGoogle Scholar
- Sinclair WK, Morton RA: X-Ray and ultraviolet sensitivity of synchronized chinese hamster cells at various stages of the cell cycle. Biophys J. 1965, 5: 1-25.PubMed CentralView ArticlePubMedGoogle Scholar
- Terasima T, Tolmach LJ: Changes in x-ray sensitivity of HeLa cells during the division cycle. Nature. 1961, 190: 1210-1211. 10.1038/1901210a0.View ArticlePubMedGoogle Scholar
- Fox MH, Read RA, Bedford JS: Comparison of synchronized Chinese hamster ovary cells obtained by mitotic shake-off, hydroxyurea, aphidicolin, or methotrexate. Cytometry. 1987, 8: 315-320. 10.1002/cyto.990080312.View ArticlePubMedGoogle Scholar
- Cartwright IM, Genet MD, Kato TA: A simple and rapid fluorescence in situ hybridization microwave protocol for reliable dicentric chromosome analysis. J Radiat Res (Tokyo). 2012, 54: 344-348.PubMed CentralView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.