Double-Strand Break Repair by Interchromosomal
Recombination: An In Vivo Repair Mechanism Utilized by
Multiple Somatic Tissues in Mammals
Ryan R. White1¤, Patricia Sung2, C. Greer Vestal1, Gregory Benedetto1, Noelle Cornelio1, Christine
Richardson1*
1 Department of Biology, University of North Carolina-Charlotte, Charlotte, North Carolina, United States of America, 2 Developmental Biology, Sloan-Kettering
Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
Abstract
Homologous recombination (HR) is essential for accurate genome duplication and maintenance of genome stability.
In eukaryotes, chromosomal double strand breaks (DSBs) are central to HR during specialized developmental
programs of meiosis and antigen receptor gene rearrangements, and form at unusual DNA structures and stalled
replication forks. DSBs also result from exposure to ionizing radiation, reactive oxygen species, some anti-cancer
agents, or inhibitors of topoisomerase II. Literature predicts that repair of such breaks normally will occur by nonhomologous end-joining (in G1), intrachromosomal HR (all phases), or sister chromatid HR (in S/G2). However, no in
vivo model is in place to directly determine the potential for DSB repair in somatic cells of mammals to occur by HR
between repeated sequences on heterologs (i.e., interchromosomal HR). To test this, we developed a mouse model
with three transgenes—two nonfunctional green fluorescent protein (GFP) transgenes each containing a recognition
site for the I-SceI endonuclease, and a tetracycline-inducible I-SceI endonuclease transgene. If interchromosomal
HR can be utilized for DSB repair in somatic cells, then I-SceI expression and induction of DSBs within the GFP
reporters may result in a functional GFP+ gene. Strikingly, GFP+ recombinant cells were observed in multiple organs
with highest numbers in thymus, kidney, and lung. Additionally, bone marrow cultures demonstrated
interchromosomal HR within multiple hematopoietic subpopulations including multi-lineage colony forming unit–
granulocyte-erythrocyte-monocyte-megakaryocte (CFU-GEMM) colonies. This is a direct demonstration that somatic
cells in vivo search genome-wide for homologous sequences suitable for DSB repair, and this type of repair can
occur within early developmental populations capable of multi-lineage differentiation.
Citation: White RR, Sung P, Vestal CG, Benedetto G, Cornelio N, et al. (2013) Double-Strand Break Repair by Interchromosomal Recombination: An In
Vivo Repair Mechanism Utilized by Multiple Somatic Tissues in Mammals. PLoS ONE 8(12): e84379. doi:10.1371/journal.pone.0084379
Editor: Michael Lichten, National Cancer Institute, United States of America
Received April 3, 2012; Accepted November 22, 2013; Published December 13, 2013
Copyright: © 2013 White et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: RW was a recipient of the North Carolina Biotechnology Center Undergraduate Biotechnology Research Fellowship. This work was supported in
part by funds provided to CR by the Concern Foundation, National Institutes of Health/National Cancer Institute CA100159, the Alexander and Margaret
Stewart Trust, Columbia University, and University of North Carolina-Charlotte. The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: caricha2@uncc.edu
¤ Current address: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
Introduction
topoisomerase II inhibitors also promote chromosomal breaks
[10–14]. Some environmental and/or dietary compounds may
promote DSBs, and the recent observations that bioflavonoids
can stabilize DNA DSBs and lead to illegitimate repair and
genome rearrangements in cultured cells underscores the
importance of understanding DSB repair processes in vivo
[15–18].
DSBs are potent inducers of recombination and increase
both homologous recombination (HR) and non-homologous
end-joining (EJ) events by several orders of magnitude [19,20].
These two major DSB repair pathways differ based on their
requirement for a donor DNA template with significant
Faithful repair of DNA damage, including double-strand
breaks (DSBs), is crucial to genome stability and normal cell
survival and proliferation [1]. Chromosomal breaks can occur in
a programmed manner through meiosis, immunoglobulin classswitch recombination, and V(D)J recombination [2–4]. In
addition,
reactive
oxidative
species
may
promote
10,000-20,000 DNA damaged sites per cell per day [5–7], and
DNA replication errors or stalls may promote another 10-50
DSBs per cell [8,9]. Exposure to ionizing radiation (IR),
alkylating agents, and chemotherapeutic drugs such as
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Interchromosomal DSB Repair in Vivo
sequences suitable for DSB repair, and this type of repair can
occur within progenitor populations capable of proliferation and
multi-lineage differentiation.
sequence homology; thus, their relative activity changes with
each stage of the cell cycle. Studies in multiple organisms have
demonstrated that EJ is most efficient in G1 and in noncycling
somatic cells while homology-directed DSB repair is favored in
both S/G2 utilizing a sister chromatid and intrachromosomal HR
[19,21–26]. In vivo systems have been developed to detect EJ,
sister chromatid, and intrachromosomal HR that arise both
spontaneously and in response to induced DSBs [27–30].
Homologs are utilized for HR-directed DSB repair with lower
efficiency although this is increased in organisms that exhibit a
high degree of mitotic pairing, supporting the hypothesis that
proximity of homologous sequences is an important factor in
determining template choice [31–33]. While repair of specific
DSBs by more distant homologous repeat sequences on
heterologous chromosomes (i.e. interchromosomal HR) has
been examined in vivo using mitotic yeast and tobacco [34,35],
studies in mammalian cells have been limited to cultured cell
assays [36–39]. Whether repair of DSBs in vivo in mammals
occurs by interchromosomal HR at significant and detectable
frequencies has not been demonstrated.
If cells are exposed to irradiation, chemotherapeutic agents,
or even environmental factors and metabolites, multiple DSBs
at unlinked loci will occur in the same cell at the same time.
Repair of multiple breaks using interchromosomal HR in vivo
has the potential to result in reciprocal exchanges that may be
viable, inherited by daughter cells in the next cell division, or
inherited through the germ line. Genome analysis of plants
suggests that translocations are a regular mechanism of plant
evolution [40,41]. In mammals, one third of the genome is
composed of repetitive elements [42]. The presence of Alu
elements elevates recombination rates [43], and Alu-Alu
mediated recombination has been associated with founder
mutations and evolution [44–49]. In somatic cells,
translocations can be tumorigenic, and are a hallmark of
human hematopoietic malignancies and some soft-tissue
sarcomas [36,50–56]. Thus, such events would likely be
suppressed in somatic cells in vivo where a selective pressure
exists to maintain genome stability and avoid immortalization.
Specialized cell types within mammals may preferentially utilize
different pathways of repair, particularly as more differentiated
cells spend less time in S phase of the cell cycle [57–60] or as
proliferation rates change with age [61,62].
To directly test the potential for multiple DSBs to promote
interchromosomal HR in vivo in mammals, we developed a
mouse model with three transgenes--two nonfunctional green
fluorescent protein (GFP) reporter transgenes each containing
a recognition site for the I-SceI endonuclease, and a
tetracycline-inducible I-SceI endonuclease transgene. Induced
expression of I-SceI and the resulting induction of DSBs within
the GFP reporters may produce a functional GFP gene if
interchromosomal HR is utilized for repair. In this system, GFP
+ recombinant cells were observed in all seven organs
examined--pancreas, liver, spleen, kidney, thymus, heart, and
lung--with highest numbers in thymus, kidney, and lung. Bone
marrow cultures demonstrated interchromosomal HR within
multiple colony types including early progenitor CFU-GEMM.
This is a direct demonstration that somatic cells in vivo
maintain the potential to search genome-wide for homologous
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Results
In vivo mouse model
Constructs were designed to introduce two defective green
fluorescent protein (GFP) genes and a tetracycline-responsive
(TET-ON) inducible I-SceI endonuclease gene construct onto
heterologous chromosomes in the mouse genome. 1S-GFP
and 2S-GFP reporter constructs each contain a unique 18bp
restriction site for the endonuclease I-SceI [63,64] in the 5’ and
3’ ORF regions, respectively, with 460bp homology to each
other between the two restriction sites (Figure 1A). The TETON I-SceI endonuclease gene is on a single auto-regulated bidirectional expression vector with the tet operator regulating
both a TK-rtTAN repressor of the transactivator gene (vector
kindly provided by Craig Strathdee) [65] and an I-SceI gene
(Figure 2A) [64,66]. Presence of the transgenes within mice
was shown by both Southern Blotting and PCR of DNA isolated
from tail tips. Founder mice containing each transgene were
crossed with wild type, and those that inherited single insertion
sites at Mendelian ratios and with the lowest copy number as
estimated by both Southern blotting and Q-PCR as compared
against a standard (Figure 1B and Methods) were maintained
for further breeding. Taken together these analyses estimated
4-5 copies of 1S-GFP and 2-4 copies of 2S-GFP. Mice were
screened for an intact I-SceI site at both the 1S-GFP and the
2S-GFP reporters using PCR primers that flank each I-SceI site
and digestion of the PCR product with I-SceI endonuclease
(Figure 1A, 1C). Individually 1S-GFP and 2S-GFP positive lines
were crossed to each other, and then crossed to the I-SceI
transgenic line over generations, and inheritance of the three
transgenes in expected Mendelian ratios supports unlinked
loci. Breeding resulted in triply positive transgenic GS lines for
analysis.
DSB-induced interchromosomal HR occurs in mouse
embryonic fibroblasts
Mouse embryonic fibroblasts (MEFs) were harvested at day
E13.5. MEFs from each GS mouse were divided and cultured
in one of 3 conditions: (1) cultured in media without DSB
induction, (2) cultured in the presence of tetracycline (2 μg/mL)
to induce DSBs through I-SceI expression, or (3) transfected
with 30μg I-SceI expression vector CBAS [20] to induce DSBs
through I-SceI expression. I-SceI RNA transcripts and protein
were detectable by RT-PCR and Western blotting, respectively,
following addition of tetracycline to culture media of MEFs
(Figure 2B) or to H2O provided transgenic mice in subsequent
experiments (see below).
Individual GFP+ MEFs were detectable by inverted
fluorescent microscopy as early as 4 days following the
addition of tetracycline (Figure 3A). Cells were analyzed by
fluorescent activated cell sorting (FACS) 6-10 days posttetracycline. Untreated MEFs had an undetectable number of
GFP+ cells. By contrast, intermediate/bright GFP+ cells were
greater than 12% of the treated cells (compared against
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Figure 1. Structure and confirmation of the 1S and 2S GFP transgenes. (A) For each construct schematic, the numbers of
bases are indicated to show the lengths of homology between the two as well as the relative positions of the engineered I-SceI
restriction sites. The 3’UTR sequences of the two constructs do not share homology and are indicated as a hatched box of 1270 bp
for 1S-GFP and a grey box of 535 bp for 2S-GFP; these non-homologous sequences allow for PCR amplification specific to each
transgene. Nested PCR primer pairs used for verification of intact construct sequences and for analysis of GFP+ hematopoietic
colonies are indicated. Primers 1F-4R followed by 2F-3R amplify sequence flanking the I-SceI site in 1S-GFP. Primers 1F-7R
followed by 5F-6R amplify sequence flanking the I-SceI site in 2S-GFP. (B) Southern blotting to estimate copy number utilized a
GFP ORF DNA fragment of 3.1 kb and diluted to pg amounts that approximated 0, 0.2, 1.0, and 5.0 copies per genome spiked into
10µg non-transgenic mouse DNA. Genomic DNA from single transgenic mice (either 1S-GFP or 2S-GFP) was digested with
restriction endonucleases within the GFP promoter and ORF of both transgenes to yield a 3.1 kb fragment. Band intensities are
consistent with 4-5 copies of 1S-GFP and 2-4 copies of 2S-GFP, and were confirmed with Q-PCR data on the same samples (data
not shown). (C) PCR reactions flanking each DSB site in the two GFP constructs confirm intact I-SceI recognition sites. Nested PCR
as described in Materials amplified each transgene shown in the left side lane of each image. Digestion with I-SceI endonuclease
produced the expected sizes indicated in the middle lane of each image. Right side Marker lane PhiX.
doi: 10.1371/journal.pone.0084379.g001
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Figure 2. Structure and confirmation of the tetracycline inducible I-SceI transgene. (A) For details of the bicistronic I-SceI
transgene construct refer to [65]. (B) MEFs derived from GS mice were cultured in media supplemented with TET at 2μg/mL for 48
hours. Total protein extracts were harvested and analyzed by Western blotting. By 48 hours post-TET, detectable quantities of ISceI endonuclease can be observed. As a negative controls, total protein extracts were harvested from cultured E14 ES cells or
uncultured MEFs from GS mice. Loading control: Western blotting for β-actin.
doi: 10.1371/journal.pone.0084379.g002
these mice had undetectable levels of GFP+ cells in all organs
examined, similar to the non-transgenic controls. However, two
of the 15 mice contained GFP+ populations of cells in multiple
tissues (data not shown). In these mice, it is possible that the ISceI transgene became activated. Alternatively, it is possible
that an early progenitor cell in utero underwent spontaneous
interchromosomal HR giving rise to a GFP+ progenitor cell that
contributed to multiple tissues, or was a cell type that gave rise
to cells capable of infiltrating multiple organs, e.g. circulating
hematopoietic cells.
untreated cells with a gate set at 0.1%; n=12) (Figure 3B).
Individual GFP+ cells were FACS sorted and confirmed to be
GFP+ by inverted fluorescent microscopy (Figure 3C).
DSB-induced interchromosomal HR occurs in vivo in
multiple somatic cell types
GS mice at least 3 months of age (n=47) were administered
tetracycline through H20 for 21d to allow an extended period of
I-SceI expression and subsequent induction of DSBs. Mice
were then taken off tetracycline for 7d-21d prior to analysis.
This waiting period would restrict analysis to viable GFP+ cells
after cells with unstable repair structures would be cleared from
the in vivo tissues. A total of seven organs--pancreas, liver,
spleen, kidney, thymus, heart, and lung--were analyzed for
GFP+ recombinants by FACS (Figure 4). Mice were analyzed
in batches, and each batch included an age-matched nontransgenic mouse (n=8). Gates for determination of GFP+ cells
were set such that negative controls had ≤3 events per million,
and then the same gates were used to score GFP+ cells from
GS tetracycline-treated mice. This analysis directly
demonstrated that GFP+ cells, as determined by >3 GFP+ cells
per million by FACS, were readily detectable in multiple tissues
from 40 of the 47 mice treated and analyzed (Figures 4,5;
Table S1). Despite variance in GFP+ numbers detected
between mice, all organs had significantly increased GFP+
cells as compared to the age-matched negative controls
(Figure 5). For comparison, constitutively expressing EGFP
mice consistently contained >45% GFP+ cells in all tissues
examined (data not shown) [67]. These data demonstrate that
somatic cell types in vivo retain the potential to repair DSBs
with a homologous sequence on a heterologous chromosome.
Furthermore, the potential for interaction between sequences
on heterologous chromosomes in wild-type cells has not been
eliminated by epigenetic factors or chromatin remodeling
associated with differentiation programs.
Additionally, age-matched GS mice that were not
administered tetracycline were analyzed (n=15). 13 of 15 of
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Impact of aging on DSB-induced interchromosomal HR
in multiple somatic cell types
Close examination of the variance of numbers of GFP+ cells
detected in tetracycline-treated GS mice indicated that 7 of the
47 mice contained no detectable GFP+ cells in any organs
analyzed, similar to non-transgenic controls. All 7 mice were
older. Thus, we separated analysis of the 47 mice GS mice into
two age cohorts, young (≤ 5months old, n=16) and old (≥ 8
months, n=31) (Figures 6A and 6B, respectively). Regardless
of age, statistically significant numbers of GFP+ cells were in
most organs examined, as compared to negative control mice.
Comparison of GFP+ cell numbers by age (Figure 6C)
indicated that in 5 of the 7 organs examined (pancreas, kidney,
spleen, lung, and thymus), overall numbers of detectable GFP+
cells were lower in the cohort of older mice (Figure 6C). The
decrease in detectable number of GFP+ cells was significant in
3 of these (pancreas, lung, thymus). However, two organs
(heart and liver) appeared to have an overall slight increase in
numbers GFP+ cells in older mice, although the trend did not
reach statistical significance. Decreases in transgene
expression levels with age has been observed in multiple other
models. A similar mechanism of transgene shutdown may be
involved in this model, but only occur in a subset of tissue
types. It is possible that certain organs contain specific cell
types or progenitor cells capable of DSB-induced
interchromosomal HR, even within older mice. Further
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Figure 3. Analysis of GFP+ MEFs post-TET. (A) Phase contrast and matched fluorescent microscopy images of MEFs in culture
—magnification 400X. Top row-untreated MEFs. Second row-96 hrs post-electroporation with I-SceI expression plasmid. Third and
fourth rows-96 hrs after addition of tetracycline to the culture medium (+TET). (B) Representative FACS plot of MEFs with GFP
positivity in log scale on the x axis plotted against number of cells on the y axis. Upper plot--untreated MEFs. Lower plot-- +TET
treated MEFs. In this sample, the GFP+ population is 12.4%. (C) Confirmation of GFP+ cells after FACS single cell sorting for GFP+
MEFs. Cells within the GFP+ gate indicated in B lower panel were sorted and then viewed by fluorescent microscopy—
magnification 400X.
doi: 10.1371/journal.pone.0084379.g003
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Figure 4. Representative FACS analysis plots of three GS mice for spleen, pancreas, kidney, liver, and thymus. GFP
positivity is shown on log scale on the X axis plotted against nonspecific PerCP-Cy5-5 on the Y axis to visualize individual cells.
Age-matched negative control mice were not provided TET (-TET). Two representative age-matched mice contain all 3 transgenes
and were provided TET as described in text (+TET). Establishment of gates is described in text.
doi: 10.1371/journal.pone.0084379.g004
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Figure 5. Quantitative analysis of GFP+ cells in all mice analyzed. The number of GFP+ cells in each organ of analyzed mice
was determined. Establishment of gates is described in text. From FACS analysis, the average number of GFP+ recombinant cells
per million cells and the standard deviation of each was calculated for seven organs and represented in bar graph form. Negative
controls are shown in red bars (n=8), and +TET are shown in green bars (n=47). H=heart, P=pancreas, Li=liver, K=kidney,
S=spleen, Lu=lung, T=thymus. Organs with statistically significant increased numbers of GFP+ cells groups are indicated by **
above the error bars.
doi: 10.1371/journal.pone.0084379.g005
determination of the specific cell types that are GFP+ within
each of the mice could provide this information.
Given the variance in GFP+ numbers detected between mice
(Figures 5, 6; Table S1), statistical significance of the
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probabilities associated with covariance among the traits was
calculated for each pair of traits separately in the young and old
cohorts (Table S2). In the young cohort, only a single strong
positive correlation of covariance between spleen and kidney
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Figure 6. Quantitative analysis of GFP+ cells by age. (A) In the young mouse cohort (age<5.5 months), negative controls are
shown in red bars (n=5), and +TET are shown in grey bars (n=16). Organs with statistically significant increased numbers of GFP+
cells groups are indicated by ** above the error bars. (B) In the older mouse cohort (age>8 months), negative controls are shown in
red bars (n=11) and +TET are shown in black bars (n=31). (C) Comparison of +TET young mice (grey bars) versus +TET old mice
(black bars) from A and B. Organs with statistically significant different numbers of GFP+ cells by age are indicated by ** above the
error bars. For all panels, H=heart, P=pancreas, Li=liver, K=kidney, S=spleen, Lu=lung, T=thymus.
doi: 10.1371/journal.pone.0084379.g006
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(p=0.002) was noted. In the old cohort, a larger number,
although weaker, of positive correlations of covariance were
noted; these were between heart and pancreas (p=0.021) or
thymus (0.021), as well as between spleen and kidney (0.021)
or thymus (p=0.021).
repair sites (Figure 1A). Because the 3’ UTR ends of the
transgene sequences are unique, primers could selectively
amplify each of the two transgenes (Figure 1A). A total of 22
individual BM colony PCR products were cloned and
sequenced. Because each transgene is inserted in multiple
copies, PCR will amplify both GFP+ recombinant and parental
non-recombinant copies of the transgenes. These were
distinguishable following TA cloning and sequencing of multiple
TA clones from each BM colony PCR. This analysis verified
that all 22 BM colonies contained a repaired GFP+ wild-type
sequence on at least one allele. In 6 of 22 colonies this
analysis detected HR repair at only one allele (4 at 1S-GFP
and 2 at 2S-GFP). In 16 of 22 colonies this analysis detected
HR repair at both alleles; however given the multiple copy
inserts, these likely represented independent events.
DSB-induced interchromosomal HR occurs in vivo in
hematopoietic multi-lineage progenitor cell types
Hematopoiesis is characterized by a hierarchy of cells, with
hematopoietic stem cells (HSC) possessing the highest
proliferative potential and thought to be the targets of aberrant
interchromosomal DSB repair events leading to mutagenic
chromosomal rearrangements. Our previous in vitro studies
demonstrated that early stem and progenitor cells are more
proficient than terminally differentiated myeloid cells in
repairing DSBs by interchromosomal HR [68]. Here, we
determined the potential for hematopoietic multi-lineage
progenitor cells to utilize this mechanism of repair in vivo. GS
mice (ages 3-5 months) were administered tetracycline, then
bone marrow cells harvested, and subsequently seeded into
methylcellulose colony forming assays that support proliferation
of myeloid, erythroid, or B-cell progenitors [68–70]. Total
numbers of hematopoietic CFUs were scored and classified
based on their morphology, and individual GFP+ CFUs
determined by inverted fluorescent microscopy (Figure 7).
Mature colonies derived from individual precursors included the
colony forming unit- granulocyte-erythrocyte-monocytemegakaryocte (CFU-GEMM), granulocyte-monocyte (CFUGM), granulocyte (CFU-G), monocyte (CFU-M), erythrocyte
(CFU-E), and pre-B (CFU-pre-B). Colonies that contain mixed
cell populations are presumed to derive from immature
progenitor cells capable of differentiation into multiple cell
types. Colonies that contain a single cell population are
presumed to derive from more differentiated progenitors that
only have the capacity to expand a single cell type.
Following DSBs, GFP+ recombinants were readily obtained
from all sub-populations assayed. Strikingly, the results parallel
observations previously made in studies of DSB-induced
interchromosomal HR using genetically engineered murine ES
cells differentiated in vitro into hematopoietic colonies [68]. The
highest average number of GFP+ recombinant colonies (32 ±
15) was observed in the multi-potent CFU-GEMM cells scored
by this assay (Table 1). Observed numbers of GFP+
recombinants decreased with increased differentiation status
with the lowest average number of GFP+ recombinant colonies
(5 ± 5) observed in the terminally differentiated but actively
proliferating monocytic cells (p value = 0.02) (Table 1). The
average frequency of recombination in this in vivo system was
estimated to be 8.0 x 10-5 in CFU-GEMM cells, 5.5 x 10-5 in
CFU-GM cells, 6.5 x 10-5 in CFU-G cells, and decreasing to
1.25 x 10-5 in CFU-M cells. Overall these data demonstrate that
both multipotent and terminally differentiated cell types retain
the potential to repair DSBs with a homologous sequence on a
heterologous chromosome in vivo.
Because CFU represent clonal populations, the recombinant
HR repair products could be verified at the sequence level.
DNA was extracted from individual BM colonies, and nested
PCR used to amplify across the two I-SceI endonuclease DSB
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Discussion
This study presents an in vivo model that directly
demonstrates that DSB-induced interchromosomal HR occurs
at readily detectable rates. GFP+ recombinant cells were
readily detectable in a broad range of somatic cell types.
Variability in numbers of GFP+ recombinant cells was observed
between the multiple somatic cell types and mice in all cohorts
examined. Such variability could be due to differences in GFP
expression, recombination rates, clonal expansion of individual
GFP+ recombinants, or I-SceI transgene induction, expression,
or stability. This mouse model initiates I-SceI expression in vivo
using a single bicistronic TET-ON system [65]. The
experiments in MEFs with this system show strong and specific
induction, but in vivo kinetics could be different. In addition,
individual mice self regulate feeding and thus vary dosage to
tetracycline. However, similar inter-mouse variability in the in
vivo mouse model of spontaneous intrachromosomal/sister
chromatid HR suggests that I-SceI is not the major determinant
of these results [30].
Intrachromosomal HR may occur if homologous repeat
sequences lie on the same chromosome in the same direct
repeat orientation such as repetitive elements within several kb
of each other. Several studies have used Arabidopsis and N.
tabacum models to detect spontaneous and DSB-induced
sister chromatid and intrachromsomal HR with spontaneous
frequencies estimated at 10-5 to 10-4 [29,35,71,72] and up to
10,000X stimulation by I-SceI expression [29,35]. Further,
similar to in vitro findings, SSA was a predominant mode of
DSB repair with ectopic joining contributing to a smaller subset
of repair events [35]. In mice, spontaneous intrachromosomal
and sister chromatid HR have been demonstrated utilizing a
yellow fluorescent protein (YFP) reporter or LacZ/βgalactosidase reporter construct [27,30,73–76]. These studies
demonstrated median spontaneous HR frequencies of 5 per
106 cells in the pancreas [30,73–76]. Ionizing radiation or the
interstitial cross-linking agent mitomycin-C led to an increase of
recombination suggesting that non-specific DNA damage is
also sufficient to promote intrachromsomal HR, at least in
pancreatic cells [75]. Although comparisons between different
model systems are difficult, these results are surprisingly
similar to the findings presented here suggesting that both
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Interchromosomal DSB Repair in Vivo
Figure 7. DSB-induced GFP+ recombinants in hematopoietic subpopulations isolated from bone marrow of GS
mice. Colonies were scored by inverted fluorescent microscopy and faint background fluorescence of negative controls was
subtracted out of total repair frequency. Representative phase contrast and fluorescent microscopy images of GFP+ recombinants
from bone marrow CFC assay. Granulocyte-erythrocyte-macrophage-megakaryocyte (GEMM), Granulocyte-macrophage (CFUGM), Granulocyte (CFU-G), Macrophage (CFU-M), Pre-B cell (Pre-B), and Burst forming unit-erythroid (BFU-E). Magnification
400X.
doi: 10.1371/journal.pone.0084379.g007
types of HR repair are utilized with roughly the same overall
efficiency, although likely in different cell types or at different
stages of the cell cycle [60].
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Cytologic studies indicate that nuclei are ordered, and
chromosomes/genomes generally exist within defined nuclear
territories [77,78], and single DSBs remain stable in these
defined regions [79,80]. Genetic studies seem to support this
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Table 1. DSB-induced interchromosomal
hematopoietic progenitor cell populations.
HR
hematopoietic lineages is also quite prevalent with observed
GFP+ numbers decreasing with differentiation. Similarly, in
most organs the number of GFP+ cells decreased with age.
These data support other hypotheses that differentiation and
age will determine different pathways of repair or utilize
apoptotic programs with different frequencies [57–60].
Topo II is an essential cellular enzyme that catalyzes
changes in DNA topology via its cleavage-religation
equilibrium. Topo II inhibitors convert topo II into a DNAdamaging enzyme by disrupting the cleavage-religation
equilibrium, resulting in accumulation of DSBs, activation of
DNA damage sensors, cell cycle arrest, and initiation of
apoptosis or repair. A wide range of agents, including some
chemotherapeutic agents, are classified as topo II inhibitors,
and exposure to these is associated with development of
secondary leukemias [91,92]. However, they also include
benzene metabolites, bioflavinoids, anthraquinone laxatives,
podophyllin resins, quinolone antibiotics, pesticides, many
phenolic compounds, as well as certain fruits, tea, coffee, wine,
soy, and cocoa [11,12,93]. The recent observations that
bioflavinoids can stabilize DNA DSBs and promote illegitimate
repair and genome rearrangements in cultured cells has led to
the hypothesis that exposure to these agents in utero or
through unregulated high doses as dietary supplements may
promote leukemia [15–18]. Further study of this in vivo system
could determine the potential for exposure to such agents at
early stages of development to promote HR in vivo and their
long-term impact.
Rearrangements resulting from DSB repair that occurs in
germ cells can have evolutionary implications. It has been
observed that topoII has a role in DSB formation in spermatids
[94], and chromatin loop organization is similar between
spermatids and somatic cell types [89]. These observations
have led to the suggestion that DSB repair pathways and
partner choice may be more similar in meiotic and mitotic cells
than appreciated and has the potential to result in
rearrangements leading to genome variation [89,95]. That this
may be universal across multiple kingdoms, is supported by
genome analysis of plants that suggests translocations are a
regular mechanism of plant evolution [40,41]. In addition,
mutation fixation has been implicated during DSB repair in the
first zygotic cell division in mice [96]. Our demonstration that
interchromosomal HR occurs in vivo in response to DSBs at
just two loci in a broad range of cell types, particularly
progenitor cells, is a novel finding and lends further support to
the idea that exposure to the growing list of environmental
agents, dietary supplements, or groundwater contaminants that
induce or stabilize DSBs may promote potentially tumorigenic
rearrangements, accelerate genomic variation, and influence
evolution.
in
a
# GFP colonies
Bone Marrow CFC
Expt 1
Expt 2
Expt 3
avg. GFP colonies
CFU-GEMM
47
17
32
32 ± 15
CFU-GM
31
0
35
22 ± 19
CFU-G
23
49
7
26 ± 21
CFU-M
0
4
10
5 ± 5 p value = 0.02
CFU-Pre B
37
21
27
28 ± 8
BFU-E
8
0
40
16 ± 21
b
GS mice were administered tetracycline via drinking H2O for 14d. Mice were then
sacrificed, and femur bone marrow cells isolated and seeded into methylcellulose
colony forming assays. Cells were plated at 1.0 x 105 cells/plate. Each experiment
included 4 technical replicates and the total number of colonies is shown.
a. GFP+ colony numbers were normalized to account for variation of overall plating
efficiency (total number of CFC of each type) between mice.
b. Number of GFP+ CFU-M colonies observed was statistically significantly lower
as compared to the number of GFP+ CFU-GEMM observed (student’s T test).
doi: 10.1371/journal.pone.0084379.t001
model as repair of a single DSB in mouse and human cells
does not promote large scale genome rearrangements
between heterologs, although they can be associated with
regional loss of heterozygosity (LOH) and insertions with
sequences of unknown origin [20,31–33,81]. Similarly, multiple
DSBs on the same chromosome do not significantly promote
large-scale genome rearrangements in mouse or human cell
lines, although the efficiency of repair decreases as the
distance between two DSBs increases (up to 9 kb apart)
[82,83].
By contrast, cytological analysis indicates chromosome
movement is more fluid in DNA repair deficient cells [79].
Chromosome movement has also been observed in the
presence of multiple induced DSBs on heterologous
chromosomes in mitotic yeast [84] or following global exposure
of cells to ionizing radiation or topo II inhibitors [85–87], leading
to foci suggestive of repair centers (“repairosomes” [84,88]).
The steps by which such repairosomes are initiated by
chromatin remodeling programs as a normal step in DNA repair
or the biological understanding of how translocations are
formed within the ordered nucleus remain unclear [2,89,90]. It
is not clear if chromosome movement is in response to multiple
breaks in different loci or after prolonged or persistent damage.
The established nuclear matrix and chromatin loop structures
may also influence choice of recombination partners during
DSB repair [89]. In support of the cytologic data, our genetic
study here indicates that in vivo interaction of DNA sequences
and recombination is promoted by multiple DSBs.
A wider range of HR mechanisms are used to repair DSBs
on
heterologous
chromosomes
as
compared
to
intrachromosomal HR. In addition, intrachromosomal HR is not
typically associated with the genome rearrangements observed
in human tumors. DSBs in cultured ES cells and multiple in
vitro differentiated hematopoietic cell types can stimulate
interchromosomal HR as a repair pathway [68]. We observed
with this in vivo system that repair by HR in multiple
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Materials and Methods
Ethics Statement
All studies were approved by IACUC (protocol #AAAA0123
Columbia University; protocol #08-035 University of North
Carolina at Charlotte). All studies were conducted under
supervision of appropriate regulatory bodies and in accordance
11
December 2013 | Volume 8 | Issue 12 | e84379
Interchromosomal DSB Repair in Vivo
template for second round of PCR following the same protocol.
PCR primers for each: Sce1F 5’-gtccgaactctaaactgctga-3’;
Sce2R 5’-ACCAGTATGCCAGAGACATC-3’; GFP 1F 5’aaggccaagagggccaa-3’;
GFP
2F
5’TGGACGGCGACGTAAAC-3’;
GFP
3R
5’gtgctcaggtagtggttg-3’;
GFP
4R
5CTCTGTTCCACATACACTTC-3’;
GFP
5F
5’tgaaccgcatcgagctgag-3’;
GFP
6R
5’GACCATGTGATCGCGTTC-3’;
GFP
7R
5’TTCTGATAGGCAGCCTG-3’. Southern blotting to determine
copy number utilized a plasmid fragment of full length GFP
ORF of 3.07 kb and diluted to pg amounts that approximated
0.2, 1.0, 5.0, 10, 20, and 100 copies per genome spiked into
10µg non-transgenic mouse DNA. Genomic DNA of transgenic
mice was digested with restriction endonucleases that flank the
GFP promoter and ORF of both transgenes. The GFP probe
fragment was an Sph-Not I fragment homologous to both
transgenes. Q-PCR for copy number estimation utilized a GFP
ORF fragment diluted to pg amounts that approximated 0.2,
1.0, 5.0, 10, 20, and 100 copies per genome to amplify a 296
bp fragment of GFP DNA. Genomic DNA isolated from
transgenic mice was utilized for Q-PCR. Fluorescent detection
of PCR products was reported using a SYBR® Green PCR kit
(Quanti Tect) in 20μL reactions established according to the
manufacturer’s recommended protocol. A standard curve was
generated (n=3) using the control plasmid GFP ORF DNA
according to the manufacturer’s protocol (QuantiTect). Q-PCR
analysis was simultaneously analyzed by a 96 well 7500 Fast
Real-Time PCR System (Applied Biosystems) in which
transgenic mouse genomic DNA was compared against the
standard curve and statistical analysis performed according to
the Applied Biosystems protocol for 7500 Fast Real-Time PCR
System protocol.
to established NIH guidelines for ethical treatment of animals in
research.
Transgenic Mice
Transgenic mice for study were generated by establishing
three independent transgenic lines of mice: (1) the tetracyclineregulated I-SceI expression gene, (2) 1SGFP with I-SceI cut
site 1, and (3) 2SGFP containing I-SceI cut site 2 (1). TET-ISceI – XbaI-PstI fragment of CBAS containing the I-SceI gene
[64,66] sequence was inserted into NheI-BamHI digested
pBIG3i bicistronic tetracycline-regulated vector (kindly provided
by Craig Strathdee) [65]. DNA was digested with BspHI and the
fragment was provided to the Columbia University Transgenic
Mouse facility (2). 1SGFP – SacII-HindIII fragment of
pCAGGS-NZE-GFP containing the GFP sequence was subcloned into SacII-HindIII digested pBluescript SK+, creating
SKRGFP(Sac2H3). Single-stranded oligomers BHI-∆1-ISceINcoI
P1
(5’GATCTGGATCCACCGGTCGCAATTACCCTGTTATCCCTAC
CATGGAGTAC-3’)
and
BHI-∆1-ISceI-NcoI
P2
(5’GTACTCCATGGTAGGGATAACAGGGTAATTGCGACCGGT
GGATCCAGATC-3’) were annealed and digested with BamHI
and NcoI. This BamHI-NcoI fragment containing the I-SceI
recognition site was ligated into the BamHI-NcoI digested
SKRGFP, creating SKRGFP(Sac2H3)∆1-S. The SacII-HindIII
fragment of SKRGFP(Sac2H3)∆1-S was subcloned back into
the SacII-HindIII digested pCAGGS-NZE-GFP plasmid, to
create pCAGGS-GFP∆1-S. DNA was digested with SalI and
PstI, and the 3433 bp fragment was provided to the Columbia
University Transgenic Mouse facility (3). 2SGFP -- A PvuII site
was engineered in pCAGGS-NZE-GFP using annealed singlestranded
oligomers
GFP-Pvu2-1
(5’CGCCGACCACTACCAGCTGAACACCCCCATCGGCGAC-3’)
and
GFP-Pvu2-2
(5’GTCGCCGATGGGGGTGTTCAGCTGGTAGTGGTCGGCG-3
’and QuikChangeII Site-Directed Mutagenesis Kit (Stratagene),
following manufacturer’s protocol, creating pGFP-Pvu2. Singlestranded
oligomers
SCE1
(5’-PhosATTACCCTGTTATCCCTA)and
SCE2
(5’-PhosTAGGGATAACAGGGTAAT-3’) were annealed and ligated into
the PvuII blunt end digested pGFP-Pvu2, creating pGFP-Pvu2S. DNA was digested with SalI and PstI, and the 3433 bp
fragment was provided to the Columbia University Transgenic
Mouse facility. The Columbia University Transgenic Mouse
facility generated transgenic mice in F1 (C57BL/6J-CBA)
hybrids, and mice were transferred to University of North
Carolina at Charlotte.
The two GFP lines were intercrossed and the resulting line
crossed with mice containing the tetracycline regulated I-SceI
expression transgene. The resultant triply positive transgenic
line was denoted “GS” and used for further study. Genotyping
for presence of all three transgenes was performed by PCR
and Southern blotting of mouse tail tip genomic DNA and
subsequent digestion of PCR products with I-SceI
endonuclease (New England Biolabs) to confirm intact I-SceI
sites. Amplification was performed by 94°C 5 min; followed by
40 cycles of 94°C 30s, 60°C 30s, 72°C 2 min; and 72°C 15
min. For nested PCR 5uL of the first PCR product was used as
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MEFs
Mouse embryonic fibroblasts were isolated from day E13.5 of
GS mice and washed with phosphate buffered saline (PBS).
The head was removed from isolated embryos and used for
DNA genotyping. The body was minced well and 10mL of
0.25% Trypsin-EDTA (Gibco, Grand Island, NY) added.
Solution was triturated with a pipette and added to 25 mL of
medium [Dulbecco’s Modified Eagle Medium (Gibco), 15% FBS
(Gemini Bio-Products, West Sacramento, CA), 1.2% 200mM LGlutamine (Gemini Bio-Products), 1.2% Non-essential Amino
Acids (Gibco), and 1.2% Penicillin-Streptomycin (Gibco)]. Cells
were then collected by centrifugation (1000 rpm x 10 min),
resuspended into 4mL medium, and cultured on a 6-well dish
at 37°C with 5%CO2. MEFs were then passaged onto 10cm
dishes after initial growth. Tetracycline HCl (Barr Laboratories)
was dissolved in 1x PBS to 1mg/mL and passed through a 0.2
micron filter. MEFs were given a final concentration of 2μg/mL
for up to 6 days.
DSB induction in Mice
Tetracycline HCl (Barr Laboratories) was dissolved into .5X
PBS/H20/ sucrose at 10mg/mL and passed through a 0.2
micron filter. Mice were administered tetracycline at 2mg/mL in
a water bottle for up to 21 days.
12
December 2013 | Volume 8 | Issue 12 | e84379
Interchromosomal DSB Repair in Vivo
Flow cytometry and statistical analysis
DNA Sequence Analysis of HR Recombinants from BM
CFCs
MEFs were trypsinized and collected by centrifugation (1000
rpm x 10 min). Cells were resuspended in 1x PBS at a
concentration of 1.0x106 cells/mL. Sections of individual organs
were harvested and a single cell suspension generated in 5%
Bovine Serum Albumin (Gemini Bio-Products)/1x PBS.
Suspensions were passed through a 53μM nylon mesh filter
(Spectrum Laboratories Inc) and analyzed on a FACSAriaII for
GFP positivity. To assess statistical significance of increased
numbers of GFP+ cells among organs in tetracycline treated
mice (Table S1), we utilized a non-parametric t-test for all mice
versus negative controls (Figure 5), and then separately in the
young and old cohorts versus negative controls (Figure 6). To
assess statistical significance of the probabilities associated
with covariance of the number of GFP+ cells in organs of
individual mice, we calculated Spearman’s nonparametric
correlation coefficients for each pair of organs separately in the
young and old cohorts, and utilized the false discovery rate
procedure to control the proportion of false positive results
(Table S2).
Individual CFU-GEMM expressing GFP were identified by
inverted fluorescent microscopy and isolated. Genomic DNA
from 24 individual CFU-GEMMs was extracted from each with
DNeasy Tissue Kit (Qiagen) followed by whole genome
amplification (WGA) with Repli-G Kit (Qiagen) as previously
described [68]. 1.0μg of WGA DNA template was used for
PCR. Each 25μL PCR reaction contained template DNA, 10X
reaction buffer, 1.5mM MgCl2, 200μM each dNTP, 0.48μM
each primer, 2.5 units Taq DNA polymerase. PCR primer sets
are indicated in Figure 1 and in Methods above. Amplification
was performed by 94°C 5 min; followed by 40 cycles of 94°C
30s, 55°C 30s, 72°C 2 min; and 72°C 15 min. For nested PCR
5uL of the first PCR product was used as template for second
round of PCR following the same protocol. PCR reaction
products were cloned with the TA cloning system (Invitrogen)
and blue-white screening used to determine which individual
clones to amplify, isolate DNA, and sequence by Sequetech
(Mountain View, CA) using M13 forward and M13 reverse
primers. Sequencing of up to 10 white colonies from each PCR
reaction/TA cloning reaction was sufficient to identify GFP+
recombinants among parental GFP sequences.
Western Immunoblot analysis
Protein was isolated from pelleted cells using Total Protein
Extraction Kit (Millipore). Cell lysate proteins were then
separated on a 10% NuPage Bis-Tris SDS-Page gel
(Invitrogen) and transferred to Amersham Hybond-P
membrane (GE Healthcare Life Sciences). The membranes
were then blocked in 5% Non-Fat dry milk in 1X tris buffered
saline (Bio-Rad). Membranes were probed with a mouse
monoclonal IgG anti-HA antibody to detect the HA tag within ISceI (Cell Signaling Technology) at 1:100 dilutions for 20-22
hours at 4°C or a mouse monoclonal IgG anti-β-actin antibody
(Santa Cruz Biotechnology) at 1:400 dilution for 1 hour at room
temperature. Blots were subsequently exposed to an antimouse IgG HRP-linked secondary antibody (Cell Signaling
Technology) at 1:1000 dilutions for 1 hour at room temperature.
Blots were washed 3x for five minutes each in a 1x TBS-.05%
Tween 20 solution. Membranes were developed using
SuperSignal® West Pico Chemiluminescent Substrate (Thermo
Scientific).
Supporting Information
Table S1. Number of GFP+ cells detected per million
analyzed by FACS in young and old cohorts. Individual mice
are noted with young cohort mice indicated by Y and old cohort
mice indicated by O. Organs from which technical error led to
no sample recovered for FACS analysis are noted as nd (no
data). These values were the basis for the covariance of traits
analysis in Table S2.
(DOCX)
Table S2. Covariance of GFP+ cells in organs of young
and old cohorts. To assess statistical significance of the
probabilities associated with covariance, Spearman’s
nonparametric correlation coefficients for each pair of traits
separately in the young and old cohorts (Table S1), and utilized
the false discovery rate procedure to control the proportion of
false positive results. Calculated p-values in the young mouse
cohort are represented within the top diagonal half of the
matrix. Calculated p-values in the old mouse cohort are
represented within the bottom diagonal half of the matrix. pvalues <0.05 are denoted with **.
(DOCX)
Bone Marrow-CFC Assay
GS mice (ages 3-5 months) were administered tetracycline
through H2O for 14d. Mice were then sacrificed, and femur
bone marrow (BM) cells isolated and seeded into
methylcellulose colony forming assays [69,70]. Whole BM was
flushed from femurs into IMDM supplemented with 2% FBS
and disrupted into a single cell suspension by a 22G needle
and syringe. Cell viability counts were performed using .05%
trypan blue staining. Total viable BM cells were plated at 1.0 x
105 cells per 35mm low adherence tissue culture dishes in
hematopoietic
differentiation
medium
(STEMCELL
Technologies) containing IMDM, 1% methylcellulose, 15% nonES qualified FBS, 100U/mL penicillin, 100μg/mL streptomycin,
2mM L-glutamine, 150μM monothioglycerol, 1% bovine serum
albumin, 10μg/mL insulin, 200μg/mL transferrin, 150ng/mL
mSCF, 30ng/ml mIL-3, 30ng/mL mIL-6, and 3U/ml hEPO for 14
days.
PLOS ONE | www.plosone.org
Acknowledgements
We thank Craig Strathdee for providing the bicistronic TET-ON
vector backbone. We thank Dr. Larry Leamy for assistance with
statistical analysis. We gratefully acknowledge Victor Lin and
the Columbia University Transgenic Mouse facility for
generation of the relevant transgenic mouse lines used in this
study. We gratefully acknowledge Norman LeFebvre and the
staff at the University of North Carolina at Charlotte vivarium
facility for assistance with animal husbandry.
13
December 2013 | Volume 8 | Issue 12 | e84379
Interchromosomal DSB Repair in Vivo
Author Contributions
Analyzed the data: RRW CGV GB NC CR. Contributed
reagents/materials/analysis tools: PS CR. Wrote the
manuscript: RRW PS CGV CR.
Conceived and designed the experiments: RRW PS CR.
Performed the experiments: RRW PS CGV GB NC CR.
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