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Karyotype Evolution
Annu. Rev. Genet. 2015.49:183-211. Downloaded from www.annualreviews.org
Mitchell L. Leibowitz,1,3,† Cheng-Zhong Zhang,1,2,3,4,†

and David Pellman1,3,4,5,∗
1
Department of Pediatric Oncology, 2 Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215; email: david_pellman@dfci.harvard.edu
3
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
email: mleibowitz@fas.harvard.edu
4
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
email: chengz@broadinstitute.org
5
Howard Hughes Medical Institute, Boston, Massachusetts 02115
Annu. Rev. Genet. 2015. 49:183–211 Keywords

First published online as a Review in Advance on micronuclei, complex chromosomal rearrangement, chromosome bridge,
October 6, 2015
nuclear envelope rupture, single-cell sequencing, genome evolution
The Annual Review of Genetics is online at
genet.annualreviews.org Abstract
This article’s doi: Chromosomal rearrangements are generally thought to accumulate gradu-
10.1146/annurev-genet-120213-092228
ally over many generations. However, DNA sequencing of cancer and con-
Copyright c 2015 by Annual Reviews. genital disorders uncovered a new pattern in which multiple rearrangements
All rights reserved
arise all at once. The most striking example, chromothripsis, is characterized
†
These authors contributed equally to this work. by tens or hundreds of rearrangements confined to a single chromosome or
∗
Corresponding author to local regions over a few chromosomes. Genomic analysis of chromothrip-
sis and the search for its biological mechanism have led to new insights on
how chromosome segregation errors can generate mutagenesis and changes
to the karyotype. Here, we review the genomic features of chromothrip-
sis and summarize recent progress on understanding its mechanism. This
includes reviewing new work indicating that one mechanism to generate
chromothripsis is through the physical isolation of chromosomes in abnor-
mal nuclear structures (micronuclei). We also discuss connections revealed
by recent genomic analysis of cancers between chromothripsis, chromosome
bridges, and ring chromosomes.
183
INTRODUCTION
It is common to think of a mutation rate as a constant value—a rate of point mutation or chro-
Chromothripsis: an mosome rearrangement that occurs per basepair of DNA in each generation. However, recent
all-at-once mutational advances have revealed interesting complexities that challenge this simple view of mutation rates.
pattern in which a We now know that the accumulation of mutations is neither uniform across the genome (63, 68)
large number of
nor constant from one generation to the next (1, 4, 60, 170). In this review, we focus on a partic-
rearrangements are
confined to local ularly dramatic and episodic form of mutagenesis called chromothripsis (141), in which massive
regions. It is often rearrangements restricted to only one or a few chromosomes are proposed to occur through a
accompanied by one-off catastrophe during a single cell division.
copy-number losses Variable rates of mutations across the genome are evident from studies with mutation reporters
Kataegis: showers of in model organisms (88) and from mutation frequencies detected by genome sequencing (1, 10,
single nucleotide 102, 129, 171). Late-replicating and heterochromatic regions have higher mutation frequencies
changes confined to
than early replicating and euchromatic regions (17, 29, 63, 89, 97, 132, 138, 167). This differ-
local regions, often
ence in mutation frequency reflects the gradual, yet biased accumulation of mutations over many
near sites of
chromosome generations. Variation in mutation frequencies across different regions in the genome may have
rearrangement a number of origins: DNA sequence context (63, 129), such as GC content; the accessibility to
DNA repair factors (39, 145); and the time available during which a replicated sister chromatid is
present as a template for error-free DNA repair (146).
The accumulation of mutations over many generations enables a quantitative estimation of the
regional variation in mutation frequency. In general, the variation in the point mutation frequency
is relatively small: less than tenfold between infrequently and highly transcribed regions in cancer
(89), and less than threefold between early and late replicating regions (17, 86, 89, 138). It is
known that these differences in mutation frequency are not due to selection, and accounting for
such variation allows for a more accurate identification of true cancer driver mutations in the
context of selection (89).
The frequency of the generation of chromosome rearrangements also varies across the genome.
For example, ∼25% of the breakpoints found between mouse and humans originated at or near
segmental duplications (ten to several hundred kb blocks that are copied from one region of the
genome into another region; 3). Transposon-derived repeats (also known as interspersed repeats),
which are present in multiple copies throughout the genome, can account for a significant portion
of germline rearrangements (108, 168). A likely reason for this enhancement of rearrangements
in repetitive loci is that these sequences have higher chance to undergo homology-dependent
recombination events during DNA replication (127, 134). Translocations are also enriched in
late-replicating sites in the genome. For example, late-replicating common fragile sites are hot
spots for deletions and translocations in cancer (8, 29, 30, 90).
Rearrangements themselves can trigger high local concentrations of point mutations (15, 25).
Showers of single nucleotide variants (kataegis) have been observed in cancer genomes near the
junctions of chromosomal translocations (115). The mechanism of this phenomenon appears to
involve the generation of single-stranded DNA (ssDNA) by processing of the double-strand break
(DSB) that caused the rearrangement. This ssDNA is then modified by APOBEC enzymes, which
deaminate cytidine to form uracil (128, 149). Because the mutations occur on ssDNA, they are
strand-coordinated (reviewed in the accompanying review by Chan & Gordenin; 16) meaning that
Cs are mutated on one strand on one side of the DSB, whereas Cs on the other strand are mutated
on the other side of the break. This modification results in a C→T transition after DNA replication
or can result in C→T transitions or C→G transversions after base excision and translesion DNA
synthesis (149). Chromosomal breaks can also generate point mutations during gene conversion
184 Leibowitz · Zhang · Pellman

events with up to an ∼1,400-fold increase in the local occurrence of single nucleotide changes
(62). In this case, the mechanism involves replication template switching by DNA polymerases δ
and ε.
Chromoanasynthesis:
For any rearrangement breakpoint, its rearrangement partner tends to be nearby (19, 52, 79, a large series of
107). This is because chromosomes occupy territories (23, 96) within the nucleus, which creates copy-number gains
up to a tenfold enrichment for the translocation partners of a DNA break to reside within the same (and some losses) on a
chromosome relative to other chromosomes. In particular, the majority (more than 85%) of these single chromosome as
a result of template
intrachromosomal rearrangements occur between loci within 300 kb of the original breakpoint
switching
(19, 79). This means that if a break occurs, the majority of translocations are likely to occur within
approximately one ten-thousandth of the genome.

Extreme cases of localized chromosomal rearrangement occur when breaks happen repeatedly
on the same chromosome, such as in breakage-fusion-bridge (BFB) cycles. BFB cycles, first dis-
covered by Barbara McClintock (105), result from end-to-end chromosome fusions, often due to
erosion of telomere sequences (27, 50). During mitosis, the two centromeres of the dicentric chro-
mosome can be segregated into different daughter cells, creating a chromosome bridge between
the daughters. Subsequently, the bridge breaks (by poorly understood mechanisms), resulting in
chromatids with broken ends. The broken chromatid can be replicated and fused with its sister
chromatid, reinitiating the BFB cycle on the same chromosome (Figure 1a). Thus, BFB cycles
can generate multiple rearrangements on the bridging chromosome, which are often detected as
amplifications flanked by foldback inversions. These rearrangements accrue over multiple gener-
ations and thus develop in a manner expected for a classical gradual evolutionary process.
Recent genome sequencing suggests the existence of new mutational phenomena, termed chro-
mothripsis (Figure 1b; 141) and chromoanasynthesis (Figure 1c; 99), that seem to violate all the
expectations of gradual genome evolution. These phenomena involve massive rearrangement
localized to one chromosome, one chromosome arm or segment, or, in some cases, a few chromo-
somes. For chromothripsis, statistical modeling led to the hypothesis that the complex rearrange-
ments occur through a single catastrophic event, giving a burst of mutagenesis in a single step
(141)—in contrast to the BFB cycles described above. It was hypothesized that the catastrophe
initiating chromothripsis is the shattering of a chromosome followed by the reassembly of some
fragments, with the loss of others. However, the mechanism by which a chromosome could be
shattered, or even the feasibility of such an event, was unclear until recently (174).
Chromoanasynthesis is another form of highly localized complex chromosomal rearrangement
that involves small-scale changes in DNA copy number (99). Although initially it was not clear
that chromothripsis and chromoanasynthesis are distinct, there is an emerging consensus that
this is indeed the case (65, 80, 98, 173). Unlike chromothripsis, chromoanasynthesis is primarily
characterized by small-scale gains of chromosome segments, often duplication and triplication,
with some loss. Chromoanasynthesis is suggested to result from an error in DNA replication
in which damage at a DNA replication fork triggers cycles of replication template switching
(92, 99), resulting in the copying of distal DNA segments into the initial site of damage. Like
chromothripsis, chromoanasynthesis is believed to generate many complex rearrangements within
a single cell division cycle.
This review primarily focuses on chromothripsis, with an emphasis on recent advances in
understanding its mechanism. Although chromothripsis and chromoanasynthesis were first dis-
covered through genomic analyses of human diseases, the underlying mechanisms are very likely
to be relevant to other circumstances in which there is rapid and episodic karyotype evolution in
animals (12) as well as plants (148).
www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 185

a Breakage-fusion-bridge cycles b Chromothripsis
Fragmentation
1st break Breakage

Lost
(Replication)
Fusion Assembly
Bridge
Copy number
2nd break
Breakage-fusion-
bridge cycles
c Chromoanasynthesis
Template switch:
Duplication
Deletion-type
8
Inversion #1
Copy number 4
1 2 Inversion #2
0
Telomere acquisition
Copy trp
number dup
Figure 1
Complex genomic rearrangements: breakage-fusion-bridge (BFB) cycles, chromothripsis, and chromoanasynthesis. (a) BFB cycles are
initiated by loss of a terminal chromosome segment (1st break). After replication of the broken chromatid, the sister chromatids can
fuse at the break site (fusion), generating a foldback inversion (red ). The fusion creates a dicentric chromosome that can generate a new
chromosomal bridge. Bridge resolution (2nd break) can lead to further BFB cycles until the broken end acquires a telomere from, e.g., a
translocation or break-induced replication (BIR). During BFB cycles, asymmetric cleavage of the bridged chromosome can produce
DNA amplification in an inverted orientation in sequential steps, doubling the gene copy number of the terminal segment each cycle.
(b) Chromothripsis is hypothesized to be generated after a single chromosome is fragmented into many segments, followed by random
assembly of a subset of these fragments. Those segments that are not incorporated are deleted from the derivative chromosome (lost)
or, if they contain gene(s) under positive selection, might be incorporated into double-minute chromosomes (not shown).
(c) Chromoanasynthesis is proposed to arise from a series of template-switching events during DNA replication by, e.g.,
microhomology-mediated break-induced replication. Template switches (indicated in red ) can result in duplication (dup), triplication
(trp), or foldback inversions (U-turns) as well as segmental loss (not shown).
MASSIVE DAMAGE TO A SINGLE CHROMOSOME

Chromothripsis was first discovered by an insightful analysis of the chromosomal rearrangements
in a patient with chronic lymphocytic leukemia (CLL; 141). The patient’s tumor contained
42 chromosomal rearrangements involving the q arm of chromosome 4 but only one isolated
event elsewhere in the genome. The rearrangements on chromosome 4q had a number of
notable features. First, these rearrangements joined chromosome segments in random order
and orientation. In contrast to simple rearrangements that frequently involve nearby partners,
the rearrangements on chromosome 4q had partners that were just as likely to come from
distant loci as from nearby loci. Most remarkably, the clusters of complex rearrangements were

accompanied by an oscillation of DNA copy number between only two states. This pattern, which
Campbell and colleagues (141) named chromothripsis, was dominated by hemizygous regions
interspersed with islands of higher copy number that retain heterozygosity. Separately, spectral
Loss of
karyotyping (SKY) and fluorescence in situ hybridization (FISH) experiments demonstrated that heterozygosity
the rearrangements of chromothripsis are all contained within a single derivative chromosome (LOH):
that originated from one parental chromosome. loss of one parental
Since these initial observations, the unique sequence features of chromothripsis have been allele in a diploid
genome because of
observed in many tumor types (9, 75, 103, 117, 163, 171). Current estimates are that chromothripsis
DNA deletion or gene
occurs in 2% to 5% of human cancers (141, 171), with frequencies possibly reaching as high as crossover
39% in certain tumor types (103; for recent reviews, see 80, 82, 173). Initially, it was thought that
Haplotype (haploid
chromothripsis was particularly frequent in bone cancers, but recent data suggest a generally high genotype): sequence
frequency of chromothripsis in all sarcomas (9; P. Campbell, personal communication). Because of genetic variants that
cancers are often aneuploid (5, 171), either the intact homolog or the chromothriptic derivative occurs on a single
chromosome (or both) can be present at an amplified copy number. Thus, the characteristic two- parental chromosome
state DNA copy-number pattern of chromothripsis does not have to oscillate just between two Phasing: association
copies and one copy, but the number of copies at each level can vary. In general, if there are and segregation of
genetic variants to
m copies of the intact homolog and n copies of the derivative chromosome, oscillation occurs
their originating
between m and m + n copies. parental chromosomes
How accurate are these estimates of the frequency of chromothripsis? How definitively can we
distinguish chromothripsis from other forms of complex chromosomal rearrangements? Korbel
& Campbell (85) defined six criteria for the inference of chromothripsis from genomic analysis.
Importantly, they suggested statistical measures to establish several of them. The criteria are
(a) the localized clustering of breakpoints; (b) the oscillating DNA copy-number pattern; (c) the
alternation of heterozygous regions with regions showing loss of heterozygosity (LOH); (d ) the
restriction of rearrangements to a specific haplotype (i.e., one of the parental chromosomes);
(e) the random order and orientation of DNA segments; and, finally, ( f ) the ability to walk the
derivative chromosome, connecting breakpoint junctions sequentially to reveal the structure of
the derivative chromosome.
Although the criteria outlined by Korbel & Campbell (85) provide an excellent basis for a
more rigorous definition of chromothripsis, identifying chromothripsis from genomic analysis
alone remains challenging. Both the inference of rearrangements affecting a specific haplotype
(criterion d) and walking the derivative chromosome (criterion f ) require the ability to associate
(phase) rearrangements with one of the two homologous chromosomes. Such long-range phasing
information is extremely difficult to obtain from shotgun sequencing and requires cytogenetic
methods such as FISH or SKY. The other features, including those on rearrangements (criteria a
and e) and those on copy-number alterations (criteria b and c), can be validated by whole-genome
sequencing analysis. But these criteria require a threshold number of events to be set—an
operational cutoff for a phenomenon that is almost certainly a continuum of lower to higher
complexity. Further complicating the analysis are other genomic lesions that intermingle with
chromothripsis but occur independently. Such overlapping alterations can obscure the hallmark
features of chromothripsis. Finally, although we now have statistical measures to establish many
of the given criteria, it is still not clear how to properly weigh and combine the criteria into a
generally useful summary statistic—to give a binary answer as to whether or not an event is truly
chromothripsis.
For the above reasons, most studies to date combine a subset of the six criteria to detect
chromothripsis (75, 103, 171). A simple approach is to set a conservative operational cutoff.
This decreases the risk of false detection but has the trade-off of likely underestimating the true
frequency of chromothripsis. For example, the above mentioned estimate that 2% to 5% of

cancers have chromothripsis comes from the analysis of array-based copy-number data (171).
This estimate would exclude any case of copy-neutral chromothripsis, which has been shown to
occur in the germline, and exhibits all of the features of chromothripsis, with the exception of
copy-number loss (18, 28, 81, 83).
CHROMOTHRIPTIC LESIONS ARE HARD TO EXPLAIN

BY GRADUAL MUTAGENESIS
The difficulty in estimating the frequency of chromothripsis also highlights the need for
more information about its mechanism. This is especially true if the mechanism(s) generating
chromothripsis can also generate more subtle chromosomal alterations that do not meet the more
obvious criteria for chromothripsis. The first insight into the mechanism came from analyses
of the genomic features of chromothripsis, which suggested that the rearrangements are more
likely to occur in a single event rather than accumulate over many generations (e.g., like BFB
cycles).
A major piece of evidence supporting the idea that chromothripsis is a one-off event is its copy-
number pattern—many segmental deletions but little or no amplification (141). Cancer genomes
exhibit both DNA amplifications and deletions at a comparable frequency (5, 11, 120, 142, 169,
171). For example, in a pan-cancer analysis of 4,934 genomes, there were a median of 11 focal
amplifications and 12 focal deletions per genome (171). Thus, the preponderance of segmental loss
seen in chromothripsis runs contrary to expectations based on the generally random processes that
shape cancer genomes. Stephens et al. (141) extended this conceptual argument with simulations
to test the plausibility that chromothripsis could evolve through a multigenerational, gradual
process. Starting from the reference genome, the authors applied chromothriptic rearrangements
one at a time, assuming them to be independent. The simulation stipulated that once applied
to the rearranged genome, the rearrangements with a tandem duplication orientation produce
copy-number gains, and those with a deletion orientation produce copy-number losses (for more
detail, see 173). When tandem duplications overlap, increased copy-number states are generated.
Simulations based on these assumptions indicated that gradual accrual of rearrangements quickly
yields more than two copy-number states. The apparent contradiction between the multiple copy-
number states resulting from gradual evolution and the oscillating two-state copy-number pattern
in chromothripsis led to the proposal that chromothriptic rearrangements were generated all at
once.
Although compelling, these simulations are not definitive. A study by Kinsella and colleagues
(77) showed that by adjustment of the parameters of the simulation, at least in the less dramatic cases
of chromothripsis, it is possible to produce just two copy-number states by gradual accumulation
of rearrangements. For example, it is possible to generate chromothripsis by a successive accrual of
rearrangements if inversions are enriched in the simulation. This is because overlapping inversions
are capable of shuffling DNA segments into any order. A successive combination of deletions and
inversions can therefore generate all the features of chromothripsis (77). Shuffling DNA segments
by inversions is analogous to the famous pancake problem that was efficiently solved by Bill Gates
(45)—this problem asks for a particular series of flips (inversion from one terminus) of portions
of a stack of pancakes in order to generate a particular arrangement of the stack (77). Although
there is always a solution for chromothripsis resulting from a series of inversions and deletions,
the gradual model of chromothripsis based on inversions is still disfavored because of the low
frequency of inversions observed in cancer genomes (169). Overall, the study by Kinsella and
colleagues highlights the need for a better understanding of the mechanism for chromothripsis to
more accurately refine the genomic analysis (77).

WHAT MECHANISMS GENERATE CHROMOTHRIPSIS?

Any mechanism for chromothripsis needs to explain how the breaks are generated and why this
damage is so strongly localized. One early idea to be considered was that the shattering of a Micronucleus:
chromosome might occur by ionizing radiation (141). This would be unlikely during interphase, small nucleus around a
when chromosomes are decondensed and occupy fairly sizable territories (23). However, this might chromosome or
chromosomal
occur during mitosis, when chromosomes are individuated by mitotic chromosome compaction.
fragment that is not
Although plausible, it remains unclear how frequently particles would hit a chromosome in the incorporated into the
right way to generate multiple breaks on one chromosome without damaging the others (71). Other main nucleus
ideas, such as partial apoptosis (67, 158), have also been considered but are generally disfavored
because they do not easily explain the sharp localization of chromothriptic lesions.
Another proposal was that the localized damage of chromothripsis could occur through the
physical isolation of chromosomes into abnormal nuclear structures called micronuclei (22). In
metazoans, the nuclear envelope (NE) breaks down during mitosis and then reforms during mitotic
exit (61, 131). Because the NE reforms around all chromatin during telophase, any chromosome
or large chromosomal fragment that is separated from the main chromosome mass is partitioned
into its own nucleus—a micronucleus (36, 154). Micronuclei are common in cancer cell lines, with
frequencies ranging from a few percent of cells, which is typical, to very high percentages of cells in
rare cell lines (48, 155). Mutations in oncogenes or tumor suppressors that destabilize the genome,
such as those in FBXW7 (121) and TP53 (32), can cause lagging chromosomes and/or micronuclei
to form at elevated frequencies. Micronuclei are also well-described features of primary cancers
(48, 57), although we do not have quantitative information on their true in vivo frequency.
Are micronuclei a cause or a consequence of DNA damage? The evidence that micronuclei
can result from DNA breakage is very clear (35, 154). Because acentric chromosome fragments
cannot assemble kinetochores, they do not attach to the mitotic spindle and might therefore
be partitioned into micronuclei. This applies to breakage from any source—exogenous DNA
damage (37), defects in DNA replication (112, 136), or defects in DNA repair (111). The fact that
micronuclei are useful reporters for DNA damage has been used to design in vivo genetic screens
for proteins that affect DNA stability (136), and underpins a large and complicated literature on
cancer early detection, cancer risk, and a wide variety of stresses (7, 72, 110).
Although micronuclei can result from DNA damage, as was used to induce micronuclei in
many early studies, there are also data indicating that these structures have defects in DNA repli-
cation, in DNA repair and transcription, and in the accumulation of nuclear proteins (22, 57,
64, 153, 154), thus raising the possibility that micronuclei themselves might cause DNA damage.
To test whether micronuclei can cause DNA damage directly, Crasta and colleagues (22) gen-
erated micronuclei through mitotic errors and monitored the integrity of their chromosomes as
cells progressed through the cell division cycle. Mitotic errors can cause chromosomes to lag at
anaphase, leading to the incorporation of lagging chromosomes into micronuclei. Because the
chromosomes start out intact, these experiments enabled the role of the micronucleus itself in
generating DNA damage to be evaluated. Although newly generated micronuclei showed little
damage in G1-phase cells, a large fraction of S- and G2-phase cells had micronuclei that had
extensive cytological evidence of DNA damage. The damage was notably specific: It occurred
only on the missegregated chromosome that was segregated into the micronucleus. In line with
a growing body of literature (43, 69, 135), this demonstrated that errors in mitosis can generate
DNA damage, and thus potentially has significant implications for the longstanding debate about
the role of whole-chromosome aneuploidy in tumor development.
The nature of the defects in pathological micronuclei and how they generate DNA damage
remain unclear, but there has been some interesting recent progress. Most strikingly, Hatch et al.
(57) recently reported that the NE surrounding micronuclei is fragile, leading to irreversible

breakage of the NE and spillage of nuclear contents. Importantly, the rupture of the micronuclear
NE was closely correlated with the acquisition of DNA damage.
This defect in NE integrity of micronuclei is also correlated with a variety of other functional
Premature
chromosome defects. Intact micronuclei have a delay in the initiation of DNA replication, display reduced levels
compaction (PCC): of DNA replication relative to the main nucleus, and replicate asynchronously relative to the main
mitotic compaction of nucleus, with many micronuclei continuing replication into the G2 phase (22). The net result
interphase is that chromosomes in micronuclei are significantly underreplicated (see below). Micronuclei
chromosomes that
also accumulate reduced levels of various nuclear proteins, including DNA replication and repair
results in a pulverized
chromosome proteins, which we now know occurs in both intact and ruptured micronuclei (22, 57, 64, 153;
appearance when the E. Jackson, A. Spektor, D. Pellman, unpublished results). Additionally, an early electron mi-
compacted croscopy study (46) and later quantitative fluorescence analysis (22, 57, 64, 152) indicated that
chromosome is there is a reduced density of nuclear pores on micronuclei, with some variation in the extent re-
replicating
ported in different studies. How this affects nuclear transport is not clear. A general nuclear import
reporter, fluorescently labeled importin-β binding domain (IBB), showed a partial import defect
(22) that is likely to be explained by the population of cells with NE rupture, as was later described
(57). Import defects that were observed with conditional transcription factor import reporters
would have been complicated by cells with NE rupture (22, 57) and might also have been affected
by altered chromatin (57) in micronuclei, which could decrease the nuclear retention of these
reporters. Alternatively, the results with these reporters might reflect defects in specific import
pathways. In summary, micronuclei have defects in NE integrity and in the accumulation of a
number of nuclear proteins. The basis for these defects remains unclear and merits further study.
It is worth noting that micronuclei may express their defects to a variable degree in different cell
types. For example, after fertilization in amphibians and fish, apparently normal DNA replication
can occur in micronuclei called karyomeres (93). Why some micronuclei might function normally
but others do not is not known.
How NE rupture triggers DNA damage is also not known, but damage appears to occur
primarily when rupture happens after S-phase entry. Little or no damage in micronuclei occurs
in G1 cells, even if the NE ruptures (22, 57, 174; Figure 2a). We have recently confirmed this
in both unperturbed G1 cells and in serum-starved G0 cells (174). A simple hypothesis for why
DNA damage occurs when the micronucleus ruptures after the initiation of DNA replication is
that stalled or collapsed replication forks provide a substrate for cytoplasmic nucleases that cannot
attack an intact chromosome. Based on early experiments in Xenopus egg extracts, it is expected that
NE rupture blocks both the initiation and progression of DNA replication (21), thus providing
DNA structures that are substrates for several nucleases.
In addition to NE rupture, there may be other sources of DNA damage in micronuclei
(Figure 2b,c). As discussed above, there are replication defects in micronuclei, and ∼10% of
intact micronuclei exhibit cytological evidence of DNA damage (57; A. Spektor & D. Pellman,
unpublished results). Furthermore, late replication in micronuclei means that some micronuclei
enter mitosis while DNA replication is ongoing (22, 116, 133). If the NE around the micronucleus
breaks down in mitosis while the DNA contained within is still replicating, this could create an
analogous situation to NE rupture during S phase: Replication intermediates that are substrates
for cytoplasmic nucleases would now be exposed to these nucleases.
Entering mitosis during DNA replication also results in so-called premature chromosome
compaction (PCC), which generates a pulverized appearance to chromosomes (70, 73, 123). PCC
has been proposed to generate DNA damage, with the best evidence coming from the analysis
of late-replicating common fragile sites (30, 33, 101, 113). However, since its initial description,
there has been an active debate about the degree to which chromosome compaction actually
damages DNA. Gaps seen on chromosome spreads of cells that have undergone PCC (33) do

a
Hoechst GFP-NLS γ-H2AX Merged
G1
S
G2
b c
G2
Figure 2
Nuclear envelope (NE) defects and DNA damage in micronuclei. (a) Damage in micronuclei is associated with NE rupture and
requires S-phase entry. Nuclear integrity (intact or ruptured) can be monitored by the presence or absence (respectively) of green
fluorescent protein tagged with the nuclear localization signal peptide (GFP-NLS). DNA damage is detected by an antibody against the
phosphorylated-histone H2AX (γ-H2AX). Micronuclei are highlighted in boxes. The merged images indicate that DNA damage is
localized in ruptured micronuclei that have entered S phase. These images are adapted from Reference 174. (b) Models for the
acquisition of DNA damage in micronuclei. (Left path, red arrows): Delayed and asynchronous DNA replication and loss of NE
integrity. If the NE of a micronucleus ruptures while the micronuclear chromosome is still replicating, the replicating chromosome can
acquire DNA damage. This might occur from replication fork collapse and/or processing of replication intermediates by cytoplasmic
nucleases. Alternatively (right path, black arrows), if replication of an intact micronucleus continues into mitosis, DNA damage may also
occur after mitotic NE breakdown (NEBD). This damage could be caused by accessibility of replication intermediates to nucleases
after NEBD (i.e., with normal NEBD serving the same function as interphase NE rupture) or by poorly understood damaging effects
of mitotic chromosome compaction on replicating DNA [premature chromosome compaction (PCC)]. (c) Image of a metaphase spread
showing an apparently fragmented chromosome. The fragmented chromosome has a pulverized appearance, similar to the appearance
of cells known to have undergone PCC. Furthermore, the pulverized chromosome was replicating during G2, as shown by
5-bromo-2 -deoxyuridine (BrdU) incorporation (red ). This image was originally found in Reference 22.

not necessarily correspond to breaks. Instead, they could represent unreplicated regions that
lack proper chromosome condensation (118, 123, 176). Thus, whether PCC itself is damag-
ing, only accentuates preexisting damage, blocks DNA repair, or is in fact neutral needs to be
determined.
Early studies primarily used nonphysiological conditions to trigger PCC, e.g., cell fusion or
phosphatase inhibitor treatment of cells (53, 70). The new links between micronuclei and hu-
man disease provide a more physiological (or at least pathophysiological) context to motivate a
reexamination of the consequences of mitotic chromosome compaction on DNA replication.
Finally, decreased accumulation of DNA replication and repair proteins may generate DNA
damage more directly. For example, replication protein A (RPA) does not accumulate in either
intact or ruptured micronuclei ( J. Lukas, personal communication; E. Jackson & D. Pellman,
unpublished results). It has been demonstrated that depletion of RPA from cells causes them to
undergo replication catastrophe—extensive replication fork firing and subsequent DNA damage
by fork collapse, a mechanism of damage that might apply to micronuclei (156).
DIRECT EVIDENCE THAT MICRONUCLEI CAN

GENERATE CHROMOTHRIPSIS
Damage in micronuclei would not have long-term genomic consequences if micronuclei were
extruded from cells or degraded, as had been suggested in some prior studies (91, 124). How-
ever, imaging experiments showed that specifically labeled chromosomes from micronuclei can
be incorporated into a daughter cell nucleus following mitosis (22, 66). This demonstrated that
mutations from micronuclei could, in principle, be incorporated into a stably transmitted genome.
It was therefore appealing to hypothesize that the localized chromosomal damage in micronuclei
could generate chromothripsis, with rearrangements occurring after the damaged chromosome
was in a normal repair-competent daughter cell nucleus. A simple and direct test of this idea would
−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−→
Figure 3
Direct evidence that micronuclei lead to chromothripsis by combining live-cell imaging and single-cell whole-genome sequencing
(Look-Seq). (a) Live-cell imaging was used to select cells most likely to have undergone chromothripsis. Chromatin was labeled with
green fluorescent protein–conjugated histone H2B (GFP-H2B); micronuclei are highlighted in boxes; disruption of the nuclear
envelope was visualized by the loss of a nuclear-localized red fluorescent protein (RFP-NLS); reincorporation of the micronucleus was
inferred from the absence of micronuclei in either daughter. After cell division, the daughter cells were isolated and subjected to
whole-genome sequencing. DNA damage from micronuclei was measured by the detection of chromosomal rearrangements
(represented as colored arrows) in daughter cells. (b) The identity of the missegregated chromosome partitioned in the micronucleus was
inferred from the copy-number asymmetry between the two daughter cells. Depending on how the lagging chromosome segregated,
mother cells with micronuclei can be of two kinds, disomic (left scheme), or trisomic for the lagging chromosome (right scheme). The two
scenarios are expected to result in daughter cells that are at a 2:1 or 3:2 copy-number ratio for the micronucleated chromosome, given
the low level of replication of the chromosome in the micronucleus. This leads to the prediction that rearrangements as a result of
DNA damage in micronuclei should primarily be observed in the cell with the higher copy number. Daughter cells are indicated by
hatched boxes (higher copy number) or solid boxes (lower copy number). On the bottom are results from sequencing analyses of two
pairs of daughter cells, one for each scenario (2:1 and 3:2 copy-number ratios). In the plots, the chromosomes and their banding
patterns are shown in the outer circle, and DNA copy numbers for the two daughters are represented as gray histograms, with red and
blue dots representing significant gains and losses, respectively; long-range intrachromosomal rearrangements (breakpoints separated
by ≥150 kb) are shown as green links. The inner circle is for the daughter with the higher copy number of the missegregated
chromosome. On the left, chromosome 3 (Chr3) is missegregated, creating a 2:1 ratio; on the right, chromosome 8 (Chr8) is
missegregated, creating a 3:2 ratio. A large number of intrachromosomal rearrangements are almost exclusively observed on the
missegregated chromosome in the daughter cell with the higher copy number for that chromosome. This figure is adapted from
Reference 174. Abbreviations: MN, chromosomes in the micronucleus; PN, chromosomes in primary nucleus.

be to isolate daughter cells after reincorporation of a damaged chromosome from a micronucleus

and analyze the chromosomal rearrangements by whole-genome sequencing.
Our group recently established an approach (Look-Seq) combining live-cell imaging and
single-cell genome sequencing that enables this experiment to be performed (Figure 3a). This
experiment demonstrated that the formation of micronuclei is at least one mechanism underlying
chromothripsis. By imaging, we determined whether the micronuclear NE underwent rupture
and whether the chromosomes from ruptured micronuclei were reincorporated into daughter
nuclei. The daughters were then isolated and subjected to single-cell whole-genome sequencing
to identify chromothriptic rearrangements.
Although seemingly straightforward, this experiment has both technical and conceptual chal-
lenges. Because micronuclei were generated by random mitotic errors, the most significant issue
b
a
GFP-H2B RFP-NLS
G1
PN MN PN MN
S/G2
MN
rupture
G1
2 1 3 2
X 1 X 1
2122 2122
20 20 2
19 2 19
18 18
17 17
3
16 16
3 15
15
Chr8 4
14 Chr3 14
13 13 5
4
12 12
6
11 5 11
7
10 6 10
9 7 9
8 8

was determining the identity of the missegregated chromosome in the micronucleus. However,
the finding from cell biological analysis that the chromosome in the micronucleus is poorly repli-
cated provided a solution to this problem. Any chromosome in the mother cell’s primary nucleus is
MMBIR:
microhomology- normally replicated and evenly segregated. Preexisting chromosome abnormalities in the mother’s
mediated primary nucleus, for example, a trisomy, is also transmitted to both daughters. By contrast, the
break-induced underreplicated chromosome in the micronucleus is present in a single copy, generating a copy-
replication number asymmetry for this chromosome between the daughter cells (Figure 3b).
FoSTeS: fork stalling This copy-number asymmetry then leads to a series of important conclusions and predictions.
and template switching First, the asymmetry identifies the missegregated chromosome(s), demonstrating that the mis-
segregation is a de novo event from the last cell division. Second, it predicts that chromothripsis
should be observed only in the daughter that has received the damaged chromosome (i.e., the
daughter with the higher copy-number state) or in both daughters, but restricted to regions that
have the higher copy-number state, if the damaged chromosome is fragmented and split between
the daughters. Finally, chromothriptic rearrangements should be restricted to the specific chro-
matid that was in the micronucleus, which could be identified from the haplotype copy number
for different homologs.
Consistent with these predictions, we always observed one or two chromosomes with the pre-
dicted copy-number asymmetry. Moreover, a striking enrichment of rearrangements was observed
specifically on the missegregated chromosome. In the most dramatic case, the missegregated chro-
mosome had ∼80-fold enrichment in the frequency of rearrangements compared to the normally
segregated chromosomes. Where there were informative polymorphisms near the rearrangements,
it was demonstrated that the rearrangements were linked to the missegregated homolog. In ex-
amples in which the missegregated chromosome was distributed to one daughter, rearrangements
were detected only in the daughter with the higher copy number for the affected chromosome, as
predicted. These examples bear a strong resemblance to cases of germline chromothripsis, where
there is extensive rearrangement of a chromosome without copy-number loss (80).
In one case, two chromosomes were missegregated into a micronucleus, resulting in derivative
chromosomes in the daughters containing a complex admixture of fragments from both chro-
mosomes. In another example, chromothripsis involved only a single chromosome arm, likely
explained by the micronucleus having contained an acentric chromosome fragment generated
by the breakage of a chromosome bridge (58). These examples demonstrate that micronuclei can
generate chromothripsis that spans multiple chromosomes or is restricted to a single chromosome
arm, providing an explanation of the spectrum of chromothripsis that is observed in cancer and
germline disorders.
In several cases, the missegregated chromatid was split between the two daughter cells. This
generated the hallmark two-state oscillating copy-number pattern across the affected chromo-
some: higher copy number where the segments of the fragmented chromatid were retained and
lower copy number where they were lost. Importantly, segments that were lost from one cell
were usually retained in the other cell, generating a largely reciprocal pattern between the two
daughters. Such reciprocal distribution of fragments provides direct evidence that the mechanism
for chromothripsis can involve the shattering of chromosomes from micronuclei.
It was initially unclear whether chromothripsis occurred through a mechanism involving
chromosome fragmentation or from DNA replication errors, such as those generated by
microhomology-mediated break-induced replication (MMBIR) or fork stalling and template
switching (FoSTeS); MMBIR and FoSTeS are reviewed in Reference 172. Chromoanasynthesis
is believed to occur via these mechanisms (99). Although the Look-Seq experiment suggests
that micronuclei primarily generate chromothripsis via chromosome fragmentation, there were
some rearrangements that might reflect co-occurring MMBIR. For example, at one long-range

rearrangement junction, we identified eight short (∼50–500 bp) inserted segments from all over
the affected chromosome. Such templated insertions are hallmark features of MMBIR (55).
However, the single-cell sequencing data do not have the resolution to unambiguously determine
whether these short insertions are true copy-number gains, as expected for MMBIR, or result
from the ligation of fragmented breakpoint ends.
Altogether, the Look-Seq experiment demonstrated that micronuclei could generate extensive
chromosomal rearrangements, which in some cases have all the known hallmarks of chromothrip-
sis. There are many further mechanistic questions that should now be tractable with this approach.
Cell biological experiments indicate that rupture of micronuclei during the G1 phase generates
little if any DNA damage. This should now be verified by genome sequencing of daughters after
the division of a cell with G1 micronuclear rupture. Because rupture of micronuclei seems to
terminate normal nuclear processes, such as transcription and replication, it is appealing to think
that DNA breakage and the generation of chromosomal translocations or DNA repair are tempo-
rally separated. This predicts that damaged micronuclei that do not reincorporate into a daughter
cell nucleus should not be reassembled and would not undergo rearrangement. In general, the
Look-Seq approach is a powerful way of relating phenotype to genotype and may be useful for
studying a variety of problems in mutagenesis and genome stability.
CONDITIONS THAT FAVOR CHROMOTHRIPSIS

What conditions might favor the development of chromothripsis? Given the important role of
TP53, the gene that encodes the tumor suppressor protein p53, in maintaining genome integrity
(87, 94, 159), it is not surprising that TP53 loss has been linked to chromothripsis (125). However,
despite its relationship with TP53 status, chromothripsis is not always associated with general
genome instability (171). This is highlighted by the cases of germline chromothripsis (83) and by
pan-cancer genome analyses.
Perhaps some congenital cases of chromothripsis originate from rapid cell divisions in the early
embryo that are under reduced cell cycle checkpoint surveillance. Of interest in this regard is that
depletion of the pluripotency factor Oct4 from embryonic stem cells promotes the formation of
micronuclei, apparently because of a nontranscriptional role of Oct4 as a cyclin-dependent kinase
inhibitor (175).
Polyploidy, which itself can promote tumorigenesis (41, 51), may also favor chromothripsis.
This might be expected because of the buffering effect of having more chromosome sets, dilut-
ing the deleterious impact of aneuploidy or chromothripsis (31, 143, 157). Moreover, because
polyploidy in mammalian cells is accompanied by extra centrosomes, polyploidy increases the
frequency of lagging chromosomes (42, 43). Indeed, there is recent evidence that chromothrip-
sis is more frequent after the in vitro transformation of tetraploid cells as compared to isogenic
diploid cells (103a). The extent to which this holds true in vivo is an interesting question for future
research.
DIVERSE GENOMIC OUTCOMES FROM CHROMOTHRIPSIS
Double-Minute Chromosomes
Starting with the first paper on chromothripsis, there has been a strong suggestion that chromoth-
ripsis might generate double-minute chromosomes (125, 141). Double-minute chromosomes
are small circles of DNA that lack centromeres and are usually derived from megabase-scale
chromosomal fragments (14, 20, 56, 140, 164). In cancer, amplification of DNA contained in

double minutes is frequently observed. In these contexts, double-minute chromosomes carry a

gene that is under strong positive selection, typically an oncogene (e.g., EGFR or MYC; 6, 47,
144, 160–162) or a gene conferring drug resistance (e.g., DHFR; 2, 24, 74). They are replicated
Double-minute
chromosomes: small, once and only once during S phase, just like the other chromosomes (162). However, because
acentric, circular they lack centromeres, the new copies can be asymmetrically segregated, leading to increased
chromosomes that copy number in one daughter and loss in the other. Cells with the higher copy number of the
often appear as paired oncogene-containing double minute are selected for, and, over many generations, double minutes
circles in metaphase
can reach hundreds of copies per cell (40, 114, 137, 147).
chromosome spreads
In contrast with the mechanism for amplification of double minutes, the mechanism(s) gen-
Aneugens: mutagenic
erating the extrachromosomal circular fragments has been less clear, although it is believed to
agents that cause
aneuploidy involve the formation of chromosomal breaks (166). In Stephens et al. (141), the amplification of a
complex double-minute chromosome containing MYC and multiple segments from chromosome
Clastogens:
mutagenic agents that 8 was identified. Intriguingly, in this tumor chromosome 8 underwent chromothripsis and the
cause chromosome segments present in the double minute and those in the derivative chromosome were mutually
breaks exclusive. This raised the possibility that the fragments that were assembled into the derivative
chromosome and those assembled into the double minute were generated simultaneously from the
same shattered chromatid. Subsequent work identified more examples of complex double-minute
chromosomes in cancer linked to chromothripsis (40, 125).
Indeed, the Look-Seq experiments (174) demonstrated that circularized chromosome frag-
ments of the right sizes to be nascent double-minute chromosomes are generated from shattered
chromosomes in micronuclei. In retrospect, this makes intuitive sense: If the broken ends of frag-
mented chromosomes can be stitched together, there seems to be no reason why the ends of one
fragment would not be ligated together to form circular structures. Interestingly, the hypothesis
that double-minute chromosomes could be generated from pulverized-appearing chromosomes
in micronuclei was raised in an early study (133). This study noted a correlation between what
appeared to be damaged chromosomes from micronuclei (pulverized on chromosome spreads)
and the subsequent formation of double-minute chromosomes after treatment of cells with
aneugens or clastogens.
In summary, chromosome fragmentation in micronuclei is one mechanism to generate circular
chromosomes that could become double minutes if the circles contain an oncogene. If multiple
circles are formed from a fragmented chromosome containing an oncogene, this should increase
the chance that the oncogene would be captured by one circle and subsequently generate an
amplified double minute.
Chromothripsis and Breakage-Fusion-Bridge Cycles

It has been noted that chromothripsis sometimes occurs near the telomeric ends of chromosomes
(141). This raised the possibility that chromosome bridges formed after telomere erosion, and BFB
cycles might have a role in generating chromothripsis. Recently, Li and colleagues (95) reported
a series of findings that indicate a fascinating back-and-forth interplay between BFB cycles and
chromothripsis in patients with a subtype of acute lymphoblastic leukemia (ALL).
The starting point for these studies was the observation of an association between a Robertso-
nian translocation between chromosome 15 and chromosome 21 rob(15;21) and iAMP21 ALL,
a poor prognosis subgroup bearing an intrachromosomal amplification of chromosome 21. The
Robertsonian translocation joins two acrocentric chromosomes in a manner that brings the two
centromeres into close proximity. Remarkably, children born with rob(15;21) have a 2,700-fold
increase in the risk of developing iAMP21 ALL but no increased risk of developing other ALL

subtypes or other cancers. Genomic analysis indicated that chromothripsis of the rob(15;21) chro-
mosome occurred early, followed by duplication of the derivative chromosome.
Interestingly, the copy number on the derivative chromosome oscillated between three copy-
Robertsonian
number states rather than two. This led to the suggestion that chromosome shattering affected translocation:
both sister chromatids (i.e., after DNA replication), generating segmental copy-number gains reciprocal
in addition to extensive loss and rearrangement. The authors speculate that the two juxtaposed translocation between
centromeres do not function as a single unit, making the chromosome pseudodicentric. This might two acrocentric
chromosomes near the
cause the rob(15;21) chromosome to form attachments to microtubules from both spindle poles.
centromere, leading to
If both rob(15;21) chromatids form these abnormal attachments to the spindle, both chromatids a large metacentric
could lag and be partitioned together into a micronucleus. Shattering and reincorporation of chromosome
fragments from both sisters would then generate a derivate chromosome with zero (loss), one Acrocentric:
(basal), and two (gain) copies. chromosomes with
This is a plausible model for how chromothripsis might generate small-scale copy-number centromeres near one
gains, although it is worth noting that the presence of a duplicated sequence breaks down the end
sharp distinction between MMBIR-based mechanisms and chromosome shattering. It may now
be possible to directly test the idea that shattered replicated sister chromatids can generate copy-
number gain. This could be tested with a Look-Seq type experiment, starting with micronucleated
cells that rupture late during the cell cycle.
Unlike the cases of congenital rob(15;21), genomic analyses of sporadic cases of iAMP21 ALL
suggest that they are initiated by BFB cycles, which are then followed by chromothripsis. This
order of events was deduced in the following way (Figure 4): BFBs can be inferred by their
characteristic foldback inversion rearrangements, accompanied by subtelomeric sequence loss.
Gene amplification from BFBs typically proceeds in 2n copy-number steps (54, 76), generating
big jumps in copy number across some rearrangement breaks. By contrast, chromothripsis gen-
erates small copy-number steps across rearranged segments. If chromothripsis follows the BFBs,
large copy-number steps are preserved and are primarily associated with foldback inversions,
but the BFB pattern is then peppered with sporadic small-scale copy-number changes and re-
arrangements from chromothripsis. However, if chromothripsis precedes the BFBs, most of the
small-scale changes from chromothripsis are amplified according to the typical BFB pattern, and
the chromothriptic rearrangements can also be associated with large copy-number steps due to this
amplification.
This work may be telling us something biologically interesting about chromothripsis, chromo-
some bridges, and, possibly, micronuclei. In sporadic iAMP21 ALL, it is possible that the BFBs
and subsequent chromothripsis events are independent. But it is worth considering the possibility
that they are mechanistically related. It is known, for example, that chromosome bridges can be
broken in a manner that generates micronuclei, which could easily link bridge resolution to chro-
mothripsis. It is also interesting to consider the possibility that chromosome bridges may share
common properties with micronuclei that might generate chromothripsis. Indeed, we have pre-
liminary evidence that like micronuclei, chromosome bridges undergo NE rupture and defective
DNA replication (N. Umbreit & D. Pellman, unpublished).
Chromothripsis, Ring Chromosomes, and Neochromosomes

Further evidence linking chromosomal bridges, BFBs cycles, and chromothripsis is provided by
Garsed and coworkers (44) in the study of the evolution of ring chromosomes and the generation
of giant neochromosomes. Ring chromosomes contain centromeres but lack telomeres. They are
seen in a variety of contexts, including cancer (49, 50, 78, 104). These structures can be formed

a Chromothripsis c
before BFB cycles
Starting chromosome Fragmentation
Copy
1 0
number
Breakage (telomere attrition) Reassembly
(Replication) (Replication)
BFB #1
End association Foldback #1 (FB1) End association FB1
Bridge Bridge
Daughter a Daughter b Daughter a

Breakage Breakage
Fusion FB1 Fusion FB1

BFB #2 FB2 FB2
FB1 FB1
Copy 4 Copy 4
2 2 2
number 0 number 0
Terminal gain Terminal loss
Bridge Bridge
Breakage Breakage
BFB #3
FB1 FB1
FB2 FB2
FB1 FB1
Fusion FB3 Fusion FB3
FB1 FB1
FB2 FB2
FB1 FB1
8 8
Copy 2 4 Copy 4
2
number number 0
Chromothripsis
after BFB cycles
Foldback inversions (BFB signature)
b Chromothripsis rearrangement junctions
Chromothriptic deletions
7 8
4 3
2 1

by circularization of a single chromosome but can also contain fragments from multiple chro-
mosomes (49, 119). They are prevalent in certain tumor types, such as well- and dedifferentiated
liposarcomas (WD/DDLPS; 59, 100, 150, 165). A peculiar feature of ring chromosomes is that any
Ring chromosomes:
odd number of sister chromatid exchanges results in a double-sized, dicentric ring chromosome, circular chromosomes
whereas for linear chromosomes, sister-chromatid exchanges do not alter the chromosome size with one centromere
(Figure 5a,b). Ring chromosomes are known to evolve in patients or in vitro into linear structures but no telomeres
called neochromosomes. How either structure forms has been unclear. (ends)
Because of the large size of the neochromosomes, Garsed and colleagues (44) were able
to isolate these marker chromosomes from WD/DDLPS cell lines by fluorescence-activated
cell sorting (FACS) and then perform whole-chromosome sequencing of the neochromosomes.
Sequencing of the neochromosomes provided base-level resolution of their structure; analyses
of these structures generated evidence for chromothripsis at multiple steps in the generation
of the neochromosome. The neochromosomes contained heavily amplified core sequences from
chromosome 12. These fragments have the same copy number but are derived from many individ-
ual segments originating from dispersed regions and assembled apparently at random, indicating
an origin from chromothripsis.
The segments in the neochromosome were often amplified to approximately 2n copies, a pat-
tern suggestive of BFB cycles. However, no enrichment was observed for foldback inversions as
expected for BFB cycles involving the ends of linear chromosomes. In light of the fact that each
neochromosome was likely to have originated from a ring chromosome, this pattern suggested that
the core was likely amplified by BFB cycles occurring on the ring chromosome before lineariza-
tion (Figure 5c–e). In contrast to BFBs on linear chromosomes that primarily generate foldback
inversions, BFBs on ring chromosomes are expected to generate noninverted-type translocations
(head-to-tail or tail-to-head; Figure 5d ).
Remarkably, in contrast to the prediction that BFBs on ring chromosomes would result in
noninverted-type translocations, the neochromosomes contained almost an equal number of
inverted-type and noninverted-type translocations; the inverted-type translocations are also not all
foldback inversions, as expected for sister-chromatid fusions. Moreover, they contained many more
breakpoints than would be expected from a model in which breakpoints were generated solely from
ring chromosome BFBs. Although the model remains somewhat speculative, simulations suggested
that the cells underwent both chromothripsis and BFB cycles contemporaneously (Figure 5f ).
←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
Figure 4
Breakage-fusion-bridge (BFB) cycles and chromothripsis. (a) Segmental amplification by a series of BFB cycles. Each fusion between
the sister chromatids generates a dicentric chromosome that can result in a chromosomal bridge and lead to a new break. After the
initial BFB (BFB #1), each additional BFB amplifies the terminal segment by twofold; thus, after many rounds of BFB cycles, the
amplified segments have copy numbers that peak at 2n . (b) If a chromothripsis event occurs after a series of BFB cycles, chromothriptic
deletions are overlaid on the BFB amplifications. In the final copy-number profile, the large copy-number jumps (>1) are generated by
BFB amplifications and are associated with foldback inversions ( green), whereas chromothriptic rearrangements are associated only
with single-level copy-number changes (red ). The single-level copy-number changes in chromosomal segments that are present at
multiple copies must have occurred after the amplification of these segments. (c) If chromothripsis occurred prior to BFB cycles,
chromothriptic rearrangements can be amplified by subsequent BFB cycles, resulting in large copy-number jumps that are not
associated with the foldback inversions typical of BFB cycles. In the example shown, a chromothripsis event results in the deletion of
three segments (dashed boxes) and two rearrangement junctions (red bars); the derivative chromosome (lacking one telomere) fuses with
its sister chromatid and undergoes three subsequent BFB cycles. The BFB cycles generate foldback inversions and amplifications; one
rearrangement junction generated by the earlier chromothripsis event is amplified by the BFB cycles to have a copy-number step of
eight. The presence of large copy-number jumps at chromosomal breaks that are not associated with foldback inversions indicates that
these breaks have been generated prior to the BFB amplifications.

a No crossover or Proper segregation

even number
of crossovers
Daughter a
Starting chromosome
Daughter b
Odd number
b
of crossovers
c Bridge
BFB cycles Chromothripsis
Breakage
d f c
Head-tail Tail-head b
+ d
a
f e
Replication
e
e
c
b
Sister-chromatid fusion –f

Finally, one neochromosome contained chromothriptic segments present in a single copy. It is

likely that this chromothripsis event occurred during the latest stage of neochromosome evolution.
The multiple putative chromothripsis events in ring chromosomes have a number of interesting
implications. First, chromothripsis is an appealingly simple mechanism to explain the formation
of complex ring chromosomes and neochromosomes, mechanisms that until now have been mys-
terious. Indeed, single-cell sequencing suggests that damaged chromatids from micronuclei can
reassemble into circular structures and might potentially generate ring chromosomes with se-
quences from one or multiple chromosomes (174). Second, the analysis by Garsed et al. (44)
independently strengthens the case for a mechanistic link between the formation of chromosome
bridges and the generation of chromothripsis. Third, these results illustrate the likelihood that
chromothripsis in many cases might not be an isolated event but rather is an event that triggers a
secondary storm of mutagenesis. This hypothesis could be tested by looking for co-occurrences
of complex events, such as chromothripsis and BFB cycles, on a single chromosome. Overall,
the results highlight a potentially general role that chromothripsis could play in generating rapid
karyotypic change.
THE CONSEQUENCES OF CHROMOTHRIPSIS

Chromothripsis seems like a dangerous activity for any organism that values the integrity of its
chromosomes. However, the observation of chromothripsis in the germline and in many cancers
suggests that it is not always deleterious and may have a spectrum of phenotypic consequences. It
is thus reasonable to ask whether and how chromothripsis could provide benefits to cells. In tu-
morigenesis, the equivalent question is how frequently chromothripsis is a driver of tumorigenesis
rather than a passenger. To quantitatively assess the contribution of chromothripsis to tumorige-
nesis is difficult because of the complexity of cancer genomes, but the available data indicate that
chromothripsis, like any other mutation, can be beneficial, neutral, or deleterious.
The most obvious mechanism by which chromothripsis can drive tumorigenesis is by initiating
the formation of double-minute chromosomes. This can not only amplify a single oncogene
but also create potent amplicons carrying multiple oncogenes (44, 125, 130). The high number
of rearrangements associated with chromothripsis also means it might have a higher frequency
of generating functional oncogenic fusions that can drive tumorigenesis. This, however, is not
frequently observed (141, 151), as might be expected given that the coding sequence is only ∼1% of
the genome. Another way that chromothripsis promotes cancer is by deletion of tumor suppressors.
In a survey of The Cancer Genome Atlas (TCGA) Single Nucleotide Polymorphism (SNP) array
←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
Figure 5
Evolution of ring chromosomes. (a) Sister-chromatid exchanges in ring chromosomes can alter the structure of the chromosome.
With an even number of crossovers, the sister chromatids can be separated. (b) By contrast, an odd number of sister-chromatid
exchanges fuse the two chromatids into a dicentric ring chromosome that is double the size of the original ring. (c) Resolution of a
dicentric ring chromosome can either trigger breakage-fusion-bridge (BFB) cycles or lead to chromothripsis. (d ) Breakage of a
dicentric ring chromosome into two pieces (by the unknown mechanisms that sever chromosome bridges) can generate two smaller
ring chromosomes if the broken ends of each piece are fused together. For both fragments, the translocation is noninverted, i.e., has
either a head-to-tail orientation or a tail-to-head orientation. (e) If the broken ends remain free until DNA replication is complete,
sister chromatids can fuse between each other, creating ring chromosomes with local foldback inversions as in linear BFB cycles. ( f ) A
dicentric ring chromosome can also be fragmented into multiple pieces, followed by random reassembly into a new ring chromosome.
In all three scenarios (d–f ), the resulting ring chromosome can undergo further evolution because of the unstable nature of ring
chromosomes. Large ring chromosomes were previously observed in primary WD/DDLPS (well- and dedifferentiated liposarcomas)
tumors, and the cell lines derived from these tumors contained large, linear chromosomes that were inferred to have evolved from the
ring chromosome in the primary tumors.

data, 72% of chromothripsis events were found to cause copy-number changes in regions that are
recurrently disrupted in cancer (171). Notably, CDKN2A, one of the most commonly inactivated
tumor suppressors in cancer, was disrupted by chromothripsis in 20 of 22 glioblastomas that
Haploinsufficient:
the condition in which underwent one or more rounds of chromothripsis (171). Other tumor suppressors found to be
a single functional disrupted by chromothripsis included FBXW7 and WRN (141). Chromothripsis could facilitate
copy of a gene is not tumor suppressor loss as one step in the classical two-step inactivation of both alleles (84), or it
enough to sustain the could directly promote cell growth by inactivating haploinsufficient tumor suppressors (26).
wild-type phenotype
Tumor suppressor inactivation can also be accomplished by focal or arm-level deletions. How-
ever, recent work (26) highlights the complex additivity of gene dosage changes that result from
large-scale chromosome gains and losses. In this sense, arm-level gains or losses are a blunt instru-
ment. By contrast, chromothripsis can, in principle, allow selective pressure to pick and choose
segments for deletion, allowing a more fine-tuned optimization of beneficial, growth-promoting
effects. Consistent with this hypothesis, Li et al. (95) demonstrated that the copy-number profile
of chromosome 21 in ALL patients after chromothripsis mimics the average copy-number profile
chromosome 21 across thousands of cancers.

Chromothripsis that is beneficial to tumorigenesis is in fact deleterious to the individual.
However, a recent study uncovered chromothripsis in which an individual derived benefit: the
purging of dominant deleterious mutations in a somatic cell population. McDermott et al. (106)
reported a case in which a patient with WHIM (warts, hypogammaglobulinemia, infections,
and myelokathexis) syndrome, an autosomal-dominant combined immunodeficiency disease
caused by a gain-of-function mutation of the chemokine receptor CXCR4, was spontaneously
cured after the disease-causing mutation was eliminated by chromothripsis. Chromothripsis
occurred in a hematopoietic stem cell that populated the myeloid lineage but not the lymphoid
lineage, generating mosaic hematopoiesis. It is worth noting that this example of chromothripsis
eliminated 163 other genes along with the disease gene. Although in this case the patient bene-
fitted, the risks from chromothripsis at present seem to preclude the induction of chromothripsis
as a therapeutic strategy.
Although the potential for chromothripsis to generate beneficial (growth-promoting) muta-
tions is clear, it seems likely that at the cellular level, most events will be neutral or deleterious. This
carries the implication that the cellular events leading to chromothripsis may be more common
than the observed frequency of chromothripsis observed in clones of cancer cells. Thus, the true
frequency of chromothripsis may be found only by single-cell analysis. It is worth emphasizing that
only ∼1% of the human genome encodes proteins. This means that copy-number-neutral chro-
mothripsis, a common outcome from damaged micronuclei, might have surprisingly mild pheno-
typic effects, despite the extensive chromosome rearrangement. This is underscored by the known
cases of congenital chromothripsis, which are viable, albeit with developmental defects. Moreover,
one recent study even identified several phenotypically normal, or near-normal, mothers that have
copy-number-neutral chromothripsis involving rearrangements between multiple chromosomes
(28). These women came to medical attention only after giving birth to affected children who
received only a subset of their derivative chromosomes and thus had copy-number imbalance.
The fact that individuals with complex multichromosome chromothripsis can be viable and
transmit the rearranged chromosome through the germline may have implications for organismal
evolution. Interestingly, plants can become aneuploid and generate micronuclei during a process
called genome elimination. Genome elimination is an incompletely understood phenomenon in
which kinetochore incompatibility between parents, for example different variants of the cen-
tromeric histone CENP-A, triggers loss of one parental genome during early mitotic divisions
after fertilization (126). Genome elimination has been used as a strategy to accelerate plant breed-
ing and is thought to mimic what occurs during some interspecies crosses. Chan and colleagues

(148) observed that in Arabidopsis thaliana strains engineered to undergo genome elimination, a
trisomic chromosome frequently contained rearrangements and oscillating copy-number patterns.
These patterns have been termed genome restructuring but in fact are very similar or identical to
Genome elimination:
chromothripsis in mammals. The authors proposed that the mechanism might involve micronuclei loss of one set of
because micronuclei are commonly observed during genome elimination. They therefore posited parental chromosomes
that micronucleation and chromothripsis may play a more general role in genome evolution and
species divergence.
Consistent with this idea is another potential link between mitotic chromosome segregation
errors and rapid karyotype evolution. Gibbons underwent rapid karyotype evolution ∼5 million
years ago (12). At this time, a retrotransposon called a LAVA (L1ME5-AluSz6-VNTR-Alu-like;

13) element spread throughout the genome, disrupting mitotic chromosome segregation genes
at a surprisingly higher frequency than expected by random chance. This raises the interesting
possibility that early in gibbon evolution, chromosome missegregation, possibly accompanied by
chromothripsis, could have contributed to the rapid karyotype evolution. Consistent with this
possibility, most of the unique rearrangements between gibbon genomes lack sequence signa-
tures of homology-driven rearrangements and could therefore have originated from chromosome
shattering and end-joining.
SUMMARY
In this review, we have tried to summarize recent progress on the causes and consequences of
chromothripsis, one of the most surprising biological discoveries made from cancer genome se-
quencing. The past few years have seen rapid progress in defining at least one mechanism for
chromothripsis, which involves the physical isolation of chromosomes or chromosome arms in
micronuclei. Testing this idea has spurred the development of an experimental approach com-
bining live-cell imaging with single-cell genome sequencing. This approach may have a number
of applications in the study of mutagenesis and other heterogeneous cellular phenomena. How-
ever, many questions about the mechanism(s) of DNA damage in micronuclei remain unsolved,
as do those about how and when rearrangements are generated. Recent genomic analyses also
underscore the relationship between chromothripsis and BFB cycles, raising interesting questions
about the structure of chromosome bridges and the mechanisms leading to bridge breakage. In
general, the work on chromothripsis highlights the deep connection between nuclear architecture
and integrity in the maintenance of genome stability (109).
Defining the mechanisms that cause chromothripsis is also important for understanding its true
frequency. Although damaged micronuclei can generate patterns of rearrangement with all the
hallmark features of chromothripsis, they can also generate less extensive rearrangement patterns
that ex post facto would be hard to recognize as chromothripsis. Indeed, the identification of
chromothripsis from genomic data requires stringent statistical cutoffs that could underestimate
its true frequency. Thus, one appealing hypothesis is that chromothripsis might be the tip of the
iceberg, an extreme outcome of mutational processes that are more common than the few percent
incidences in cancer would suggest.
The extent of rearrangement, and the fact that it occurs from a single event, has led to interesting
analogies being made between chromothripsis and Eldredge & Gould’s concept of punctuated
equilibrium (34). Although appealing, it is not yet clear whether chromothripsis would impact
evolutionary dynamics in a genuinely unique way. The simplest way to think about chromothripsis
is that it is just another mutation that occurs at a definable rate (e.g., related to the rate of forming
micronuclei), and results in a distribution of fitness effects. This would affect evolutionary dynamics
like any other mutational process. However, if chromothripsis were to commonly affect the rate

of beneficial (growth-promoting) mutations or to alter the magnitude and/or distribution of their

fitness effects, it would be justified to view it differently from other mutational processes. The
degree to which chromothripsis might trigger downstream mutagenesis, a possibility raised by the
Punctuated
equilibrium: a studies on chromothripsis and BFBs, should now be possible to test by single-cell analysis.
theory in evolutionary Although chromothripsis has been identified and mainly studied in the context of human
biology hypothesizing disease, in principle it could contribute to the evolution of karyotypes in any context. The evolution
that speciation occurs of karyotypes between related species is typically characterized by a high frequency of sequence
rapidly between
inversions and by the transposition of large syntenic blocks of chromosomes (122). Multiple
extended periods of
stasis mechanisms, including nonallelic homologous recombination (38, 139), are likely to be involved.
However, given that chromothripsis can generate inversions and can also transpose large segments
Syntenic: describing
blocks of genes in the between chromosomes in one step, we speculate that it might also play a general role in the
same or adjacent evolution of karyotypes.
relative positions in
the genomes of
DISCLOSURE STATEMENT
different organisms
The authors are not aware of any affiliations, memberships, funding, or financial holdings that
might be perceived as affecting the objectivity of this review.
ACKNOWLEDGMENTS
M.L.L. was supported by the National Science Foundation Graduate Research Fellowship under
grant no. DGE1144152. C.Z.Z. was supported by funds from the Dana-Farber Cancer Insti-
tute Single-Cell Genomics Center. D.P. was supported by the Claudia Adams Barr Program
in Innovative Cancer Research. D.P. is an HHMI investigator and is supported by NIH grant
GM083299-18.
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GE49-FrontMatter ARI 5 November 2015 16:10
Contents Annual Review of

Genetics
Volume 49, 2015

Brachypodium distachyon as a Genetic Model System
Elizabeth A. Kellogg p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 1
Genetic Dissection of the Host Tropism of Human-Tropic Pathogens

Florian Douam, Jenna M. Gaska, Benjamin Y. Winer, Qiang Ding,
Markus von Schaewen, and Alexander Ploss p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p21
From Genomics to Gene Therapy: Induced Pluripotent Stem Cells

Meet Genome Editing
Akitsu Hotta and Shinya Yamanaka p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p47
Engineering of Secondary Metabolism
Sarah E. O’Connor p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p71
Centromere Associations in Meiotic Chromosome Pairing
Olivier Da Ines and Charles I. White p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p95
Chromosome-Membrane Interactions in Bacteria
Manuela Roggiani and Mark Goulian p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 115
Understanding Language from a Genomic Perspective
Sarah A. Graham and Simon E. Fisher p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 131
The History of Patenting Genetic Material
Jacob S. Sherkow and Henry T. Greely p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 161
Chromothripsis: A New Mechanism for Rapid Karyotype Evolution
Mitchell L. Leibowitz, Cheng-Zhong Zhang, and David Pellman p p p p p p p p p p p p p p p p p p p p p p p 183
A Uniform System for the Annotation of Vertebrate microRNA Genes
and the Evolution of the Human microRNAome
Bastian Fromm, Tyler Billipp, Liam E. Peck, Morten Johansen, James E. Tarver,
Benjamin L. King, James M. Newcomb, Lorenzo F. Sempere, Kjersti Flatmark,
Eivind Hovig, and Kevin J. Peterson p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 213
Clusters of Multiple Mutations: Incidence and Molecular Mechanisms
Kin Chan and Dmitry A. Gordenin p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 243
The Genetics of Nitrogen Use Efficiency in Crop Plants
Mei Han, Mamoru Okamoto, Perrin H. Beatty, Steven J. Rothstein,
and Allen G. Good p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 269
Eukaryotic Mismatch Repair in Relation to DNA Replication
Thomas A. Kunkel and Dorothy A. Erie p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 291
v
Population Genomics for Understanding Adaptation

in Wild Plant Species
Detlef Weigel and Magnus Nordborg p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 315
Nonsense-Mediated mRNA Decay: Degradation of Defective
Transcripts Is Only Part of the Story
Feng He and Allan Jacobson p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 339
Accelerating Discovery and Functional Analysis of Small RNAs
with New Technologies
Lars Barquist and Jörg Vogel p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 367

Meiotic Silencing in Mammals
James M.A. Turner p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 395
Neural Regulatory Pathways of Feeding and Fat

in Caenorhabditis elegans
George A. Lemieux and Kaveh Ashrafi p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 413
Accessing the Inaccessible: The Organization, Transcription,
Replication, and Repair of Heterochromatin in Plants
Wei Feng and Scott D. Michaels p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 439
Genetic and Epigenetic Regulation of Human Cardiac
Reprogramming and Differentiation in Regenerative Medicine
Paul W. Burridge, Arun Sharma, and Joseph C. Wu p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 461
Giving Time Purpose: The Synechococcus elongatus Clock in a Broader
Network Context
Ryan K. Shultzaberger, Joseph S. Boyd, Spencer Diamond, Ralph J. Greenspan,
and Susan S. Golden p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 485
The Biology and Evolution of Mammalian Y Chromosomes
Jennifer F. Hughes and David C. Page p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 507
Conservation of Planar Polarity Pathway Function Across
the Animal Kingdom
Rosalind Hale and David Strutt p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 529
Understanding Metabolic Regulation at a Systems Level: Metabolite
Sensing, Mathematical Predictions, and Model Organisms
Emma Watson, L. Safak Yilmaz, and Albertha J.M. Walhout p p p p p p p p p p p p p p p p p p p p p p p p p p 553
Integrative and Conjugative Elements (ICEs): What They
Do and How They Work
Christopher M. Johnson and Alan D. Grossman p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 577
General Stress Signaling in the Alphaproteobacteria
Aretha Fiebig, Julien Herrou, Jonathan Willett, and Sean Crosson p p p p p p p p p p p p p p p p p p p p p 603
vi Contents
Gene Positioning Effects on Expression in Eukaryotes

Huy Q. Nguyen and Giovanni Bosco p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 627
Asymmetry of the Brain: Development and Implications
Véronique Duboc, Pascale Dufourcq, Patrick Blader, and Myriam Roussigné p p p p p p p p p p p 647
Modulation of Chromatin by Noncoding RNA
Victoria H. Meller, Sonal S. Joshi, and Nikita Deshpande p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 673
Cell Competition During Growth and Regeneration
Rajan Gogna, Kevin Shee, and Eduardo Moreno p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 697
An online log of corrections to Annual Review of Genetics articles may be found at

http://www.annualreviews.org/errata/genet
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GE49CH09-Pellman ARI 30 October 2015 15:13

Mitchell L. Leibowitz,1,3,† Cheng-Zhong Zhang,1,2,3,4,†

Annu. Rev. Genet. 2015. 49:183–211 Keywords

184 Leibowitz · Zhang · Pellman

approximately one ten-thousandth of the genome.

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 185

a Breakage-fusion-bridge cycles b Chromothripsis

1st break Breakage

MASSIVE DAMAGE TO A SINGLE CHROMOSOME

186 Leibowitz · Zhang · Pellman

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 187

CHROMOTHRIPTIC LESIONS ARE HARD TO EXPLAIN

188 Leibowitz · Zhang · Pellman

WHAT MECHANISMS GENERATE CHROMOTHRIPSIS?

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 189

190 Leibowitz · Zhang · Pellman

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 191

DIRECT EVIDENCE THAT MICRONUCLEI CAN

192 Leibowitz · Zhang · Pellman

be to isolate daughter cells after reincorporation of a damaged chromosome from a micronucleus

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 193

194 Leibowitz · Zhang · Pellman

CONDITIONS THAT FAVOR CHROMOTHRIPSIS

DIVERSE GENOMIC OUTCOMES FROM CHROMOTHRIPSIS

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 195

double minutes is frequently observed. In these contexts, double-minute chromosomes carry a

Chromothripsis and Breakage-Fusion-Bridge Cycles

196 Leibowitz · Zhang · Pellman

Chromothripsis, Ring Chromosomes, and Neochromosomes

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 197

Daughter a Daughter b Daughter a

Fusion FB1 Fusion FB1

198 Leibowitz · Zhang · Pellman

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 199

a No crossover or Proper segregation

BFB cycles Chromothripsis

200 Leibowitz · Zhang · Pellman

Finally, one neochromosome contained chromothriptic segments present in a single copy. It is

THE CONSEQUENCES OF CHROMOTHRIPSIS

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 201

chromosome 21 across thousands of cancers.

202 Leibowitz · Zhang · Pellman

years ago (12). At this time, a retrotransposon called a LAVA (L1ME5-AluSz6-VNTR-Alu-like;

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 203

of beneficial (growth-promoting) mutations or to alter the magnitude and/or distribution of their

204 Leibowitz · Zhang · Pellman

dominant non-homologous repair following chromosomal breakage in karyotypically balanced germline

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 205

206 Leibowitz · Zhang · Pellman

are not “lost” by cells. Cell Res. 22:932–35

chromosome is a frequent event in cancer. Cell 155:567–81

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 207

208 Leibowitz · Zhang · Pellman

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 209

rearrangement in human breast cancer genomes. Nature 462:1005–10

210 Leibowitz · Zhang · Pellman

www.annualreviews.org • A New Mechanism for Rapid Karyotype Evolution 211

Contents Annual Review of

Volume 49, 2015

Genetic Dissection of the Host Tropism of Human-Tropic Pathogens

From Genomics to Gene Therapy: Induced Pluripotent Stem Cells

Population Genomics for Understanding Adaptation

Lars Barquist and Jörg Vogel p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 367