Biotechnology Advances 31 (2013) 9941001

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Biotechnology Advances
journal homepage: www.elsevier.com/locate/biotechadv

Research review paper

Advances in genetic modication of pluripotent stem cells

Andrew Fontes, Uma Lakshmipathy
Primary and Stem Cell Systems, Life Technologies, 5781 Van Allen Way, Carlsbad, CA 92008, USA

a r t i c l e i n f o a b s t r a c t

Available online 12 July 2013 Genetically engineered stem cells aid in dissecting basic cell function and are valuable tools for drug discovery, in
vivo cell tracking, and gene therapy. Gene transfer into pluripotent stem cells has been a challenge due to their
Keywords: intrinsic feature of growing in clusters and hence not amenable to common gene delivery methods. Several
Stem cells advances have been made in the rapid assembly of DNA elements, optimization of culture conditions, and
Embryonic stem cells DNA delivery methods. This has lead to the development of viral and non-viral methods for transient or stable
Induced pluripotent stem cells
modication of cells, albeit with varying efciencies. Most methods require selection and clonal expansion
Genetic modication
that demand prolonged culture and are not suited for cells with limited proliferative potential.
Choosing the right platform based on preferred length, strength, and context of transgene expression is a critical
step. Random integration of the transgene into the genome can be complicated due to silencing or altered regu-
lation of expression due to genomic effects. An alternative to this are site-specic methods that target transgenes
followed by screening to identify the genomic loci that support long-term expression with stem cell proliferation
and differentiation. A highly precise and accurate editing of the genome driven by homology can be achieved
using traditional methods as well as the newer technologies such as zinc nger nuclease, TAL effector nucleases
and CRISPR. In this review, we summarize the different genetic engineering methods that have been successfully
used to create modied embryonic and induced pluripotent stem cells.
2013 Elsevier Inc. All rights reserved.

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 995
2. Gene insertion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 996
2.1. Random genomic integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 996
2.1.1. Naked plasmid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 996
2.1.2. Lentivirus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 996
2.1.3. Transposon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 997
2.2. Non-integrating technology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 997
2.2.1. Episomal vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 997
2.2.2. Adenovirus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 997
2.2.3. Minicircle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 997
2.2.4. BacMam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 997
2.3. Site-specic genomic integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 998
2.3.1. Adeno-associate virus (AAV) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 998
2.3.2. PhiC31 integrase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 998
3. Gene targeting and editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 998
3.1. Homologous recombination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 998
3.2. Zinc nger nucleases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 999
3.3. TAL effectors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1000
3.4. Crispr/CAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1000
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1000

Corresponding author at: Primary and Stem Cell Systems, 5781 Van Allen Way, Carlsbad, CA 92008, USA. Tel.: +1 760 268 7465.
E-mail address: uma.lakshmipathy@lifetech.com (U. Lakshmipathy).
URL: http://www.lifetechnologies.com (U. Lakshmipathy).

0734-9750/$ see front matter 2013 Elsevier Inc. All rights reserved.
http://dx.doi.org/10.1016/j.biotechadv.2013.07.003
 A. Fontes, U. Lakshmipathy / Biotechnology Advances 31 (2013) 9941001
1. Introduction
The ability of pluripotent stem cells to indenitely proliferate in
culture and differentiate into multiple cell types under the right cues
provides an ideal source for genetic modication for various down-
stream applications. This enables scientists to dissect basic biology
and explore the potential use of pluripotent cells in regenerative medi-
cine and drug discovery. However, a key challenge lies in identifying the
ideal platform suited for the intended application. Various viral and
non-viral platforms have been utilized for expression of exogenous
genes and for targeting endogenous DNA in human embryonic stem
cells (hESC) and induced pluripotent stem cells (iPSC), albeit with
varying efciencies. Methods that have been widely used for murine
embryonic stem cells (mESC) have largely been suboptimal for hESC
thus necessitating further optimization of culture conditions (Braam
et al., 2008).
The fundamental unit for gene delivery into cells is a plasmid DNA
or vector carrying the transgenes of choice. The primary architecture
of such plasmid DNA comprises a transgene of interest driven by a
promoter of choice. Promoter choice is dependent on the type of
expression needed. Constitutive promoter is expressed in all cell
types, an inducible promoter can be activated or inactivated in the
Fig. 1. (A) High throughput efcient cloning systems that can rapidly assemble plasmids of choice and (B) deliver to cells via efcient nontoxic methods, are critical for successful
gene modication for gene insertion or targeted gene editing of stem cells.
995
presence of small molecules, and a lineage specic promoter is active
in specic cell types. Traditional restriction endonuclease-mediated
cloning processes are rapidly being replaced by recombination-
mediated cloning methods such as Multisite Gateway or Lego that
enable speedy assembly of multiple DNA fragments. The base plasmid
also carries a drug resistance gene which can be utilized for screening
cells that harbor the plasmid and a bacterial origin of replication and
an antibiotic resistance gene important for propagating the plasmid
in bacteria.
An additional factor that is critical for successful gene modication is
efcient gene delivery methods to introduce the DNA fragments into
pluripotent stem cells. Chemical-based reagents such as Lipofectamine
2000, Fugene HD, Gene Jammer, etc. offer the advantage of direct addi-
tion to the culture media but suffer from poor efciencies. Advances to
traditional electroporation devices such as Amaxa Nucleofector and
Neon electroporation system have allowed higher efciency of transfec-
tion of hESC (Lakshmipathy et al., 2004; Liu et al., 2009). In cases where
chemical and electroporation methods pose a challenge, viral delivery
systems have been utilized. A modied Lentivirus system has been
reported to achieve rapid generation of stable clones in both murine
as well as human ESC (Suter et al., 2006). The combination of modular
cloning methods, optimal vector design and efcient gene delivery
996 A. Fontes, U. Lakshmipathy / Biotechnology Advances 31 (2013) 9941001

into target cells is critical for modifying hard-to-transfect ESCs (Fig. 1).
In addition, choices of culture conditions and media systems are equally
important factors. Although ESCs and iPSCs can be cultured under
feeder-free media systems prior to transfection, recovery and selection
of feeders has been the most traditional method used to maintain and
clone out the genetically modied stem cells.
Gene modication of cells can be broadly classied into two major
categories based on application, (1) gene insertion and (2) gene
targeting. Gene insertion methods are most widely used to deliver
DNA fragments such as cDNA or shRNA for overexpression or knock-
down of specic genes, respectively. The platform of choice is large-
ly dependent on length and strength of expression required. The
wide range of gene modication approaches offers unique advan-
tages that can be utilized to robustly express exogenous genes at
levels signicant enough to alter cellular function. Here, we review the
various methods that have been successfully utilized to alter hESCs and
iPSCs.
2. Gene insertion
2.1. Random genomic integration
Randomly integrating technologies enable users to create stable
systems leading to lasting expression with or without the use of anti-
biotic selection. These platforms result in the random insertion of se-
lected DNA fragments into the host genome without the use of DNA
homology. Random genomic integration provides a valuable tool for
long-term expression in human ES cells despite their rapid and in-
nite dividing capabilities. However, consequences of random inser-
tion leading to variable copy number per cell are inconsistent
integration sites and unpredictable expression patterns. In addition,
the locus of insertion can result in partial or complete silencing in
human ES cells, which can occur during routine culture and maintenance
as well as throughout differentiation. A major risk with these methods
is insertional mutagenesis resulting in genome instability and toxicity
(Baum et al., 2006).
2.1.1. Naked plasmid
Randomly integrating platforms have progressed with the optimiza-
tion of transfection system for ES cells. Using solely plasmid DNA pro-
vides a relatively simple integrating engineering platform since they
require no additional recombination or preparation prior to transfec-
tion. As an integrating system, plasmids provide stable expression of
complex cassettes with or without selection. The use of plasmid for
random integration has the potential to be used in ES cells for a variety
of applications including the overexpression of exogenous cassettes
(Wobus and Boheler, 2005). In human ES cells, plasmid insertion re-
mains limited by efcient electroporation methods, which will progres-
sively decrease in efciency with increased vector size (Moore et al.,
2010). Furthermore, the recovery of colonies after single-cell transfec-
tion remains a complex factor for ES cell transfection. Despite these hur-
dles, scientists have been able to identify locations within the genome
where limited silencing occurs using random integration of plasmid
DNA (Costa et al., 2005). One site, deemed the Envy locus, has shown
to remain un-silenced by expression of GFP using a constitutive pro-
moter at all levels of differentiation in the absence of selection in
mouse ES cells. Although cumbersome to identify, this site offers a plat-
form for high expression of reporters or complex gene cassettes.
2.1.2. Lentivirus
To circumvent electroporation roadblocks, viral platforms offer an
attractive alternative to plasmid transfection. Recombinant Lentivirus
for gene delivery is replication incompetent with the ability to infect a
wide variety of cell types including human embryonic stem cells. The
mechanism of entry requires attachment to common glycoprotein on
the cell exterior to facilitate cell membrane fusion. Lentivirus has been
used as a gene modication tool in human ES cells since Dr. James
Thomson's lab showed expression of GFP in ESC with minimal silencing
of upon differentiation to hematopoietic precursors (Ma et al., 2003).

Fig. 2. Integrational methods are most commonly used for the creation of transient or stably modied human ESC. (A) Lentiviruses can be used to create PGK-GFP H9 ESC where
single or multiple copies of this gene can randomly integrate into any part of the host chromosome. (B) Episomal vectors, a non integrating system with the plasmids maintained
extra chromosomally, were used to create a stable H9 ESC dual reporter expressing GFP and Tag RFP both driven by EF1a promoters. Site-specic integration method using PhiC31
integrase was used to insert Oct4-eGFP into a placed target site on chromosome 13. (C) Site-specic integration method using PhiC31 integrase was used to insert Oct4-eGFP into a
placed target site on chromosome 13.
 A. Fontes, U. Lakshmipathy / Biotechnology Advances 31 (2013) 9941001
With improved ease of use, Lentivirus typically requires only one over-
night transfection. This allows for minimal manipulation of ESCs grown
in adherent cell culture systems and cells cultured on feeder layers.
However, murine embryonic broblast feeder layers show more robust
transduction compared to the variable transduction and expression
observed within the ESC colony (Fig. 2A).
With the ability to transfect dividing or non-dividing cells, Lentivirus
provides a tool for pluripotent cells as well as differentiation inter-
mediates and expression of markers by lineage specic promoters.
Overexpression using Lentivirus can provide a selection tool for
pluripotency as well as an editing tool, as shown with microRNAs intro-
duced into ESC via Lentivirus, to identify and monitor the repression and
expression of key pluripotency genes (Xu et al., 2009). Along with high
transfection efciency, there is an increased risk of insertional mutagen-
esis and multiple proviral integrations that can cause alternative
splicing and aberrant transcripts (Moiani et al., 2012). Additionally,
differential expression can result due to variable copy number without
selecting for individual clones. Lentivirus load capacity is relatively small
with decreased transfection efciency as well as recombination in direct
correlation with higher payload.
2.1.3. Transposon
Non-viral vectors, such as Sleeping Beauty (SB) transposon, achieve
efcient delivery and integration into the host genome. The SB transpo-
son system is comprised of a catalytic component and a cargo-containing
component. The cargo-containing component is anked by inverted
terminal repeats that encode non-identical direct repeats that are recog-
nized by transposons to facilitate transposition (Ivics et al., 1997). When
this construct is co-delivered with a construct expressing SB transposon,
the cargo containing the gene of interest anked by the direct repeats is
excised from the donor plasmid and inserted randomly into the host
genome. This method has been used to generate modied human
embryonic stem cells (Wilber et al., 2007) and modied ESCs used to fur-
ther study differentiation (Orban et al., 2009). Although the transposon
systems such as Sleeping Beauty, Tol2 and PiggyBac result in random
integration (Huang et al., 2010), it is thought to less likely integrate
into transcribed genes or regulatory regions observed with viral systems
(Mitchell et al., 2004).
2.2. Non-integrating technology
Human embryonic stem cells have the potential to become valuable
clinical tools for therapeutics, clinical research, and diagnostics. However,
the majority of cell engineering tools utilize integrating platforms that
can cause genomic effects removing the possibility of downstream appli-
cations. To reassure clinical relevancy it is crucial to have non-integrating
engineering platforms available for early research.
2.2.1. Episomal vectors
The EpsteinBarr Nuclear Antigen 1 (EBNA) region has been utilized
for stable expression in mammals for a variety of applications for
decades (Yates et al., 1985). The trans acting EBNA1 element requires
an origin of replication (OriP) for plasmid replication to occur. The
vector containing OriP replicates once per cell cycle with the binding
of multiple EBNA homodimers to the exogenous OriP. However, in pri-
mate and human cells, the stable expression of EBNA expressing vectors
previously required the creation of a cell line expressing EBNA. Upon
transfection of a plasmid containing the OriP, the vector would replicate
with the genomic DNA. In the past ten years, scientists have optimized
this combination for stable expression in human ES cells (Ren et al.,
2006). Expression by a two-step integrating system, however, negates
the use of a non-integrating system for human ES cells, which are
prone to continued silencing and differential expression. In 2009, a
vector containing both the EBNA and OriP was introduced for the
creation of stable expressing cell lines in human ESC (Thyagarajan et al.,
2009). Expression remained stable in the presence of antibiotic selection
997
as well as during random differentiation of embryoid bodies. The vector
system offers an efcient method to create reporter lines as shown via
GFP expression driven by the POU5F1 (Oct4) promoter (Fig. 2B).
These vectors, although limited by the identical electroporation
issues detailed above, face additional size constraints. To contain both
the EBNA and OriP genes with a selection cassette, the vector backbone
is typically above 10 kB in size. For stable expression, the inclusion of a
selection cassette is required. Although the plasmid replicates once per
cell cycle, the vectors localize in the cytoplasm during cell division. This
results in an uneven distribution of plasmid copy number between the
daughter cells. Furthermore, uneven distribution can lead to heteroge-
neity in exogenous gene expression within the pooled population of
cells.
2.2.2. Adenovirus
Adenovirus vectors can transduce both dividing and non-dividing
cells but are limited in the payload they can deliver (Russell, 2000).
Gutless adenoviruses can carry a larger payload, but are cumbersome
requiring the co-infection of a helper virus making the subsequent pu-
rication processes hard (Alba et al., 2005). Further efciency of trans-
duction is dependent on the expression of coxsackie and adenovirus
receptor on cells. While this method has been used to achieve efcient
gene transfer in mouse embryonic stem cells (Kawabata et al., 2005), in
the case of human cells, it has also been successfully used to transduce
neural stem cells derived from human ESCs.
2.2.3. Minicircle
Regular plasmid vectors contain bacterial elements such as antibiotic
resistance genes and origins of replication. These elements are excised
out of the vector via an intramolecular recombination catalyzed by the
PhiC31 integrase to generate a minicircle DNA (Jia et al., 2010). The
resulting mammalian expression minicircle, which is comprised of pro-
moters and genes, has shown to have higher and longer expression but
eventually turns over thus providing an ideal non-integrating footprint
free system (Chen et al., 2003). This method has been used for the gen-
eration of iPSCs from somatic cells (Jia et al., 2010) and for modication
of adult stem cells such as neural stem cells (Madeira et al., 2013), but
has limited use for generating gene modied ESCs.
2.2.4. BacMam
Additional viral vectors are utilized in non-integrating gene modica-
tion platforms. The baculovirus is a non-integrating DNA insect virus
with the ability to infect mammalian and insect cells with high efciency.
The virus historically has been utilized for recombinant protein produc-
tion (Kost et al., 2005). In mammalian systems, however, the baculovirus
does not retain the ability to replicate and become infectious, offering a
valuable transient over-expression tool. The incorporation of a mamma-
lian promoter or a mammalian expression system within the baculovirus
genome denotes the viral platform BacMam (Baculoviral Mammalian
expression). The BacMam virus has become a standard gene transfer
technique due to its safety and ease of transfection and virtually zero
cytotoxic effects on human cells (Gao et al., 2002; Kost et al., 2005). The
baculovirus is relatively large compared to typical viral capsid and is a
double-stranded DNA virus. Viral entry is proposed to occur via the G64
glycoprotein causing endocytosis and eventual migration to the nucleus.
With advances in stem cell research scientists require increasingly
more complex expression cassettes. The baculoviral system has the
capacity for extremely large DNA cassettes (N 35 kB) providing a exi-
ble system for the introduction of complex engineering fragments
(Fornwald et al., 2007). Transient expression provides a fast and ef-
cient system for the identication of specic lineages during differenti-
ation. BacMam can be used to overexpress markers using lineage
specic promoters enabling ES cell scientists to create more throughput
differentiation protocols. Additionally, baculovirus has been used to
overexpress proteins to directly drive differentiation and trigger osteo-
genesis (Chuang et al., 2007).
998 A. Fontes, U. Lakshmipathy / Biotechnology Advances 31 (2013) 9941001
2.3. Site-specic genomic integration
Site-specic modication is an ideal method to avoid variable
expression patterns and copy number variation as a result of random
integration. These tools enable the user to locate specic sites within
the chromosome where silencing is minimized. In order to identify spe-
cic locations within the genome these platforms rely on methods that
have preferential insertion into the mammalian genome. Additionally,
selection is recommended to identify single copy insertions of the
gene of interest and eliminate false positives. Despite the added selec-
tion, these platforms require a screening step for multiple copy variants.
2.3.1. Adeno-associate virus (AAV)
AAV allows for site-specic modication utilizing a single-stranded
DNA genome. The recombination event for insertion occurs with a rela-
tively high efciency (1%), an improvement from solely homologous
recombination of plasmid vectors (Hirata et al., 2002). Additional
advantages of using AAV include the low level of innate cell immune
response from the presence of the virus in humans. This establishes
AAV as a more relevant platform for downstream clinical applications
compared to other viral models. The AAV virus is limited in payload
capacity, typically carrying no more than a 1 kB cassette. Payload chal-
lenge is increasingly more relevant due to the need for more complex
cassettes containing polycistronic sets or enhancing elements.
With the increased recombination efciency compared to DNA
targeting site identication, AAV offers a relatively efcient gene editing
tool with less cumbersome assembly required by Zinc Finer Nucleases
(ZFN). In pluripotent stem cells, AAV vectors have shown the ability to
modify genes for the creation and correction of mutations at the HPRT
loci (Khan et al., 2010).
2.3.2. PhiC31 integrase
Additional site-specic technologies rely on integrase-mediated
recombination. PhiC31 integrase is a bacteriophage integrase that
nds native attachment P (attP) sites within bacteria. Human cells
contain a number of pseudo attP sites which allow for localized recom-
bination into a specic attP site in human cells. Although there are a
variety of pseudo attP sites within the genome there are specic hotspots
with a higher likelihood of recombination. The location identied on
chromosome 13 is a known intronic region unaffected by chromatin
remodeling during differentiation (Chalberg et al., 2006; Thyagarajan
et al., 2008). Targeting the chromosome 13 locus results in a similar
expression and characteristics of the ROSA locus (Irion et al., 2007).
Although the site has the capability to accept a high payload, the limiting
factor remains to be the electroporation of large DNA vectors. As men-
tioned above, the most efcient method for transfecting DNA into ES
cells remains to be electroporation. This requires single-cell suspension
and clone generation that can cause genomic defects such as karyotypic
abnormalities when not kept in the correct conditions. For this reason,
additional means of insertion for the PhiC31 integrase, such as viral,
have been explored.
The integrase is introduced into human ESCs with a plasmid DNA
cotransfected with a target plasmid carrying the gene of interest.
PhiC31 integrases mediate the insertion of the target plasmid into
pseudo sites in the mammalian genome. The resulting drug selected
stable clones show robust expression and are less prone to silencing
with extended culture or with differentiation (Fig. 2C). One of the
PhiC31 hotspots in hESC is located on chromosome 13 and genes
inserted into this site show sustained expression. This feature has
been utilized to place a R4 integrase target site to create a target ESC
line that can be rapidly retargeted to generate modied ESC expressing
genes of interest (Liu et al., 2009; Macarthur et al., 2012; Thyagarajan
et al., 2008). Active expression at a single genomic locus in human ES
cells is a valuable tool for differentiation studies, gain or loss of function
assays, as well as disease model creation.
3. Gene targeting and editing
All cells have endogenous repair mechanism to repair DNA double
strand breaks either via non-homologous end joining (NHEJ) or homol-
ogous recombination (HR). The relatively inaccurate NHEJ double-
strand break repair machinery has been utilized to create gene disrup-
tion for the generation of gene knock-outs. The most accurate method
is HR which corrects the damaged chromosome using the undamaged
sister chromatid as a template (Fig. 3A). Targeted gene editing to correct
single base pair mutations of gene disruption by insertional mutagene-
sis utilizes this repair machinery to replace or modify specic chromo-
somal regions with extra chromosomal donor DNA containing the
modication or gene replacement of interest (Capecchi, 1989). This
method has also been used to insert reporters and genes in specic pro-
moter locations and safe harbor sites for sustained gene expression.
Targeted gene editing is therefore the method of choice to modify
human ESCs and iPSCs to generate correct disease phenotypes to create
cell models, and insert or delete genes to create knock-in or knock-out
cell lines to dissect basic developmental biology. The basic methods to
achieve targeted gene editing are outlined in Fig. 3B.
3.1. Homologous recombination
Gene targeting using traditional methods via homologous recom-
bination has been extensively used to specically alter genes in the
case of animal models such as the mouse. This method involves the
introduction of a targeting construct homologous to the target gene
sequence with the desired mutation and oxed drug selectable markers
into a germ-line competent embryonic stem cell line (Capecchi, 1989;
Thomas and Capecchi, 1987). The combination of positive and negative
drug selection is then utilized to exclude clones with randomly inserted
targeted constructs and positively select for mutant embryonic stem
cell. Following the subsequent removal of the drug selection cassette
via Cre recombinase (Gu et al., 1993; Hasty et al., 1991) mutant cells
are injected into a normal blastocyst to produce a heterozygous chime-
ric mouse and in-bred to generate homozygous mutant mice. Homozy-
gous mutant cells can also be directly created by inactivation of both
alleles of the gene (Mortensen et al., 1992). Despite this method being
of low efciency and laborious due to the requirement of targeting con-
structs with long homology arms and multiple rounds of drug selection
to isolate desired clones, it has been used to generate several knock-in
and knock-down cell lines and transgenic mice. Since the rst successful
establishment of human embryonic stem cells by Thompson in 1998
(Thomson et al., 1998), this technology was used to knock down
genes (Di Domenico et al., 2008; Irion et al., 2007; Urbach et al., 2004;
Zwaka and Thomson, 2003). It has also been used to successfully used
to knock in reporter genes into specic endogenous promoters to create
lineage reporter ESC lines (Davis et al., 2008; Elliott et al., 2011;
Goulburn et al., 2011; Xue et al., 2009; Zwaka and Thomson, 2003).
Here, the targeting construct comprises of a core region with the
reporter gene and a drug selection cassette anked with homology
arms. Following transfection into cells, positive clones are identied
based on drug selection and true targeted clones identied by PCR
analysis. Finally, the drug selection cassette is oxed out to eliminate
the potential of any interference it may cause to the reporter gene or
other genes in the host cell genome (Davis et al., 2009). Conventional
gene targeting via HR has also been used to insert RFP at human homo-
log of the mouse ROSA26 locus in hESC and expression has shown to be
sustained both in undifferentiated and differentiated cells thus
suggesting this region to be a safe harbor loci (Irion et al., 2007).
Spontaneous gene targeting occurs at a very low frequency in mam-
malian cells with an efciency of 1 in a million cells but the presence of a
double-strand break is recombinogenic and increases the HR frequency
by several thousand fold (Jasin, 1996). This feature has been harnessed
for the development of novel and efcient targeting methods.
 A. Fontes, U. Lakshmipathy / Biotechnology Advances 31 (2013) 9941001 999

Fig. 3. (A) The highly recombinogenic double strand break recruits an endogenous double-strand DNA repair machinery that can be utilized to achieved deletion, and insertion of
precise editing of the genomic loci. (B) Targeted gene editing can be carried out using traditional homologous recombination or via ZFN, TALENS, and CRISPR that rely on molecular
scissors to precisely create double-strand breaks at specic genomic sites.

3.2. Zinc nger nucleases
Zinc nger (ZF) motifs are articial DNA-binding proteins made up
of approximately 30 amino acids with conserved Cys2His2 residues
that chelate to zinc ion thus stabilizing the tertiary structure for the
alpha helix of the motif to bind to the major grove of the DNA double
helix (Pavletich and Pabo, 1991). Key amino acids at the start of the
alpha helix of each ZF motif can be changed to generate different triplet
sequences to confer specicity to the DNA recognition site; and multiple
ZF motifs are linked in tandem to facilitate specic binding to longer
DNA sequences to generate Zinc nger proteins or ZFP (Tan et al.,
2003). This platform technology can then be linked to additional
functionality to activate or repress genes and also create non-specic
double-strand breaks using FolkI nuclease to create Zinc nger nucleases
that can recognize and cleave specic target sequences (Kim et al.,
1996). Since dimerization of FokI domain is required for its activity,
ZFN pairs are designed to bind to the DNA region of interest in the oppo-
site orientation (Vanamee et al., 2001). The utility of this technology is
best served when the ZFN-induced double-strand break is restricted to
the target site. In order to increase specicity, the original ZFN design
has been signicantly modied to facilitate a unique and specic
targeting at essentially any locus (Miller et al., 2007).
Knock-out of PIG-A, a disease related gene mutated in hematopoietic
stem cells from patients with paroxysmal nocturnal hemoglobinuria,
1000 A. Fontes, U. Lakshmipathy / Biotechnology Advances 31 (2013) 9941001
was achieved in ESC and iPSC both via ZFN alone to create site-specic
break followed by error-prone NHEJ and with a donor DNA via inser-
tional mutagenesis (Zou et al., 2009). Knock-in of eGFP reporter was
also achieved in the previously targeted Oct4 locus in human ESC and
the resulting Oct4-eGFP cells retained pluripotency and differentiation
potential (Hockemeyer et al., 2009). The same study also reported the
targeting of one ESC line and two iPSC lines at the transcriptionally inac-
tive PITX3 locus that is not expressed in pluripotent state but turned on
after differentiation. In addition to the creation of knock-out and knock-
in cell lines, ZFN technology has been used for gene and shRNA insertion
into the safe harbor locus AAVS1 on chromosome 19 for over expression
of knock-down of specic genes (DeKelver et al., 2010; Hockemeyer
et al., 2009). The knockout of CCR5 gene in CD34+ cells conferring resis-
tance to HIV infection demonstrates the potential of ZFN in potential
clinical applications (Holt et al., 2010). However, its widespread use
is hindered due to the challenges associated with designing DNA
sequences for nger design that confer sequence specicity thus elimi-
nating off target effects.
3.3. TAL effectors
Transcription activator-like effectors (TALE), rst identied in the
plant pathogen Xanthamonas, recognize DNA in a modular manner
(Boch et al., 2009; Moscou and Bogdanove, 2009) and hence have
recently gained popularity for DNA targeting because it confers
higher specicity. Specic DNA sequence recognition is achieved by
a central repetitive region consisting of varying numbers of identical
repeat units of typically 3335 amino acids with two variable amino
acids termed the repeat-variable diresidues (RVD). It is thought that
these RVDs specically contact base pairs for target recognition, albeit
with a minor mismatch. The code that constitutes most frequent asso-
ciations can be used to predict TALE binding sites for custom design spe-
cic to target DNA sequences of choice. Similar to the ZFN technology,
the combination of the TALE and FokI nuclease is designed in pairs to
bind opposing DNA target sites separated by spacer sites that are used
to design TAL effector nucleases, or TALENs (Bogdanove and Voytas,
2011), and to successfully target endogenous genes in human cell
lines (Cermak et al., 2011; Miller et al., 2011). Knock-in of eGFP at the
endogenous Oct4 and PITX3 promoters and gene insertion of constitu-
tive eGFP at the safe-harbor AAVS1 sites were targeted in ESCs and
iPSCs using TALENs and the targeting efciencies were found to be
comparable (Hockemeyer et al., 2011) to the frequencies previously
observed for these sites with ZFN (Hockemeyer et al., 2009). Given
the powerful combination of high targeting efciency and simpler
recognition code for effective design of sequence specic TALENs, this
method holds a huge potential for the modication of pluripotent
stem cells for various downstream applications.
3.4. Crispr/CAS
Recently, a new class of genome engineering tools that harnesses the
ability of RNA to program sequence-specic DNA cleavage was reported.
Based on the prokaryotic CRISPR (clustered regularly interspaced short
palindromic repeats), this minimal 3-component platform comprises
of Cas9 (codon optimized and attached to nuclear localization signals),
and two noncoding RNAs: pre-crRNA (array containing nuclease guide
sequences or spacers interspaced by identical direct repeats), and an
89-nucleotide tracrRNA. Fig. 3A outlines the basic schematic of the
CRISPR cleavage. Directed by the two noncoding short RNAs, Cas9 nucle-
ases have been shown to precisely and efciently cleave endogenous
genomic loci in human and mouse cells (Cong et al., 2013). Further,
this system was used to target the AAVS1 locus in induced pluripotent
stem cells with targeting rates of 24% (Mali et al., 2013). Recently,
this tool was utilized for the disruption of ve genes simultaneously in
mouse ES cells as well as insertion into mouse zygotes for the generation
of mice with multiple point mutations at specic targets (Wang et al.,
2013). The advantage of this method over all the previous gene-
targeting systems is that although specicity and efciency maybe
similar or better, this robust method allows simultaneous editing of
multiple target loci in the mammalian genome.
The methods outlined above for the creation of genetically
engineered embryonic stem cells and induced pluripotent stem cells aid
in uncovering key aspects of basic stem cell biology and understanding
human disease. Modied stem cells also serve as a relevant in vitro cell
model to develop safe drugs and toxicity screening methods. As advances
in genetic modication of stem cells continue, we approach the realiza-
tion of their unparalleled potential in regenerative medicine and drug
discovery.
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