Genes In Mouse Embryonic Stem Cells Research Articles

NR5A2 connects zygotic genome activation to the first lineage segregation in totipotent embryos

Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to the inner cell mass (ICM) where pluripotent epiblast arises, and extraembryonic trophectoderm. However, how ZGA is connected to the first lineage segregation in mammalian embryos remains elusive. Here, we investigated the role of nuclear receptor (NR) transcription factors (TFs), whose motifs are highly enriched and accessible from the 2-cell (2C) to 8-cell (8C) stages in mouse embryos. We found that NR5A2, an NR TF strongly induced upon ZGA, was required for this connection. Upon Nr5a2 knockdown or knockout, embryos developed beyond 2C normally with the zygotic genome largely activated. However, 4–8C-specific gene activation was substantially impaired and Nr5a2-deficient embryos subsequently arrested at the morula stage. Genome-wide chromatin binding analysis showed that NR5A2-bound cis-regulatory elements in both 2C and 8C embryos are strongly enriched for B1 elements where its binding motif is embedded. NR5A2 was not required for the global opening of its binding sites in 2C embryos but was essential to the opening of its 8C-specific binding sites. These 8C-specific, but not 2C-specific, binding sites are enriched near genes involved in blastocyst and stem cell regulation, and are often bound by master pluripotency TFs in blastocysts and embryonic stem cells (ESCs). Importantly, NR5A2 regulated key pluripotency genes Nanog and Pou5f1/Oct4, and primitive endoderm regulatory genes including Gata6 among many early ICM genes, as well as key trophectoderm regulatory genes including Tead4 and Gata3 at the 8C stage. By contrast, master pluripotency TFs NANOG, SOX2, and OCT4 targeted both early and late ICM genes in mouse ESCs. Taken together, these data identify NR5A2 as a key regulator in totipotent embryos that bridges ZGA to the first lineage segregation during mouse early development.

A One-step strategy to target essential factors with auxin-inducible degron system in mouse embryonic stem cells.

The self-renewal and pluripotency of embryonic stem cells (ESCs) are conferred by networks including transcription factors and histone modifiers. The Auxin-inducible degron (AID) system can rapidly and reversibly degrade its target proteins and is becoming a powerful tool to explore novel function of key pluripotent and histone modifier genes in ESCs. However, the low biallelic tagging efficiency and a basal degradation level of the current AID systems deem it unsuitable to target key pluripotent genes with tightly controlled expression levels. Here, we develop a one-step strategy to successfully target and repress the endogenous pluripotent genes in mouse ESCs and replace their expression with AID fused transgenes. Therefore, this work provides an efficient way for employing the AID system to uncover novel function of essential pluripotent and chromatin modifier genes in ESCs.

Lactate Activates Germline and Cleavage Embryo Genes in Mouse Embryonic Stem Cells.

Lactate was recently found to mediate histone lysine lactylation and facilitate polarization of M1 macrophages, indicating its role in metabolic regulation of gene expression. During somatic cell reprogramming, lactate promotes histone lactylation of pluripotency genes and improves reprogramming efficiency. However, the function of lactate in cell fate control in embryonic stem cells (ESCs) remains elusive. In this study, we revealed that lactate supplementation activated germline genes in mouse ESCs. Lactate also induced global upregulation of cleavage embryo genes, such as members of the Zscan4 gene family. Further exploration demonstrated that lactate stimulated H3K18 lactylation accumulation on germline and cleavage embryo genes, which in turn promoted transcriptional elongation. Our findings indicated that lactate supplementation expanded the transcriptional network in mouse ESCs.

MMTR/Dmap1 Sets the Stage for Early Lineage Commitment of Embryonic Stem Cells by Crosstalk with PcG Proteins.

Chromatin remodeling, including histone modification, chromatin (un)folding, and nucleosome remodeling, is a significant transcriptional regulation mechanism. By these epigenetic modifications, transcription factors and their regulators are recruited to the promoters of target genes, and thus gene expression is controlled through either transcriptional activation or repression. The Mat1-mediated transcriptional repressor (MMTR)/DNA methyltransferase 1 (DNMT1)-associated protein (Dmap1) is a transcription corepressor involved in chromatin remodeling, cell cycle regulation, DNA double-strand break repair, and tumor suppression. The Tip60-p400 complex proteins, including MMTR/Dmap1, interact with the oncogene Myc in embryonic stem cells (ESCs). These proteins interplay with the stem cell-related proteome networks and regulate gene expressions. However, the detailed mechanisms of their functions are unknown. Here, we show that MMTR/Dmap1, along with other Tip60-p400 complex proteins, bind the promoters of differentiation commitment genes in mouse ESCs. Hence, MMTR/Dmap1 controls gene expression alterations during differentiation. Furthermore, we propose a novel mechanism of MMTR/Dmap1 function in early stage lineage commitment of mouse ESCs by crosstalk with the polycomb group (PcG) proteins. The complex controls histone mark bivalency and transcriptional poising of commitment genes. Taken together, our comprehensive findings will help better understand the MMTR/Dmap1-mediated transcriptional regulation in ESCs and other cell types.

A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes

The rate of RNA polymerase II (RNAPII) elongation has an important role in the control of alternative splicing (AS); however, the in vivo consequences of an altered elongation rate are unknown. Here, we generated mouse embryonic stem cells (ESCs) knocked in for a slow elongating form of RNAPII. We show that a reduced transcriptional elongation rate results in early embryonic lethality in mice. Focusing on neuronal differentiation as a model, we observed that slow elongation impairs development of the neural lineage from ESCs, which is accompanied by changes in AS and in gene expression along this pathway. In particular, we found a crucial role for RNAPII elongation rate in transcription and splicing of long neuronal genes involved in synapse signaling. The impact of the kinetic coupling of RNAPII elongation rate with AS is greater in ESC‐differentiated neurons than in pluripotent cells. Our results demonstrate the requirement for an appropriate transcriptional elongation rate to ensure proper gene expression and to regulate AS during development.

Embryonic Stem Cells Derived Kidney Organoids as Faithful Models to Target Programmed Nephrogenesis

The kidney is a complex organ that is comprised of thousands of nephrons developing through reciprocal inductive interactions between metanephric mesenchyme (MM) and ureteric bud (UB). The MM undergoes mesenchymal to epithelial transition (MET) in response to the signaling from the UB. The secreted protein Wnt4, one of the Wnt family members, is critical for nephrogenesis as mouse Wnt4−/− mutants fail to form pretubular aggregates (PTA) and therefore lack functional nephrons. Here, we generated mouse embryonic stem cell (mESC) line lacking Wnt4 by applying the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated systems 9 (Cas9). We describe here, differentiation of the wild type and Wnt4 knockout mESCs into kidney progenitors, and such cells induced to undergo nephrogenesis by the mouse E11.5 UB mediated induction. The wild type three-dimensional (3D) self-organized organoids depict appropriately segmented nephron structures, while the Wnt4-deficient organoids fail to undergo the MET, as is the case in the phenotype of the Wnt4 knockout mouse model in vivo. In summary, we have established a platform that combine CRISPR/Cas9 and kidney organoid technologies to model kidney development in vitro and confirmed that mutant organoids are able to present similar actions as in the in vivo studies.

1025 - A Quantitative Perspective of Transcription in Pluripotent and Differentiated Cells

The differentiation of embryonic stem cells (ESC) requires three fundamentally distinct transitions in transcriptional state: 1. the activation of genes that are fully silent in ESC but transcribed in the differentiated state, 2. the silencing of genes that are transcribed in ESC but must be fully inactive in the differentiated cells, and 3. The increased or decreased transcription of genes that are actively transcribed in both populations. Because distinct mechanisms are likely to regulate each type of transition, the genes included in each category must be carefully delineated before the mechanisms can be elucidated and fully appreciated. However, genes in categories 1 and 2 have not been separated adequately from genes in category 3 because studies of differential gene expression typically use low stringency thresholds to define differential expression; they therefore group genes that are moderately upregulated or downregulated with those that transition between active and silent states. A quantitative analysis of nascent transcript RNA-seq data sets revealed that the vast majority of differentially expressed genes in mouse ESC in comparison to three primary differentiated cell types exhibit dynamic ranges of expression of less than 10-fold, with only a small number of genes exhibiting a dynamic range of 100-fold or more. This finding raises a number of questions, one of which is the following: What are the functions of the thousands of binding sites for pluripotency transcription factors, such as Oct4 and Sox2, if the vast majority of differentially expressed genes change expression level by only a small magnitude as cells leave the pluripotent state? As expected, a small number of these binding sites appear to be involved in the regulation of the small number of genes that exhibit large dynamic ranges of expression in ESC versus differentiated cells. However, do the thousands of other binding sites support small (e.g. 2-fold) changes in expression of genes that are efficiently expressed in both the pluripotent and differentiated states? If so, do they regulate these genes by binding constitutively active promoters and enhancers or, alternatively, by activating dedicated enhancers that support small changes in gene expression? Or, do they maintain the active state of constitutively expressed genes in ESC without playing a critical role in boosting or suppressing transcription? By combining nascent transcript RNA-seq with pluripotency factor ChIP-seq data sets and CRISPR/Cas9 disruption of individual Oct4:Sox2 composite binding sites, insights into these and other unanswered questions are beginning to emerge.

Pluripotent stem cells as a source of osteoblasts for bone tissue regeneration

Appropriate and abundant sources of bone-forming osteoblasts are essential for bone tissue engineering. Pluripotent stem cells can self-renew and thereby offer a potentially unlimited supply of osteoblasts, a significant advantage over other cell sources. We generated mouse embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) from transgenic mice expressing rat 2.3 kb type I collagen promoter-driven green fluorescent protein (Col2.3GFP), a reporter of the osteoblast lineage. We demonstrated that Col2.3GFP ESCs and iPSCs can be successfully differentiated to osteoblast lineage cells that express Col2.3GFP in vitro. We harvested GFP+ osteoblasts differentiated from ESCs. Genome wide gene expression profiles validated that ESC- and iPSC-derived osteoblasts resemble calvarial osteoblasts, and that Col2.3GFP expression serves as a marker for mature osteoblasts. Our results confirm the cell identity of ESC- and iPSC-derived osteoblasts and highlight the potential of pluripotent stem cells as a source of osteoblasts for regenerative medicine.

Regulation of human and mouse telomerase genes by genomic contexts and transcription factors during embryonic stem cell differentiation

Differential regulation of telomerase reverse transcriptase (TERT) genes contribute to distinct aging and tumorigenic processes in humans and mice. To study TERT regulation, we generated mouse embryonic stem cell (ESC) lines containing single-copy bacterial artificial chromosome (BAC) reporters, covering hTERT and mTERT genes and their neighboring loci, via recombinase-mediated BAC targeting. ESC lines with chimeric BACs, in which two TERT promoters were swapped, were also generated. Using these chromatinized BACs, we showed that hTERT silencing during differentiation to embryoid bodies (EBs) and to fibroblast-like cells was driven by the human-specific genomic context and accompanied by increases of repressive epigenetic marks, H3K9me3 and H3K27me3, near its promoter. Conversely, the mouse genomic context did not repress TERT transcription until late during differentiation. The hTERT promoter was more active than its mouse counterpart when compared in the same genomic contexts. Mutations of E-box and E2F consensus sites at the promoter had little effect on hTERT transcription in ESCs. However, the mutant promoters were rapidly silenced upon EB differentiation, indicating that transcription factors (TFs) bound to these sites were critical in maintaining hTERT transcription during differentiation. Together, our study revealed a dynamic hTERT regulation by chromatin environment and promoter-bound TFs during ESC differentiation.

Sialylation Is Dispensable for Early Murine Embryonic Development in Vitro.

The negatively charged nonulose sialic acid (Sia) is essential for murine development in vivo. In order to elucidate the impact of sialylation on differentiation processes in the absence of maternal influences, we generated mouse embryonic stem cell (mESC) lines that lack CMP‐Sia synthetase (CMAS) and thereby the ability to activate Sia to CMP‐Sia. Loss of CMAS activity resulted in an asialo cell surface accompanied by an increase in glycoconjugates with terminal galactosyl and oligo‐LacNAc residues, as well as intracellular accumulation of free Sia. Remarkably, these changes did not impact intracellular metabolites or the morphology and transcriptome of pluripotent mESC lines. Moreover, the capacity of Cmas −/− mESCs for undirected differentiation into embryoid bodies, germ layer formation and even the generation of beating cardiomyocytes provides first and conclusive evidence that pluripotency and differentiation of mESC in vitro can proceed in the absence of (poly)sialoglycans.

Embryonic stem cells derived from in vivo or in vitro-generated murine blastocysts display similar transcriptome and differentiation potential.

The use of assisted reproductive technologies (ART) such as in vitro fertilization (IVF) has resulted in the birth of more than 5 million children. While children conceived by these technologies are generally healthy, there is conflicting evidence suggesting an increase in adult-onset complications like glucose intolerance and high blood pressure in IVF children. Animal models indicate similar potential risks. It remains unclear what molecular mechanisms may be operating during in vitro culture to predispose the embryo to these diseases. One of the limitations faced by investigators is the paucity of the material in the preimplantation embryo to test for molecular analysis. To address this problem, we generated mouse embryonic stem cells (mESC) from blastocysts conceived after natural mating (mESCFB) or after IVF, using optimal (KSOM + 5% O2; mESCKAA) and suboptimal (Whitten’s Medium, + 20% O2, mESCWM) conditions. All three groups of embryos showed similar behavior during both derivation and differentiation into their respective mESC lines. Unsupervised hierarchical clustering of microarray data showed that blastocyst culture does not affect the transcriptome of derived mESCs. Transcriptomic changes previously observed in the inner cell mass (ICM) of embryos derived in the same conditions were not present in mESCs, regardless of method of conception or culture medium, suggesting that mESC do not fully maintain a memory of the events occurring prior to their derivation. We conclude that the fertilization method or culture media used to generate blastocysts does not affect differentiation potential, morphology and transcriptome of mESCs.

Role of Tet proteins in enhancer activity and telomere elongation.

DNA methylation at the C-5 position of cytosine (5mC) is one of the best-studied epigenetic modifications and plays important roles in diverse biological processes. Iterative oxidation of 5mC by the ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are selectively recognized and excised by thymine DNA glycosylase (TDG), leading to DNA demethylation. Functional characterization of Tet proteins has been complicated by the redundancy between the three family members. Using CRISPR/Cas9 technology, we generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (Tet triple knockout [TKO]). Whole-genome bisulfite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs at distally located enhancers and fine-tunes the transcription of genes associated with these regions. Functional characterization of Tet TKO ESCs revealed a role for Tet proteins in regulating the two-cell embryo (2C)-like state under ESC culture conditions. In addition, Tet TKO ESCs exhibited increased telomere-sister chromatid exchange and elongated telomeres. Collectively, our study reveals a role for Tet proteins in not only DNA demethylation at enhancers but also regulating the 2C-like state and telomere homeostasis.

Designing Ago2-specific siRNA/shRNA to Avoid Competition with Endogenous miRNAs.

Relatively large amounts of transfected siRNA can compete for Ago proteins and thus compromise endogenous miRNA function, potentially leading to toxicities. Here, we show that shRNA can also perturb endogenous miRNA function similarly. More importantly, we also show that the problem can be solved by designing shRNAs in the context of pre-miR-451 structure with completely complementary stem, which significantly improves the Ago2 specificity. This shRNA was shown to be Ago2-specific, and maintain target-silencing ability while avoiding competition with endogenous miRNAs by not competing for Agos 1, 3, and 4. We conclude that modified pre-miR-451 structure provides a general platform to design shRNAs that significantly reduce perturbation of miRNA function.

Embryonic stem cells stably expressing BDNF–GFP exhibit a BDNF-release-dependent enhancement of neuronal differentiation

Brain-derived neurotrophic factor (BDNF) is known to be a crucial regulator of neuronal survival and synaptic plasticity in the mammalian brain. Furthermore, BDNF positively influences differentiation of embryonic neural precursors, as well as that of neural stem cells from adult neurogenic niches. To study the impact of cell-released BDNF on neural differentiation of embryonic stem cells (ESCs), which represent an attractive source for cell transplantation studies, we have generated mouse ESC clones overexpressing BDNF-GFP by use of knock-in technology. After neural differentiation in vitro, we observed that ESC clones overexpressing BDNF-GFP gave rise to an increased number of neurons as compared to control ESCs. Neurons derived from BDNF-GFP-expressing ESCs harbored a more complex dendritic morphology and differentiated into the GABAergic lineage more than controls. Moreover, we show that ESC-derived neurons released BDNF-GFP in an activity-dependent manner and displayed similar electrophysiological properties as cortical neurons. Thus, our study describes the generation of ESCs stably overexpressing BDNF-GFP, which are ideally suited to investigate the ameliorating effects of BDNF in cell transplantation studies of various neuropathological conditions.

Inactivation of Klf5 by zinc finger nuclease downregulates expression of pluripotent genes and attenuates colony formation in embryonic stem cells

Recent studies suggest that Klf5 is required to maintain embryonic stem (ES) cells in an undifferentiated state. However, whether Klf5 can be inactivated by novel fusion technology of zinc finger nucleases (ZFN) has never before been examined. Therefore, we used ZFN technology to target the Klf5 gene in mouse ES cells, and examined the effects of the Klf5 gene on the expression of pluripotency-related genes, Oct3/4, Nanog, and Sox2 and on the self-renewal of ES cells. In Klf5-ZFN-transfected cells, expression of the Klf5 mRNA was downregulated by ~80% compared to the control. Furthermore, expression of the Oct3/4 and Nanog mRNAs was significantly decreased in the Klf5-ZFN-targeted cells. RT-PCR analysis, however, showed no significant change in the level of Sox2 mRNA, but a decreased trend was evident in the Klf5-ZFN-targeted cells. Moreover, we observed the spontaneous differentiation of Klf5-ZFN-transfected cells and quantitative analysis revealed a significant decrease in colony formation in Klf5-ZFN-transfected cells. In conclusion, our data suggest that ZFN methodology is an effective approach to target the Klf5 gene and that Klf5 plays an important role in the maintenance of ES cell self-renewal.

Abstract 2644: In vivo and in vitro stem cell models suggest a role for LGR5 in regulating intestinal epithelial lineage specification.

Abstract The stem cell marker Leucine Rich Repeat Containing G-protein Coupled Receptor 5 (LGR5) is frequently upregulated in human colon cancer. Numerous observations implicate LGR5 in stem cell maintenance during intestinal development, tissue homeostasis and cancer, however the precise role of LGR5 in these processes is still unclear. To explore the role of LGR5, we generated mouse embryonic stem cells (ESCs) in which one or both alleles of Lgr5 were deleted and replaced with either β-galactosidase or green fluorescent protein (gfp) reporter genes, or the human LGR5 gene. These cell lines were used in three complimentary systems to differentiate and/or isolate cell lineages. The first system was an in vivo model in which subcutaneous xenografts of murine ESCs grew and formed tumors (teratomas) containing cellular structures from all three germ cell layers. Immunostaining showed that a subset of E-cadherin-positive epithelial cells also expressed Lgr5 reporter genes. Teratomas derived from Lgr5 null ESCs showed an increase in E-cadherin-positive epithelial structures, and gene expression profiling of Lgr5 null teratomas showed an upregulation of epithelial genes including Cdh1, Epcam, Cldn7, Krt5, and Krt14 compared with control teratomas. In contrast, ESCs constitutively overexpressing a secreted form of LGR5 ectodomain formed teratomas with fewer epithelial structures and reduced expression of epithelial genes compared to control teratomas. The second system used in vitro differentiation of ESCs towards an intestinal epithelial lineage, followed by 3D culturing, to derive intestinal organoids. Lgr5+/+ (WT), Lgr5lacZ/+ (Het), or Lgr5lacZ/gfp (Null) ESCs are being examined for their ability to adopt an intestinal fate and form organoids in vitro. A third system used ex vivo culture of murine intestinal crypts isolated from humanized LGR5 heterozygous mice to form intestinal organoids. In summary, the morphological and gene expression changes observed in teratomas implicate a role of LGR5 in regulating epithelial tissue homeostasis. The ability to grow and manipulate organoid cultures ex vivo/in vitro will allow us to use various soluble reagents and detailed microscopy to further assess the role of the Lgr5 pathway in intestinal cell lineage specification as well as tumorigenesis. Citation Format: Courtney M. Williams, Jessica L. Harper, Hui Huang, Pat Boland, Qing Zhang, George D. Yancopoulos, Zhe Li, O. Gavin Thurston. In vivo and in vitro stem cell models suggest a role for LGR5 in regulating intestinal epithelial lineage specification. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2644. doi:10.1158/1538-7445.AM2013-2644

BMP Induces Cochlin Expression to Facilitate Self-renewal and Suppress Neural Differentiation of Mouse Embryonic Stem Cells

BMP4 maintains self-renewal of mouse embryonic stem cells (ESCs) in collaboration with LIF. Here, we report the identification of a novel key BMP target gene, cochlin (Coch) in mouse ESCs. Coch can be significantly up-regulated by BMP4 specifically in ESCs but not in somatic differentiated cells, and this up-regulation is dependent on the BMP signaling mediators Smad1/5 and Smad4. Overexpression of Coch can partially substitute BMP4 to promote self-renewal of mouse ESCs together with LIF, whereas knockdown of Coch impairs self-renewal marker gene expression even in the presence of both BMP4 and LIF. Further studies showed that COCH could mimic BMP4 in repressing neural differentiation of mouse ESCs upon LIF withdrawal and the inhibitory effect of BMP4 on neural differentiation is compromised by Coch knockdown. Taken together, our data suggest that COCH is a part of the downstream target network of BMP signaling and serves as another important effector to fine-tune mouse ESC fates.

Pluripotent Stem Cell Models of a Cardiac Sodium Channelopathy

Mutations in the gene encoding the cardiac sodium (Na+) channel, SCN5A, have been implicated in multiple arrhythmia syndromes, such as long-QT syndrome type 3 (LQT3) and Brugada syndrome (BrS). Carriers of the SCN5A-1795insD mutation exhibit both features of LQT3 and BrS. Transgenic mice carrying the mouse equivalent (1798insD) of the human SCN5A-1795insD mutation recapitulate the electrophysiological characteristics observed in patients. Recent advances in the pluripotent stem cells (PSCs) field have created new opportunities for modelling cardiac genetic diseases. However, it is unclear whether PSCs can model genetic disorders affecting the cardiac Na+ channel due to the immaturity of the PSC- derived cardiomyocytes (CMs). To address this issue, we generated multiple PSC lines containing a Na+ channel mutation causing a cardiac Na+ channel overlap syndrome.Methods: We generated mouse embryonic stem cells (mESCs) and mouse induced pluripotent stem cells (miPSCs), both wild type (scn5a-wt) and carrying the heterozygous scn5a-1798insD mutation (scn5a-het). Human iPSCs (hiPSCs) both from a patient carrying the SCN5A-1795insDmutation (SCN5A-het) and an unaffected individual were also created. Finally, human and mouse PSCs were differentiated into CMs and used for patch-clamp experiments.Results: In both mESC and miPSC cardiomyocytes, scn5a-het showed a significant decreased INa density compared to Scn5a-wt, while Na+ channel gating properties were unchanged. Action potential (AP) measurements revealed a reduced upstroke velocity and longer AP duration in Scn5a-het myocytes. These characteristics reflected those in primary CMs isolated from adult Scn5a-het mice. Finally, SCN5A-het myocytes revealed similar changes to those observed in the mouse PSC-CMs.Conclusions: Here we demonstrated that ESC- and iPSC derived cardiomyocytes recapitulate the electrophysiological characteristics of a cardiac Na+ channel mutation associated with both LQT3 and BrS and that the immaturity of PSC cardiomyocytes does not preclude their use as an accurate disease model.

Efficient conditional and promoter-specific in vivo expression of cDNAs of choice by taking advantage of recombinase-mediated cassette exchange using FlEx gene traps

Recombinase-mediated cassette exchange (RMCE) exploits the possibility to unidirectionally exchange any genetic material flanked by heterotypic recombinase recognition sites (RRS) with target sites in the genome. Due to a limited number of available pre-fabricated target sites, RMCE in mouse embryonic stem (ES) cells has not been tapped to its full potential to date. Here, we introduce a universal system, which allows the targeted insertion of any given transcriptional unit into 85 742 previously annotated retroviral conditional gene trap insertions, representing 7013 independent genes in mouse ES cells, by RMCE. This system can be used to express any given cDNA under the control of endogenous trapped promoters in vivo, as well as for the generation of transposon ‘launch pads’ for chromosomal region-specific ‘Sleeping Beauty’ insertional mutagenesis. Moreover, transcription of the gene-of-interest is only activated upon Cre-recombinase activity, a feature that adds conditionality to this expression system, which is demonstrated in vivo. The use of the RMCE system presented in this work requires one single-cloning step followed by one overnight gateway clonase reaction and subsequent cassette exchange in ES cells with efficiencies of 40% in average.

Floxin, a resource for genetically engineering mouse ESCs

We describe a method for the highly efficient and precise targeted modification of gene trap loci in mouse embryonic stem cells (ESCs). Through the Floxin method, gene trap mutations are reverted and new DNA sequences inserted using Cre recombinase and a shuttle vector, pFloxin. Floxin technology is applicable to the existing collection of 24,149 compatible gene trap cell lines, which should enable the high-throughput modification of many genes in mouse ESCs.