Name: structure-function studies in mouse embryonic stem cells using recombinase-mediated cassette exchange
Uploaded: 2017-04-27T15:00:00
Description: Watch this Scientific Journal Video about Structure-function Studies in Mouse Embryonic Stem Cells Using Recombinase-mediated Cassette Exchange at JoVE.com

We thank Jinke D&#39;Hont, Frederique Van Rockeghem, Natalie Farla, Kelly Lemeire, and Riet De Rycke for their excellent technical support. We also thank Eef Parthoens, Evelien Van Hamme, and Amanda Goncalves from the Bioimaging Core Facility of the Inflammation Research Center for their expert assistance. We acknowledge members of our research group for valuable discussions. This work was supported by the Belgian Science Policy (Belspo Interuniversity Attraction Poles - Award IAP VII-07 DevRepair; https://devrepair.be), by the Queen Elisabeth Medical Foundation, Belgium (GSKE 2008-2010; http://www.fmre-gske.be), and by the Concerted Research Actions (GOA 01G01908) of Ghent University, Belgium (http://www.ugent.be/en/ghentuniv). SG is a postdoctoral fellow of the Flanders Research Funds (FWO-V).

All experiments on mice were conducted according to institutional, national, and European animal regulations.
1. Isolation of RMCE-compatible KO mESCs
<ol>
	<li>Breed heterozygous KO mice with RMCE-compatible mice, such as ROSALUC mice10 or ROSA26-iPSC mice21. Both RMCE-compatible mice were maintained on a mixed 129/C57BL6/Swiss background. 
	NOTE: Crossing with heterozygous KO mice is advised to overcome embryonic lethality in homozygous KO mice.</li>
	<li>Us...

<ol>
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S., Hulpiau, P., Saeys, Y., van Roy, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Metazoan+evolution+of+the+armadillo+repeat+superfamily.">Metazoan evolution of the armadillo repeat superfamily.</a> Cell Mol Life Sci. , (2016).</li><li>Valenta, T., Hausmann, G., Basler, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+many+faces+and+functions+of+beta-catenin.">The many faces and functions of beta-catenin.</a> EMBO J. 31, 2714-2736 (2012).</li><li>Pieters, T., van Hengel, J., van Roy, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functions+of+p120ctn+in+development+and+disease.">Functions of p120ctn in development and disease.</a> Front Biosci. 17, 760-783 (2012).</li><li>Keirsebilck, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+cloning+of+the+human+p120ctn+catenin+gene+(CTNND1):+Expression+of+multiple+alternatively+spliced+isoforms.">Molecular cloning of the human p120ctn catenin gene (CTNND1): Expression of multiple alternatively spliced isoforms.</a> Genomics. 50, 129-146 (1998).</li><li>Capecchi, M. 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S., Dymecki, S. 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L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ground+state+of+embryonic+stem+cell+self-renewal.">The ground state of embryonic stem cell self-renewal.</a> Nature. 453, 519-523 (2008).</li><li>Chen, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-renewal+of+embryonic+stem+cells+by+a+small+molecule.">Self-renewal of embryonic stem cells by a small molecule.</a> Proc Natl Acad Sci U S A. 103, 17266-17271 (2006).</li><li>Pieters, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+and+User-Friendly+Pluripotin-based+Derivation+of+Mouse+Embryonic+Stem+Cells.">Efficient and User-Friendly Pluripotin-based Derivation of Mouse Embryonic Stem Cells.</a> Stem Cell Rev. 8, (2012).</li><li>Yang, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pluripotin+combined+with+leukemia+inhibitory+factor+greatly+promotes+the+derivation+of+embryonic+stem+cell+lines+from+refractory+strains.">Pluripotin combined with leukemia inhibitory factor greatly promotes the derivation of embryonic stem cell lines from refractory strains.</a> Stem Cells. 27, 383-389 (2009).</li><li>Haenebalcke, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ROSA26-iPSC+Mouse:+A+Conditional,+Inducible,+and+Exchangeable+Resource+for+Studying+Cellular+(De)Differentiation.">The ROSA26-iPSC Mouse: A Conditional, Inducible, and Exchangeable Resource for Studying Cellular (De)Differentiation.</a> Cell Rep. 3, (2013).</li><li>Tucker, K. L., Wang, Y., Dausman, J., Jaenisch, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+transgenic+mouse+strain+expressing+four+drug-selectable+marker+genes.">A transgenic mouse strain expressing four drug-selectable marker genes.</a> Nucleic Acids Res. 25, 3745-3746 (1997).</li><li>Nyabi, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+mouse+transgenesis+using+Gateway-compatible+ROSA26+locus+targeting+vectors+and+F1+hybrid+ES+cells.">Efficient mouse transgenesis using Gateway-compatible ROSA26 locus targeting vectors and F1 hybrid ES cells.</a> Nucleic Acids Res. 37, 55 (2009).</li><li>Katzen, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gateway((R))+recombinational+cloning:+a+biological+operating+system.">Gateway((R)) recombinational cloning: a biological operating system.</a> Expert Opin Drug Discov. 2, 571-589 (2007).</li><li>Schaft, J., Ashery-Padan, R., vander Hoeven, F., Gruss, P., Stewart, A. 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Our mESC isolation method is user-friendly and does not require advanced skills or equipment, such as microsurgery of blastocysts. Thus, this technology is accessible to a large proportion of the scientific community. Anyone with basic cell culture experience can propagate ICM outgrowths and establish mESCs lines. However, the flushing and handling of blastocysts requires some practice. A mouth pipette is used to transfer blastocysts and consists of a micropipette, a micropipette holder, tubing, and an aspirator mouthpie...

It is estimated that mammalian genomes contain about 20,000 protein-coding genes. Alternative splicing and posttranslational modifications further increase the protein repertoire. Proteins have a modular structure1 and often contain multiple interaction domains, which allow their recruitment into different protein complexes and their participation in multiple cellular processes2. One example is the multi-functional protein called p120ctn. p120ctn is encoded by the Ctnnd1 gene and consists of a large central armadillo repeat domain flanked by an N-terminal and a C-terminal region. The armadillo domain of p120ctn binds to a highly conserved juxtamembrane domain of classical cadherins, which are involved in cell-cell adhesion, but it also binds to the transcriptional repressor Kaiso. The N-terminal domain of p120ctn interacts with different kinases, phosphatases, small RhoGTPases, and microtubule-associated proteins3. Interestingly, as a result of alternative splicing, p120ctn isoforms can be generated from four alternative start codons4. p120ctn isoform 1A is the longest, as it is translated from the most-5&#39; start codon and contains the full-length N-terminal segment. In p120ctn isoforms 3 and 4, this N-terminal segment is deleted partially and completely, respectively. Understanding the precise role of proteins (or protein isoforms) and their domains in different cellular functions remains a challenge.
Gene targeting in mESCs enables the study of the function of a protein through the genetic deletion of the corresponding gene and has widely contributed to the identification of developmentally important and disease-relevant genes and pathways. This breakthrough in reverse genetics was the result of advances in the fields of mESC isolation and gene targeting due to homologous recombination5. Homologous recombination is a process in which DNA fragments are exchanged between two similar or identical nucleic moieties after double-stranded (ds) DNA breaks. Normally, HR is inefficient because dsDNA breaks are infrequent. Recently, the efficiency of homology-directed gene targeting could be increased using site-specific nucleases6,7, but unfortunately, these are prone to off-target effects8. A more reliable technique to enable gene targeting is RMCE, which is based on site-specific recombination systems such as Cre/loxP or FLPe/Frt. LoxP and Frt sequence are found in bacteriophage P1 and Saccharomyces cerevisiae, respectively, and consist of 34 bp, including an asymmetric 8 bp sequence that determines the orientation of the site. On the other hand, the orientation of, for instance, two loxP sites within a DNA stretch will determine whether the floxed DNA becomes excised or inversed upon Cre-mediated recombination9. Moreover, Cre can also induce a translocation if two sites are located on different chromosomes. RMCE takes advantage of heterospecific recombination sites that do not cross-react and that are embedded in a genomic locus. In the presence of a donor plasmid that contains a DNA fragment flanked by the same heterospecific sites, the recombinase will insert this DNA fragment into the RMCE-compatible genomic locus because of double-simultaneous translocation (Figure 1). Here, only correctly RMCE-targeted clones can render drug resistance thanks to a promoter on the incoming vector that restores a &#34;trapped,&#34; promoter-less Neomycin resistance gene (NeoR) present in the R26 genome of the docking cells (Figure 1)10,11. This results in a very high targeting efficiency, often close to 100%11,12. In conclusion, RMCE-based targeting is highly efficient and can be used for structure-functions studies; however, it requires a pre-engineered genomic locus.
<img alt="Figure 1" src="/files/ftp_upload/55575/55575fig1.jpg" /> 
Figure 1. Schematic Representation of RMCE-mediated Targeting. RMCE allows for the exchange of DNA segments from an incoming targeting vector to a defined genomic locus if both harbor two heterospecific Frt sites (depicted by white and red triangles). In addition, the engineered genomic locus contains a promoterless and truncated neomycin-resistance (NeoR) gene. By providing a promoter and start codon in the incoming DNA fragment, only correct recombination events restore neomycin resistance, resulting in high targeting efficiencies. <a href="http://cloudflare.jove.com/files/ftp_upload/55575/55575fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Genome engineering in mESCs allows for the generation of RMCE-compatible mice. In 1981, two groups succeeded in capturing pluripotent cells from the inner cell mass (ICM) of blastocysts and in maintaining them in culture13,14. mESCs are capable of self-renewal and differentiation into all types of embryonic and adult cells, including the germ-cell lineage. Therefore, gene targeting in mESCs enables reverse-genetic studies through the development of constitutive or conditional (using the Cre/LoxP system) KO mice. However, the classical way to isolate mouse ES cells is very inefficient. Several major improvements have greatly increased the success rate for deriving mESC lines, including the use of a defined serum-replacement (SR) medium15, alternating between mESC medium containing SR and fetal bovine serum (FBS)16, and the use of pharmacological compounds such as pluripotin or 2i17. Pluripotin, a small synthetic molecule, allows for the propagation of mESCs in an undifferentiated state in the absence of leukemia inhibitory factor (LIF) and mouse embryonic fibroblasts (MEFs)18. Finally, it has been shown that mESCs can be isolated with a very high efficiency (close to 100%) when an SR/FBS medium alternation protocol is combined with LIF and pluripotin19,20. These protocols enable the efficient isolation of RMCE-compatible KO mESCs that can subsequently be used for structure-function studies.
This paper describes a method that enables one to identify the key domains or residues within a protein that are responsible for specific cellular processes. To this end, a pipeline of advanced technologies that enable efficient mESC isolation, targeting vector assembly, and mESC targeting was created. As such, large panels with protein isoforms, domain mutants, and downstream effectors can be introduced in KO mESCs and can be evaluated for their ability to rescue the in vitro KO phenotype.

<table border="0" cellpadding="0" cellspacing="0" width="766">
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	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">ROSALUC Mice</td>
			<td style="width:143px;">made in house</td>
			<td style="width:107px;"></td>
			<td style="width:245px;">frozen sperm available upon request</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">R26-iPSC mice</td>
			<td style="width:143px;">made in house</td>
			<td style="width:107px;"></td>
			<td style="width:245px;">frozen sperm available upon request</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Vessel probe</td>
			<td style="width:143px;">Fine Science Tools</td>
			<td>10160-13</td>
			<td style="width:245px;">to check for copulation plugs</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">M2 medium</td>
			<td style="width:143px;">Sigma-Aldrich</td>
			<td style="width:107px;">M7167</td>
			<td style="width:245px;">make aliquots and store at -20&#176;C</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Fine forceps (Dumont #5 Standard tip Student forceps)</td>
			<td style="width:143px;">Fine Science Tools</td>
			<td style="width:107px;">11251-10</td>
			<td style="width:245px;">spray with 70% EtOH before use (do not autoclave)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">23G needles</td>
			<td style="width:143px;">Fine-ject</td>
			<td style="width:107px;">8697</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">1-ml syringes</td>
			<td style="width:143px;">Soft-ject</td>
			<td style="width:107px;">6680</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">60-mm bacterial grade plates (for flushing)&#160;</td>
			<td style="width:143px;">Gosselin</td>
			<td style="width:107px;">BB60-01</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Mouth pipette</td>
			<td style="width:143px;">made in house</td>
			<td style="width:107px;"></td>
			<td style="width:245px;">see discussion</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Mouse embryonic fibroblasts (MEFs, TgN (DR4)1 Jae strain)</td>
			<td style="width:143px;">ATTC</td>
			<td style="width:107px;">SCRC-1045</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">TgN (DR4)1 Jae mice</td>
			<td style="width:143px;">The Jackson Laboratory</td>
			<td style="width:107px;">3208</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Mitomycin C&#160;</td>
			<td style="width:143px;">Sigma-Aldrich</td>
			<td style="width:107px;">M0503</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Phosphate buffered saline (PBS) without calcium or magnesium</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">14190-094</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="105">
			<td height="105" style="height:105px;width:272px;">Tg(DR4)1Jae/J mice</td>
			<td style="width:143px;">JAX</td>
			<td style="width:107px;">3208</td>
			<td style="width:245px;">mice that contain four drug-selectable genes and DR4 MEFS confers resistance to neomycin, puromycin, hygromycin and 6-thioguanine</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">0.1% Gelatin</td>
			<td style="width:143px;">Sigma-Aldrich</td>
			<td style="width:107px;">G1393</td>
			<td style="width:245px;">Dissolve 0.5 g in 500 ml distilled water, autoclave and store at 4&#176;C.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Trypsin (0.25%)&#160;</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">25200-056</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">2 &#956;M pluripotin</td>
			<td style="width:143px;">Cayman Chemical</td>
			<td style="width:107px;">10009557</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:272px;">pRMCE-DV1</td>
			<td style="width:143px;">BCCM/LMBP collection&#160;</td>
			<td style="width:107px;">LMBP 08870</td>
			<td style="width:245px;">public available from the BCCM/LMBP collection (http://bccm.belspo.be)&#160;</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:272px;">cre-excised pRMCE-DV1</td>
			<td style="width:143px;">BCCM/LMBP collection&#160;</td>
			<td style="width:107px;">LMBP 08195</td>
			<td style="width:245px;">public available from the BCCM/LMBP collection (http://bccm.belspo.be)&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">pCAG-FlpE-IRES-Puro-pA&#160;</td>
			<td style="width:143px;">Addgene</td>
			<td style="width:107px;">20733</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">heat-shock competent DH5&#945; bacteria&#160;</td>
			<td style="width:143px;">made in house</td>
			<td style="width:107px;"></td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Gateway pDONR221 vector</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">12536-017</td>
			<td style="width:245px;">contains kanamycin-resistance gene</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">BP clonase II mix</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">11789-020</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">LR clonase II mix</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">11791-020&#160;</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Luria Broth (LB)&#160;</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Ampicillin&#160;</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Applied Biosystems 3730XL DNA Analyzer</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">3730XL</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">G418</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">11811-023</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Lipofectamine 2000 transfection reagent</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">11668027</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Lipofectamine LTX transfection reagent</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">15338100</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Effectene transfection reagent</td>
			<td style="width:143px;">Qiagen</td>
			<td style="width:107px;">301425</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">GATEWAY pENTR 1A vector</td>
			<td style="width:143px;">Thermo Fisher</td>
			<td style="width:107px;">A10462</td>
			<td>recombination-compatible vector</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">mouse monoclonal anti-p120ctn antibody</td>
			<td style="width:143px;">BD Transduction Laboratories</td>
			<td style="width:107px;">610134</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">mouse monoclonal anti-Ecadherin antibody</td>
			<td style="width:143px;">BD Transduction Laboratories</td>
			<td style="width:107px;">610181</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">General equipment:</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Sterile dissection tools</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td style="width:245px;">fine scissors and forceps for dissecting the uterus</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Sterile pipettes: 5 ml, 10 ml and 25 ml</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">15-ml and 50-ml conical centrifuge tubes</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;width:272px;">96-well culture plates V-shaped bottom and flat bottom)&#160;</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Culture dishes: 24 wells, 12 wells and 6 wells</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Multichannel pipettes (to pipette 30, 50, 100 and 200 &#956;l)&#160;</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Sterile multichannel reservoirs</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Access to a laminar air flow</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;width:272px;">Access to an incubator at 37&#176;C with 5% CO2</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Access to an inverted microscope</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Access to a bench-top centrifuge</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Access to a stereo microscope with transmitted-light&#160;</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Culture media:</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">MEF Medium:</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td style="width:245px;">stored at 4&#176;C; warm 30 min at 37&#176;C before use</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">&#160;Dulbecco&#8217;s modified Eagle&#8217;s medium (DMEM)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">41965-062</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">10% fetal bovine serum (FBS)</td>
			<td style="width:143px;">Sigma-Aldrich</td>
			<td style="width:107px;">F-7524</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">L-glutamine (2 mM)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">25030-024&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Sodium pyruvate&#160; (0.4 mM)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">11360-039&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">penicillin (100 U/ml)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">15140-122&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">streptomycin (100 &#181;g/ml)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">15140-122&#160;</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">SR-based mESC medium:</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td style="width:245px;">stored at 4&#176;C; warm 30 min at 37&#176;C before use</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">DMEM/F12</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">31330-038</td>
			<td style="width:245px;">mixed in a 1:1 ratio</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">15% knock-out serum replacement (SR )</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">10828&#8211;028</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">L-glutamine (2 mM)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">25030-024&#160;</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">0.1 mM non-essential amino acids&#160;</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">11140-050</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">penicillin (100 U/ml)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">15140-122&#160;</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">streptomycin (100 &#181;g/ml)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">15140-122&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">&#946;-mercaptoethanol (0.1 mM)&#160;</td>
			<td style="width:143px;">Sigma-Aldrich</td>
			<td style="width:107px;">M 3148&#160;</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">2,000 U/ml recombinant mouse LIF&#160;</td>
			<td style="width:143px;">(IRC/VIB Protein Service facility)</td>
			<td style="width:107px;"></td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">FBS-based mESC medium (similar to SR-based mESC medium):</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td style="width:245px;">stored at 4&#176;C; warm 30 min at 37&#176;C before use</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">Knockout DMEM</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">10829-018&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">15% FBS</td>
			<td style="width:143px;">Hyclone</td>
			<td style="width:107px;">SH30070.03E</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Differention Medium</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td style="width:245px;">stored at 4&#176;C; warm 30 min at 37&#176;C before use</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:272px;">Iscove&#39;s Modified Dulbecco&#39;s Medium (IMDM)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">21980-032&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">15% FBS</td>
			<td style="width:143px;">Hyclone</td>
			<td style="width:107px;">SH30070.03E</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">5% CD Hybridoma Medium(1x) liquid&#160;&#160;</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">11279-023&#160;</td>
			<td style="width:245px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">&#160;2 mM L-glutamine</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">25030-024&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">0.4 mM 1-thioglycerol</td>
			<td style="width:143px;">Sigma-Aldrich</td>
			<td style="width:107px;">M-6145</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">50 &#956;g/ml ascorbic acid</td>
			<td style="width:143px;">Sigma-Aldrich</td>
			<td style="width:107px;">A-4544&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">penicillin (100 U/ml)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">15140-122&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">streptomycin (100 &#181;g/ml)</td>
			<td style="width:143px;">Gibco</td>
			<td style="width:107px;">15140-122&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">2i</td>
			<td style="width:143px;"></td>
			<td style="width:107px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">1 &#956;M Erk inhibitor PD0325901&#160;</td>
			<td style="width:143px;">Axon Medchem</td>
			<td style="width:107px;">Axon 1408</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:272px;">3 &#956;M Gsk3 inhibitor CHIR99021</td>
			<td style="width:143px;">Axon Medchem</td>
			<td style="width:107px;">Axon 1386</td>
			<td></td>
		</tr>
	</tbody>
</table>

structure-function studies in mouse embryonic stem cells using recombinase-mediated cassette exchange

Gene engineering in mouse embryos or embryonic stem cells (mESCs) allows for the study of the function of a given protein. Proteins are the workhorses of the cell and often consist of multiple functional domains, which can be influenced by posttranslational modifications. The depletion of the entire protein in conditional or constitutive knock-out (KO) mice does not take into account this functional diversity and regulation. An mESC line and a derived mouse model, in which a docking site for FLPe recombination-mediated cassette exchange (RMCE) was inserted within the ROSA26 (R26) locus, was previously reported. Here, we report on a structure-function approach that allows for molecular dissection of the different functionalities of a multidomain protein. To this end, RMCE-compatible mice must be crossed with KO mice and then RMCE-compatible KO mESCs must be isolated. Next, a panel of putative rescue constructs can be introduced into the R26 locus via RMCE targeting. The candidate rescue cDNAs can be easily inserted between RMCE sites of the targeting vector using recombination cloning. Next, KO mESCs are transfected with the targeting vector in combination with an FLPe recombinase expression plasmid. RMCE reactivates the promoter-less neomycin-resistance gene in the ROSA26 docking sites and allows for the selection of the correct targeting event. In this way, high targeting efficiencies close to 100% are obtained, allowing for insertion of multiple putative rescue constructs in a semi-high throughput manner. Finally, a multitude of R26-driven rescue constructs can be tested for their ability to rescue the phenotype that was observed in parental KO mESCs. We present a proof-of-principle structure-function study in p120 catenin (p120ctn) KO mESCs using endoderm differentiation in embryoid bodies (EBs) as the phenotypic readout. This approach enables the identification of important domains, putative downstream pathways, and disease-relevant point mutations that underlie KO phenotypes for a given protein.

The procedure to isolate RMCE-compatible KO mESC lines is depicted in Figure 2. Two consecutive breedings are required to obtain RMCE-compatible KO blastocysts. First, heterozygous KO mice are crossed with RMCE-compatible mice to obtain RMCE-compatible, heterozygous KO mice. These mice are then used for timed matings with other heterozygous KO mice to obtain 3.5-dpc, RMCE-compatible, homozygous KO blastocysts. The chance of obtaining such an embryo is one in eight, as pre...

Watch this Scientific Journal Video about Structure-function Studies in Mouse Embryonic Stem Cells Using Recombinase-mediated Cassette Exchange at JoVE.com

Structure-function Studies in Mouse Embryonic Stem Cells Using Recombinase-mediated Cassette Exchange

Proteins often contain multiple domains that can exert different cellular functions. Gene knock-outs (KO) do not consider this functional diversity. Here, we report a recombination-mediated cassette exchange (RMCE)-based structure-function approach in KO embryonic stem cells that allows for the molecular dissection of various functional domains or variants of a protein.

Gene engineering in mouse embryos or embryonic stem cells (mESCs) allows for the study of the function of a given protein. Proteins are the workhorses of ...

The overall goal of this structure-function method is to dissect at the molecular level the role of different protein domains, or disease-relevance mutations, in naive or differentiated mouse embryonic stem cells. This method can help to reveal how different residues or domains of a protein can contribute to its function in a given cellular context. The main advantage of this technique is that it allows very efficient targeting of rescue constructs to the genome of knock out embryonic stem cells, or ES cells, and the investigation of their role in different cell types.To achieve this, we combine three highly efficient technologies. These include improved mouse embryonic stem cell isolation, recombination-based targeting factor assembly, and ES cell targeting via recombination-mediated cassette exchange, or RMC. Demonstrating some of the procedures will be Jinke D'Hont, a technician from my laboratory.Recombination-mediated cassette exchange, or RMCE, allows the interchange of DNA fragments between a vector and a genomic locus. RMCE takes advantage of hetero-specific recombination sites that do not cross-react and that are embedded in a genomic locus. In the presence of a donor plasmid that contains a DNA fragment flanked by the same hetero-specific sites, the recombinase will insert this DNA fragment into the RMCE-compatible genomic locus because of double simultaneous translocation.Only upon correct recombination, the trapped promoterless Neomycin-resistance gene in the Rosa 26 docking site, will be restored via a PGK promoter in the incoming targeting vector, which renders drug-resistance. This Neomycin resistance trap system results in a very high targeting efficiency, often close to 100%The day before blastocyst isolation, add 0.1%gelatin, to 12 well-cultured plates. And incubate them at 37 degrees Celsius for five minutes.Aspirate the gelatin solution. Then seed one quarter of a vial of P2 Mouse Embryonic Fibroblasts, or MEFs, into MEF medium, and divide over the 12-well plate. Incubate the 12-well plates of MEFs in two milliliters of MEF medium at 37 degrees Celsius.And grow the cells to a confluent monolayer. Then add 10 micrograms per milliliter of Mitomycin seed to the wells. And incubate the cultures for three hours at 37 degrees Celsius, to inactivate the cells.After selecting heterozygous knock out mice containing an RMCE cassette in the Rosa 26 locus according to the text protocol, set up matings to breed RMCE-compatible heterozygous knock out mice, with heterozygous knock out mice. The following morning, check for copulation plugs by lifting the female by the base of the tale, and examine the vaginal opening for a whitish mass. If the plug is difficult to see, with an angled probe, slightly spread the lips of the vulva, then separate the plugged females from their males.To collect blastocysts at 3.5 days post-coitus, or DPC. After euthanizing the pregnant females, make a mid-ventral incision, and use fine scissors and forceps to dissect the uterus and oviduct. Next, bend a 26-gauge needle into a 45-degree angle attached to a 1 milliliter syringe filled with M2 medium.And insert the needle into the end of the uterus that is closest to the oviduct. Use fine forceps to hold the needle in place while pushing the plunger to flush the blastocysts from the uterus into the lid of a 10 centimeter dish. The uterus will swell, if the flushing is successful.Use a mouth pipette to collect all the embryos in a drop of M2 medium, and wash the embryos twice in a drop of M2 medium. Immediately after washing the embryos, use PBS, to wash the mitomycin-C inactivated cells twice. Then using a mouth pipette, plate each blastocyst onto a separate well of the mitomycin-C treated MEFs, in SRES cell medium, supplemented with pluripotent or 2I.Incubate the cultures at 37 degrees Celsius, and 5%carbon dioxide. Refresh the SREF cell medium every two to three days. Examine each blastocyst under a stereo microscope at 4X magnification, and check for hatching and detachment to the MEF layer.After 10 to 12 days of culture, under a stereo microscope, use a P10 pipette with disposable tips, to pick individual icium outgrowths. Transfer each outgrowth into approximately 10 microliters of medium to a V-shaped 96-well plate, containing 30 microliters per well of PBS. Using a multi-channel pipette, add 50 microliters of 0.25%trypsin to each well.And incubate the plate at 37 degrees Celsius and 5%carbon dioxide for three minutes. Add 100 microliters of pre-incubated FPS-containing ES cell medium, and dissociate the icium outgrowths into single cells by pipetting 10 to 15 times. Then transfer the dissociated cells to mitomycin-C treated 96 well MEF plates.The following day, change the SR-based medium. Expand the ES cells in a similar fashion from 24 to 6-well plates. After identifying rescued CDNA vectors according to the text protocol, prepare a 10 microliter LR reaction using 100 nanograms of rescue CDNA vector, 150 nanograms of pre-excised RMCEDV1 vector, and two microliters of recombinase mix, containing a phage-encoded integrase, an excisionase, and a bacterial integration host factor.Incubate the reaction at 25 degrees Celsius for two hours. To transform the recombined vectors, add 5 microliters of each mixture, to 40 microliters of heat shock competent E.Coli bacteria, in a 2 milliliter skirted screw cap tube. And incubate the sample on ice for 20 minutes.Then incubate the cells at 37 degrees Celsius for five minutes. Add one milliliter of LB medium to the tube, and incubate the cells at 37 degrees Celsius for one hour. Plate 50 microliters on agar plates with ampicillin.And grow at 37 degrees Celsius overnight. Identify colonies with the correct targeting vector by using a P200 tip to randomly pick five colonies. Transfer the tip to a glass test tube containing two to five milliliters of LB medium, and grow overnight at 37 degrees Celsius.After extracting the DNA from each colony, validate the samples by digesting 0.5 to two micrograms of DNA, and separate the samples on a 1%agarose gel. Start a culture of RMCE compatible knock out ES cells, and passage them at least twice on MEFs, in FBS-based ES cell medium. Then split the ES cells on a gelatinized six-well plate.The following day, use 1.5 milliliters of FBS-based ES cell medium to refresh the ES cells that are about 50%confluent. Combine one microgram of pre-excised RMCEDV1 targeting vector, containing rescue CDNA, and one microgram of FLIPe expression plasmid, in 250 microliters of pure DMEM medium. Add seven microliters of lipofectin-based transvection reagent to 250 microliters of pure DMEM medium.And incubate the solution for five minutes at room temperature. Combine the DNA and lipofectin solutions. And incubate the mixture at room temperature for 20 minutes.Then pipette the transvection mixture onto the refreshed ES cells, and gently swirl. One day after transvection, split all ES cells from the tube to a 10-centimeter culture dish, with a confluent layer of DR4 MEFS, and 10 milliliters of FPS-based ES cell medium. Two days after transvection, select ES cell clones with the correct FLIP-e mediated cassette exchange, by adding G418 to the medium.As shown here, massive killing of non-targeted colonies should be visible after three to five days. Colonies should appear after seven to 10 days. Pick these colonies, then expand them, and verify the clones as demonstrated earlier in this video.To differentiate ES cells into embryoid bodies, or EBs, after culturing knock out ES cells with Rosa 26-driven rescue constructs according to the text protocol, allow EBs to form in the non-adherent dishes for 30 days. Refresh the medium every two to three days by transferring the EB suspension to a 50 milliliter tube. And let the EBs settle by gravity.Remove the supernatant, add fresh medium, and transfer the EB suspension to a bacterial-grade dish. Analyze the ES cells and EBs by immunofluorescence and TEM, according to the text protocol. Using the structure function method, five pre-excised RMCEDV1 targeting vectors were generated with an efficiency of 100%and these rescue constructs were targeted via RMCE, to P120 catenin knock out ES cells, with an efficiency of 97%Cystic EB morphology can be used as a phenotypic readout to screen different rescue constructs.As proof of concept, R26-driven P120 catenin isoform 1A rescued the p120 catenin knock out phenotype. To test whether E-cadherin independent membrane anchoring of P120 catenin enabled csytic EB formation, the k-ras membrane targeting motif, CAAX, was fused to the carboxy terminus of P120 catenin, and introduced via RMCE, to P120 catenin knock out ES cells, before EBs were made from them. However, this construct serves a dominant negative that does not allow binding and stabilization of E-cadherin.And as a consequence, does not rescue the p120 catenin knock out phenotype. Epithelial-mesenchymal transition, or EMT, is an essential developmental process that also occurs during ES cell differentiation. When expressed in p120 catenin knock out ES cells, the EMT inducers, ZEB1, ZEB2, or snail that can directly repress various epithelial marker genes like E-cadherin, failed to restore cystic EB formation.Once mastered, RMCE compatible ES cells can be isolated within one month. RMCE compatible targeting vectors can be generated within one week, and targeted rescue of ES cells can be achieved within one month using this technique, if it is performed properly. After watching this video, you should have a good understanding of how to use RMCE to perform structure function studies in naive or differentiated embryonic stem cells.

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Derivation of Cardiac Progenitor Cells from Embryonic Stem Cells

Cardiac progenitor cells (CPCs) have the capacity to differentiate into cardiomyocytes, smooth muscle cells (SMC), and endothelial cells and hold great promise in cell therapy against heart disease. Among various methods to isolate CPCs, differentiation of embryonic stem cell (ESC) into CPCs attracts great attention in the field since ESCs can provide unlimited cell source. As a result, numerous strategies have been developed to derive CPCs from ESCs. In this protocol, differentiation and purification of embryonic CPCs from both mouse and human ESCs is described. Due to the difficulty of using cell surface markers to isolate embryonic CPCs, ESCs are engineered with fluorescent reporters activated by CPC-specific cre recombinase expression. Thus, CPCs can be enriched by fluorescence-activated cell sorting (FACS). This protocol illustrates procedures to form embryoid bodies (EBs) from ESCs for CPC specification and enrichment. The isolated CPCs can be subsequently cultured for cardiac lineage differentiation and other biological assays. This protocol is optimized for robust and efficient derivation of CPCs from both mouse and human ESCs.

In this protocol, derivation of cardiac progenitor cells from both mouse and human embryonic stem cells will be illustrated. A major strategy in this protocol is to enrich cardiac progenitor cells with flow cytometry using fluorescent reporters engineered into the embryonic stem cell lines.

Cardiac progenitor cells (CPCs) have the capacity to differentiate into cardiomyocytes, smooth muscle cells (SMC), and endothelial cells and hold great ...

Neural Differentiation of Mouse Embryonic Stem Cells in Serum-free Monolayer Culture

The ability to differentiate mouse embryonic stem cells (ESC) to neural progenitors allows the study of the mechanisms controlling neural specification as well as the generation of mature neural cell types for further study. In this protocol we describe a method for the differentiation of ESC to neural progenitors using serum-free, monolayer culture. The method is scalable, efficient and results in production of ~70% neural progenitor cells within 4 - 6 days. It can be applied to ESC from various strains grown under a variety of conditions. Neural progenitors can be allowed to differentiate further into functional neurons and glia or analyzed by microscopy, flow cytometry or molecular techniques. The differentiation process is amenable to time-lapse microscopy and can be combined with the use of reporter lines to monitor the neural specification process. We provide detailed instructions on media preparation and cell density optimization to allow the process to be applied to most ESC lines and a variety of cell culture vessels.

This protocol describes in detail the method for generating neural progenitors from embryonic stem cells using a serum-free monolayer method. These progenitors can be used to derive mature neural cell types or to study the process of neural specification and is amenable to multiwell format scaling for compound screening.

The ability to differentiate mouse embryonic stem cells (ESC) to neural progenitors allows the study of the mechanisms controlling neural specification as ...

Generating CRISPR/Cas9 Mediated Monoallelic Deletions to Study Enhancer Function in Mouse Embryonic Stem Cells

Enhancers control cell identity by regulating tissue-specific gene expression in a position and orientation independent manner. These enhancers are often located distally from the regulated gene in intergenic regions or even within the body of another gene. The position independent nature of enhancer activity makes it difficult to match enhancers with the genes they regulate. Deletion of an enhancer region provides direct evidence for enhancer activity and is the gold standard to reveal an enhancer's role in endogenous gene transcription. Conventional homologous recombination based deletion methods have been surpassed by recent advances in genome editing technology which enable rapid and precisely located changes to the genomes of numerous model organisms. CRISPR/Cas9 mediated genome editing can be used to manipulate the genome in many cell types and organisms rapidly and cost effectively, due to the ease with which Cas9 can be targeted to the genome by a guide RNA from a bespoke expression plasmid. Homozygous deletion of essential gene regulatory elements might lead to lethality or alter cellular phenotype whereas monoallelic deletion of transcriptional enhancers allows for the study of cis-regulation of gene expression without this confounding issue. Presented here is a protocol for CRISPR/Cas9 mediated deletion in F1 mouse embryonic stem (ES) cells (Mus musculus129 x Mus castaneus). Monoallelic deletion, screening and expression analysis is facilitated by single nucleotide polymorphisms (SNP) between the two alleles which occur on average every 125 bp in these cells.

Experimental validation of enhancer activity is best approached by loss-of-function analysis. Presented here is an efficient protocol that uses CRISPR/Cas9 mediated deletion to study allele-specific regulation of gene transcription in F1 ES cells which contain a hybrid genome (Mus musculus129 x Mus castaneus).

Enhancers control cell identity by regulating tissue-specific gene expression in a position and orientation independent manner. These enhancers are often ...

The Production of Pluripotent Stem Cells from Mouse Amniotic Fluid Cells Using a Transposon System

Induced pluripotent stem (iPS) cells are generated from mouse and human somatic cells by forced expression of defined transcription factors using different methods. Here, we produced iPS cells from mouse amniotic fluid cells, using a non-viral-based transposon system. All obtained iPS cell lines exhibited characteristics of pluripotent cells, including the ability to differentiate toward derivatives of all three germ layers in vitro and in vivo. This strategy opens up the possibility of using cells from diseased fetuses to develop new therapies for birth defects.

In this study, we generate induced pluripotent stem cells from mouse amniotic fluid cells, using a non-viral-based transposon system.

Induced pluripotent stem (iPS) cells are generated from mouse and human somatic cells by forced expression of defined transcription factors using ...

Single-cell Photoconversion in Living Intact Zebrafish

Animal and plant tissue is composed of distinct populations of cells. These cells interact over time to build and maintain the tissue and can cause disease when disrupted. Scientists have developed clever techniques to investigate characteristics and natural dynamics of these cells within intact tissue by expressing fluorescent proteins in subsets of cells. However, at times, experiments require more selected visualization of cells within the tissue, sometimes at the single-cell or population-of-cells manner. To achieve this and visualize single cells within a population of cells, scientists have utilized single-cell photoconversion of fluorescent proteins. To demonstrate this technique, we show here how to direct UV light to an Eos-expressing cell of interest in an intact, living zebrafish. We then image those photoconverted Eos+ cells 24 h later to determine how they changed in the tissue. We describe two techniques: single cell photoconversion and photoconversions of populations of cell. These techniques can be used to visualize cell-cell interactions, cell-fate and differentiation, and cell migrations, making it a technique that is applicable in numerous biological questions.

Here, we present a protocol to show how cell photoconversion is achieved through UV exposure to specific areas expressing the fluorescent protein, Eos, in living animals.

Animal and plant tissue is composed of distinct populations of cells. These cells interact over time to build and maintain the tissue and can cause ...

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and chromosome dynamics. While the germline is an excellent model, the analysis is often two dimensional due to the time and labor required for three-dimensional analysis. Major readouts in such studies are the number/position of nuclei and protein distribution within the germline. Here, we present a method to perform automated analysis of the germline using confocal microscopy and computational approaches to determine the number and position of nuclei in each region of the germline. Our method also analyzes germline protein distribution that enables the three-dimensional examination of protein expression in different genetic backgrounds. Further, our study shows variations in cytoskeletal architecture in distinct regions of the germline that may accommodate specific spatial developmental requirements. Finally, our method enables automated counting of the sperm in the spermatheca of each germline. Taken together, our method enables rapid and reproducible phenotypic analysis of the C. elegans germline.

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

We present an automated method for three-dimensional reconstruction of the Caenorhabditis elegans germline. Our method determines the number and position of each nucleus within the germline and analyses germline protein distribution and cytoskeletal structure.

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and ...

In Vitro Generation of Somite Derivatives from Human Induced Pluripotent Stem Cells

In response to signals such as WNTs, bone morphogenetic proteins (BMPs), and sonic hedgehog (SHH) secreted from surrounding tissues, somites (SMs) give rise to multiple cell types, including the myotome (MYO), sclerotome (SCL), dermatome (D), and syndetome (SYN), which in turn develop into skeletal muscle, axial skeleton, dorsal dermis, and axial tendon/ligament, respectively. Therefore, the generation of SMs and their derivatives from human induced pluripotent stem cells (iPSCs) is critical to obtain pluripotent stem cells (PSCs) for application in regenerative medicine and for disease research in the field of orthopedic surgery. Although the induction protocols for MYO and SCL from PSCs have been previously reported by several researchers, no study has yet demonstrated the induction of SYN and D from iPSCs. Therefore, efficient induction of fully competent SMs remains a major challenge. Here, we recapitulate human SM patterning with human iPSCs in vitro by mimicking the signaling environment during chick/mouse SM development, and report on methods of systematic induction of SM derivatives (MYO, SCL, D, and SYN) from human iPSCs under chemically defined conditions through the presomitic mesoderm (PSM) and SM states. Knowledge regarding chick/mouse&#160;SM development was successfully applied to the induction of SMs with human iPSCs. This method could be a novel tool for studying human somitogenesis and patterning without the use of embryos and for cell-based therapy and disease modeling.

We present here a protocol for the differentiation of human induced pluripotent stem cells into each somite derivative (myotome, sclerotome, dermatome, and syndetome) in chemically defined conditions, which has applications in future disease modeling and cell-based therapies in orthopedic surgery.

In response to signals such as WNTs, bone morphogenetic proteins (BMPs), and sonic hedgehog (SHH) secreted from surrounding tissues, somites (SMs) give ...

Assessment of Oxidative Damage in the Primary Mouse Ocular Surface Cells/Stem Cells in Response to Ultraviolet-C (UV-C) Damage

The ocular surface is subjected to regular wear and tear due to various environmental factors. Exposure to UV-C radiation constitutes an occupational health hazard. Here, we demonstrate the exposure of primary stem cells from the mouse ocular surface to UV-C radiation. Reactive oxygen species (ROS) formation is the readout of the extent of oxidative stress/damage. In an experimental in vitro setting, it is also essential to assess the percentage of dead cells generated due to oxidative stress. In this article, we will demonstrate the 2&#39;,7&#39;-Dichlorofluoresceindiacetate (DCFDA) staining of UV-C exposed mouse primary ocular surface stem cells and their quantification based on the fluorescent images of DCFDA staining. DCFDA staining directly corresponds to ROS generation. We also demonstrate the quantification of dead and live cells by simultaneous staining with propidium iodide (PI) and Hoechst 3332 respectively and the percentage of DCFDA (ROS positive) and PI positive cells.

Assessment of Oxidative Damage in the Primary Mouse Ocular Surface Cells/Stem Cells in Response to Ultraviolet-C UV-C Damage

This protocol demonstrates the simultaneous detection of reactive oxygen species (ROS), live cells, and dead cells in live primary cultures from mouse ocular surface cells. 2&#39;,7&#39;-Dichlorofluoresceindiacetate, propidium iodide, and Hoechst staining are used to assess the ROS, dead cells, and live cells, respectively, followed by imaging and analysis.

The ocular surface is subjected to regular wear and tear due to various environmental factors. Exposure to UV-C radiation constitutes an occupational ...

Three-dimensional Angiogenesis Assay System using Co-culture Spheroids Formed by Endothelial Colony Forming Cells and Mesenchymal Stem Cells

Studies in the field of angiogenesis have been aggressively growing in the last few decades with the recognition that angiogenesis is a hallmark of more than 50 different pathological conditions, such as rheumatoid arthritis, oculopathy, cardiovascular diseases, and tumor metastasis. During angiogenesis drug development, it is crucial to use in vitro assay systems with appropriate cell types and proper conditions to reflect the physiologic angiogenesis process. To overcome limitations of current in vitro angiogenesis assay systems using mainly endothelial cells, we developed a 3-dimensional (3D) co-culture spheroid sprouting assay system. Co-culture spheroids were produced by two human vascular cell precursors, endothelial colony forming cells (ECFCs) and mesenchymal stem cells (MSCs) with a ratio of 5 to 1. ECFCs+MSCs spheroids were embedded into type I collagen matrix to mimic the in vivo extracellular environment. A real-time cell recorder was utilized to continuously observe the progression of angiogenic sprouting from spheroids for 24 h. Live cell fluorescent labeling technique was also applied to tract the localization of each cell type during sprout formation. Angiogenic potential was quantified by counting the number of sprouts and measuring the cumulative length of sprouts generated from the individual spheroids. Five randomly-selected spheroids were analyzed per experimental group. Comparison experiments demonstrated that ECFCs+MSCs spheroids showed greater sprout number and cumulative sprout length compared with ECFCs-only spheroids. Bevacizumab, an FDA-approved angiogenesis inhibitor, was tested with the newly-developed co-culture spheroid assay system to verify its potential to screen anti-angiogenic drugs. The IC50 value for ECFCs+MSCs spheroids compared to the ECFCs-only spheroids was closer to the effective plasma concentration of bevacizumab obtained from the xenograft tumor mouse model. The present study suggests that the 3D ECFCs+MSCs spheroid angiogenesis assay system is relevant to physiologic angiogenesis, and can predict an effective plasma concentration in advance of animal experiments.

Three-dimensional co-culture spheroid angiogenesis assay system is designed to mimic the physiologic angiogenesis. Co-culture spheroids are formed by two human vascular cell precursors, ECFCs and MSCs, and embedded in collagen gel. The new system is effective for evaluating angiogenic modulators, and provides more relevant information to the in vivo study.

Studies in the field of angiogenesis have been aggressively growing in the last few decades with the recognition that angiogenesis is a hallmark of more ...

Efficient Neural Differentiation using Single-Cell Culture of Human Embryonic Stem Cells

In vitro differentiation of human embryonic stem cells (hESCs) has transformed the ability to study human development on both biological and molecular levels and provided cells for use in regenerative applications. Standard approaches for hESC culture using colony type culture to maintain undifferentiated hESCs and embryoid body (EB) and rosette formation for differentiation into different germ layers are inefficient and time-consuming. Presented here is a single-cell culture method using hESCs instead of a colony-type culture. This method allows maintenance of the characteristic features of undifferentiated hESCs, including expression of hESC markers at levels comparable to colony type hESCs. In addition, the protocol presents an efficient method for neural progenitor cell (NPC) generation from single-cell type hESCs that produces NPCs within 1 week. These cells highly express several NPC marker genes and can differentiate into various neural cell types, including dopaminergic neurons and astrocytes. This single-cell culture system for hESCs will be useful in investigating the molecular mechanisms of these processes, studies of certain diseases, and drug discovery screens.

Presented here is a protocol for the generation of a single-cell culture of human embryonic stem cells and their subsequent differentiation into neural progenitor cells. The protocol is simple, robust, scalable, and suitable for drug screening and regenerative medicine applications.

In vitro differentiation of human embryonic stem cells (hESCs) has transformed the ability to study human development on both biological and molecular ...