Name: using mouse oocytes to assess human gene function during meiosis i
Uploaded: 2018-04-10T15:00:00
Description: Watch this Scientific Journal Video about Using Mouse Oocytes to Assess Human Gene Function During Meiosis I at JoVE.com

This work was supported by a Research Grant from the American Society for Reproductive Medicine and from the Charles and Johanna Busch Memorial Fund at Rutgers, The State University of NJ to K.S. A.L.N. was supported by a grant from the N.I.H. (F31 HD0989597).

1. Molecular Cloning
<ol>
	<li>Obtain full-length coding sequence of the gene of interest and the plasmid in vitro transcription (pIVT) vector11. 
	NOTE: Full-length cDNA clones are commercially available from various vendors or can be generated via reverse transcription polymerase chain reaction (RT-PCR). The National Center for Biotechnology Information (NCBI) online resource provides transcript sequences for genes from the Nucleotide and Expressed sequence tagged (EST) databases...

<ol>
	<li>Thoma, M. E., 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=Prevalence+of+infertility+in+the+United+States+as+estimated+by+the+current+duration+approach+and+a+traditional+constructed+approach.">Prevalence of infertility in the United States as estimated by the current duration approach and a traditional constructed approach.</a> Fertil Steril. 99 (5), 1324-1331 (2013).</li><li>Boivin, J., Bunting, L., Collins, J. A., Nygren, K. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=International+estimates+of+infertility+prevalence+and+treatment-seeking:+potential+need+and+demand+for+infertility+medical+care.">International estimates of infertility prevalence and treatment-seeking: potential need and demand for infertility medical care.</a> Human Reproduction. 22 (6), 1506-1512 (2007).</li><li>Treff, N. R., Zimmerman, R. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+Preimplantation+Genetic+Testing+for+Monogenic+Disease+and+Aneuploidy.">Advances in Preimplantation Genetic Testing for Monogenic Disease and Aneuploidy.</a> Annu Rev Genomics Hum Genet. , (2017).</li><li>Franasiak, J. M., 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+nature+of+aneuploidy+with+increasing+age+of+the+female+partner:+a+review+of+15,169+consecutive+trophectoderm+biopsies+evaluated+with+comprehensive+chromosomal+screening.">The nature of aneuploidy with increasing age of the female partner: a review of 15,169 consecutive trophectoderm biopsies evaluated with comprehensive chromosomal screening.</a> Fertil Steril. 101 (3), 656-663 (2014).</li><li>Hassold, T., Hunt, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=To+err+(meiotically)+is+human:+the+genesis+of+human+aneuploidy.">To err (meiotically) is human: the genesis of human aneuploidy.</a> Nat Rev Genet. 2 (4), 280-291 (2001).</li><li>Scott, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blastocyst+biopsy+with+comprehensive+chromosome+screening+and+fresh+embryo+transfer+significantly+increases+in+vitro+fertilization+implantation+and+delivery+rates:+a+randomized+controlled+trial.">Blastocyst biopsy with comprehensive chromosome screening and fresh embryo transfer significantly increases in vitro fertilization implantation and delivery rates: a randomized controlled trial.</a> Fertil Steril. 100 (3), 697-703 (2013).</li><li>Scott, R. T., Upham, K. M., Forman, E. J., Zhao, T., Treff, N. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cleavage-stage+biopsy+significantly+impairs+human+embryonic+implantation+potential+while+blastocyst+biopsy+does+not:+a+randomized+and+paired+clinical+trial.">Cleavage-stage biopsy significantly impairs human embryonic implantation potential while blastocyst biopsy does not: a randomized and paired clinical trial.</a> Fertil Steril. 100 (3), 624-630 (2013).</li><li>Yang, Z., 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=Selection+of+single+blastocysts+for+fresh+transfer+via+standard+morphology+assessment+alone+and+with+array+CGH+for+good+prognosis+IVF+patients:+results+from+a+randomized+pilot+study.">Selection of single blastocysts for fresh transfer via standard morphology assessment alone and with array CGH for good prognosis IVF patients: results from a randomized pilot study.</a> Mol Cytogenet. 5 (1), 24 (2012).</li><li>Rubio, C., 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=In+vitro+fertilization+with+preimplantation+genetic+diagnosis+for+aneuploidies+in+advanced+maternal+age:+a+randomized,+controlled+study.">In vitro fertilization with preimplantation genetic diagnosis for aneuploidies in advanced maternal age: a randomized, controlled study.</a> Fertil Steril. 107 (5), 1122-1129 (2017).</li><li>Nguyen, A. 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=Identification+and+characterization+of+Aurora+Kinase+B+and+C+variants+associated+with+maternal+aneuploidy.">Identification and characterization of Aurora Kinase B and C variants associated with maternal aneuploidy.</a> Mol Hum Reprod. , (2017).</li><li>Igarashi, H., Knott, J. G., Schultz, R. M., Williams, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alterations+of+PLCbeta1+in+mouse+eggs+change+calcium+oscillatory+behavior+following+fertilization.">Alterations of PLCbeta1 in mouse eggs change calcium oscillatory behavior following fertilization.</a> Dev Biol. 312 (1), 321-330 (2007).</li><li>Database, J. S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Basic+Methods+in+Cellular+and+Molecular+Biology.+Molecular+Cloning.">Basic Methods in Cellular and Molecular Biology. Molecular Cloning.</a> JoVE. , (2017).</li><li>Carey, M. F., Peterson, C. L., Smale, S. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PCR-mediated+site-directed+mutagenesis.">PCR-mediated site-directed mutagenesis.</a> Cold Spring Harb Protoc. 2013 (8), 738-742 (2013).</li><li>Armstrong, J. A., Schulz, J. 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> Current Protocols Essential Laboratory Techniques. , (2008).</li><li>Stein, P., Schindler, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mouse+oocyte+microinjection,+maturation+and+ploidy+assessment.">Mouse oocyte microinjection, maturation and ploidy assessment.</a> J Vis Exp. (53), (2011).</li><li>Watanabe, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Geometry+and+force+behind+kinetochore+orientation:+lessons+from+meiosis.">Geometry and force behind kinetochore orientation: lessons from meiosis.</a> Nat Rev Mol Cell Biol. 13 (6), 370-382 (2012).</li><li>Shuda, K., Schindler, K., Ma, J., Schultz, R. M., Donovan, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aurora+kinase+B+modulates+chromosome+alignment+in+mouse+oocytes.">Aurora kinase B modulates chromosome alignment in mouse oocytes.</a> Mol Reprod Dev. 76 (11), 1094-1105 (2009).</li><li>Lane, S. I., Yun, Y., Jones, K. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Timing+of+anaphase-promoting+complex+activation+in+mouse+oocytes+is+predicted+by+microtubule-kinetochore+attachment+but+not+by+bivalent+alignment+or+tension.">Timing of anaphase-promoting complex activation in mouse oocytes is predicted by microtubule-kinetochore attachment but not by bivalent alignment or tension.</a> Development. 139 (11), 1947-1955 (2012).</li><li>Nguyen, A. 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=Phosphorylation+of+threonine+3+on+histone+H3+by+haspin+kinase+is+required+for+meiosis+I+in+mouse+oocytes.">Phosphorylation of threonine 3 on histone H3 by haspin kinase is required for meiosis I in mouse oocytes.</a> J Cell Sci. 127 (Pt 23), 5066-5078 (2014).</li><li>Tsafriri, A., Chun, S. Y., Zhang, R., Hsueh, A. J., Conti, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oocyte+maturation+involves+compartmentalization+and+opposing+changes+of+cAMP+levels+in+follicular+somatic+and+germ+cells:+studies+using+selective+phosphodiesterase+inhibitors.">Oocyte maturation involves compartmentalization and opposing changes of cAMP levels in follicular somatic and germ cells: studies using selective phosphodiesterase inhibitors.</a> Dev Biol. 178 (2), 393-402 (1996).</li><li>Kapoor, T. M., Mayer, T. U., Coughlin, M. L., Mitchison, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+spindle+assembly+mechanisms+with+monastrol,+a+small+molecule+inhibitor+of+the+mitotic+kinesin,+Eg5.">Probing spindle assembly mechanisms with monastrol, a small molecule inhibitor of the mitotic kinesin, Eg5.</a> Eg5. J Cell Biol. 150 (5), 975-988 (2000).</li><li>Jones, K. T., Lane, S. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+causes+of+aneuploidy+in+mammalian+eggs.">Molecular causes of aneuploidy in mammalian eggs.</a> Development. 140 (18), 3719-3730 (2013).</li><li>Fellmeth, J. E., 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=Expression+and+characterization+of+three+Aurora+kinase+C+splice+variants+found+in+human+oocytes.">Expression and characterization of three Aurora kinase C splice variants found in human oocytes.</a> Mol Hum Reprod. 21 (8), 633-644 (2015).</li><li>Rieder, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+structure+of+the+cold-stable+kinetochore+fiber+in+metaphase+PtK1+cells.">The structure of the cold-stable kinetochore fiber in metaphase PtK1 cells.</a> Chromosoma. 84 (1), 145-158 (1981).</li><li>Brunet, 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=Kinetochore+fibers+are+not+involved+in+the+formation+of+the+first+meiotic+spindle+in+mouse+oocytes,+but+control+the+exit+from+the+first+meiotic+M+phase.">Kinetochore fibers are not involved in the formation of the first meiotic spindle in mouse oocytes, but control the exit from the first meiotic M phase.</a> J Cell Biol. 146 (1), 1-12 (1999).</li><li>Joung, J., 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=Genome-scale+CRISPR-Cas9+knockout+and+transcriptional+activation+screening.">Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening.</a> Nat Protoc. 12 (4), 828-863 (2017).</li><li>Cong, 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=Multiplex+genome+engineering+using+CRISPR/Cas+systems.">Multiplex genome engineering using CRISPR/Cas systems.</a> Science. 339 (6121), 819-823 (2013).</li></ol>

Because of the rapid and increasing identification of human genetic variants associated with disease, it is essential that systems are established to evaluate their biological significance. Understanding protein function in human meiosis poses particular challenges because human oocytes are precious and rare and human sperm are not amenable to genetic manipulation. Mouse oocytes are a mammalian model system valuable for evaluating human meiotic gene function 10,23</sup...

Infertility is a condition that affects 10-15% of the human population of reproductive age 1, from which nearly one-half seek medical treatment 2. Although the etiology of infertility is diverse and in many cases multifactorial, the most common genetic abnormality in humans is embryonic aneuploidy 3. Aneuploidy is defined as the deviation (either gain or loss) of the correct number of chromosomes in a cell. The phenomenon of aneuploidy in human embryos is common and increases with advanced maternal age 4,5. Four randomized controlled trials have highlighted the benefit of selecting only chromosomally normal (euploid) embryos for uterine transfer because this strategy resulted in increased implantation rates, lower miscarriage rates and a shorter time for achieving pregnancy 6,7,8,9. Therefore, understanding the etiology of human aneuploidy can have important implications in assisted reproduction.
Although pre-implantation genetic testing for aneuploidies is beneficial in infertility treatments, a thorough understanding of how aneuploidies originate is still lacking. It is widely accepted that there is a positive correlation of meiotic aneuploidies (originated during gamete production) and maternal age, however, some women present embryonic aneuploidy rates that deviate from the mean rate for their given age 4. These cases suggest that age alone is not always predictive of the risk of generating an aneuploid embryo. Other factors may play a role in increasing the risk of embryonic aneuploidy, such as gene variants.
A key aspect of investigating the potential contribution of a gene variant to aneuploidy during oocyte meiosis is to design a system to rapidly evaluate meiotic gene function. Due to ethical constraints and limited access, it is impractical to perform these experiments using human eggs. These issues can be circumvented by using mouse oocytes, and here a series of assays to assess human gene function during meiosis I are described. By microinjecting the messenger RNA (mRNA) coding for the gene variant of interest, the localization of the human protein in the mouse egg can be visualized and used to determine if the ectopic expression of the wild-type and mutated human protein results in any phenotypic alterations that could lead to aneuploidy. These phenotypes include an increase in microtubules that attach to the improper to sister kinetochore and the inability to support chromosome alignment at metaphase of meiosis I. Importantly, this protocol can be used to investigate both gain and loss of function genetic variants by establishing specific experimental conditions to challenge key events in oocyte meiosis such as spindle building and chromosome alignment 10.

<table>
	<tbody>
		<tr>
			<td>0.2 mL Seal-Rite PCR tube</td>
			<td>USA Scientific</td>
			<td>1602-4300</td>
			<td></td>
		</tr>
		<tr>
			<td>1 kb DNA Ladder</td>
			<td>Thermo Scientific</td>
			<td>SM0313</td>
			<td></td>
		</tr>
		<tr>
			<td>100 bp DNA Ladder</td>
			<td>Thermo Scientific</td>
			<td>SM0243</td>
			<td></td>
		</tr>
		<tr>
			<td>6X DNA loading Dye</td>
			<td>Thermo Scientific</td>
			<td>R0611</td>
			<td></td>
		</tr>
		<tr>
			<td>9-well glass spot plate</td>
			<td>Thomas Scientific</td>
			<td>7812G17</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Sigma Aldrich</td>
			<td>A9539</td>
			<td></td>
		</tr>
		<tr>
			<td>Albumin from bovine serum&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>A3294&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Alexa-fluor-568 conjugated anti-mouse IgG</td>
			<td>Thermo Scientific</td>
			<td>A21050</td>
			<td>1:200 dilution</td>
		</tr>
		<tr>
			<td>Alexa-fluor-633 conjugated anti-human IgG</td>
			<td>Thermo Scientific</td>
			<td>A21091</td>
			<td>1:200 dilution</td>
		</tr>
		<tr>
			<td>Ampicillin</td>
			<td>VWR</td>
			<td>AA0356</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-vibration table</td>
			<td>Technical Manufacturing Corp</td>
			<td></td>
			<td>any standard model</td>
		</tr>
		<tr>
			<td>Anti-Acetylated Tubulin antibody</td>
			<td>Sigma Aldrich</td>
			<td>T7451</td>
			<td>1:100 diution</td>
		</tr>
		<tr>
			<td>Anti-centromeric (CREST) antibody</td>
			<td>Antibodies Incorportated</td>
			<td>15-234</td>
			<td>1:30 dilution&#160;</td>
		</tr>
		<tr>
			<td>Barrier (Filter) Pipette tips</td>
			<td>Thermo Scientific</td>
			<td>AM12635</td>
			<td>Make sure compatable with your brand of pipettors. These are compatible with Eppendorf brand pipettors.&#160;</td>
		</tr>
		<tr>
			<td>BD Difco Dehydrated Culture Media: LB Agar, Miller (Luria Bertani)</td>
			<td>Fisher Scientific</td>
			<td>DF0445-07-6</td>
			<td></td>
		</tr>
		<tr>
			<td>BD Difco Dehydrated Culture Media: LB Broth, Miller (Luria Bertani)</td>
			<td>Fisher Scientific</td>
			<td>DF0446-07-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Capillary tubing</td>
			<td>Sutter</td>
			<td>B100-75-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Center Well organ culture dish</td>
			<td>VWR</td>
			<td>25381-141</td>
			<td></td>
		</tr>
		<tr>
			<td>CO2 tank</td>
			<td></td>
			<td></td>
			<td>For incubator</td>
		</tr>
		<tr>
			<td>Confocal microscope</td>
			<td>Zeiss</td>
			<td></td>
			<td>any standard model</td>
		</tr>
		<tr>
			<td>Centrifuge (With cooling ability)</td>
			<td>Thomas Scientific</td>
			<td></td>
			<td>any standard model&#160;</td>
		</tr>
		<tr>
			<td>Cover Glass 11 x 22 mm</td>
			<td>Thomas Scientific</td>
			<td>6663F10</td>
			<td></td>
		</tr>
		<tr>
			<td>Coverslips</td>
			<td>Thomas Scientific</td>
			<td>6663-F10</td>
			<td>thickness will vary for particular microscopes</td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Sigma Aldrich</td>
			<td>D9542</td>
			<td></td>
		</tr>
		<tr>
			<td>DEPC H20</td>
			<td>Life Technologies</td>
			<td>AM9922</td>
			<td></td>
		</tr>
		<tr>
			<td>Digital Dry Bath</td>
			<td>Thermo Scientific</td>
			<td>888700001</td>
			<td></td>
		</tr>
		<tr>
			<td>Easy A high fidelity cloning enzyme</td>
			<td>Agilent</td>
			<td>600400</td>
			<td>For DNA cloning&#160;</td>
		</tr>
		<tr>
			<td>Enzymes for linearizing pIVT</td>
			<td>New England Biolabs</td>
			<td></td>
			<td>NdeI or KasI can be used</td>
		</tr>
		<tr>
			<td>Ethidium Bromide</td>
			<td>Thermo Scientific</td>
			<td>155585011</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescent Microscope&#160;</td>
			<td></td>
			<td></td>
			<td>Any Fluorescent microscope may be used</td>
		</tr>
		<tr>
			<td>Formaldehyde (37%)</td>
			<td>Thermo Fisher Scientifc</td>
			<td>9311</td>
			<td></td>
		</tr>
		<tr>
			<td>Formaldehyde RNA loading dye</td>
			<td>Ambion</td>
			<td>8552</td>
			<td></td>
		</tr>
		<tr>
			<td>Frosted Microscope Slides (Uncharged) 25X75 mm</td>
			<td>Fisher Scientific</td>
			<td>12-544-3</td>
			<td></td>
		</tr>
		<tr>
			<td>Full Length cDNA Clones</td>
			<td></td>
			<td></td>
			<td>Can be obtained from any vendor that supplies open reading frame clones</td>
		</tr>
		<tr>
			<td>Gel electrophoresis apparatus</td>
			<td>Bio-Rad</td>
			<td></td>
			<td>any standard model</td>
		</tr>
		<tr>
			<td>Glass Pasteur Pipets</td>
			<td>Fisher Scientific</td>
			<td>13-678-200</td>
			<td></td>
		</tr>
		<tr>
			<td>Globin Forward Primer for pIVT Construct</td>
			<td></td>
			<td></td>
			<td>5&#39;- GAA GCT CAG AAT AAA CGC -3&#39;.&#160; Can be purchased from any company that generates custom oligonucelotides</td>
		</tr>
		<tr>
			<td>Globin Reverse Primer for pIVT Construct</td>
			<td></td>
			<td></td>
			<td>5&#39;- ATT CGG GTG TTC TTG AGG CTG G -3&#39; Can be purchased from any company that generates custom oligonucelotides</td>
		</tr>
		<tr>
			<td>Holding pipettes</td>
			<td>Eppendorf</td>
			<td>930001015</td>
			<td>Vacutip</td>
		</tr>
		<tr>
			<td>Humidified Chamber</td>
			<td></td>
			<td></td>
			<td>Tupperware can be used</td>
		</tr>
		<tr>
			<td>Illustra Ready-To-Go RT-PCR beads</td>
			<td>GE Life Sciences</td>
			<td>27925901</td>
			<td></td>
		</tr>
		<tr>
			<td>Incubator</td>
			<td></td>
			<td></td>
			<td>any standard model with CO2 and water jacketed technology</td>
		</tr>
		<tr>
			<td>Inverted Microscope</td>
			<td>Nikon instruments</td>
			<td></td>
			<td>Any Standard model</td>
		</tr>
		<tr>
			<td>Image J (NIH) Software</td>
			<td>NIH</td>
			<td></td>
			<td>Image Analysis software</td>
		</tr>
		<tr>
			<td>Lid of 96 well plate</td>
			<td>Nalgene Nunc International</td>
			<td>263339</td>
			<td></td>
		</tr>
		<tr>
			<td>Low Adhesion 0.5 mL microcentrifgue tube</td>
			<td>USA Scientific</td>
			<td>1405-2600</td>
			<td></td>
		</tr>
		<tr>
			<td>MacVector&#160;</td>
			<td>MacVector</td>
			<td></td>
			<td>Sequence analysis software</td>
		</tr>
		<tr>
			<td>MG132</td>
			<td>Selleckchem</td>
			<td>S2619</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope slides</td>
			<td>Fisher Scientific</td>
			<td>12-544-3&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>Millenium RNA Markers-Formaldehyde&#160;</td>
			<td>Ambion</td>
			<td>AM7151</td>
			<td></td>
		</tr>
		<tr>
			<td>Milrinone</td>
			<td>Sigma-Aldrich</td>
			<td>M4659</td>
			<td>Resuspend in DMSO at 2.5mM</td>
		</tr>
		<tr>
			<td>Mineral Oil</td>
			<td>Sigma-Aldrich</td>
			<td>M5310</td>
			<td>Only used embryo-tested, sterile-filtered</td>
		</tr>
		<tr>
			<td>Monastrol</td>
			<td>Sigma-Aldrich</td>
			<td>M8515</td>
			<td>Resuspend in DMSO at 100 mM</td>
		</tr>
		<tr>
			<td>Mouthpiece</td>
			<td>Biodiseno</td>
			<td>MP-001-Y</td>
			<td></td>
		</tr>
		<tr>
			<td>N2 tank</td>
			<td></td>
			<td></td>
			<td>for antivibration table</td>
		</tr>
		<tr>
			<td>Nail Polish; Clear</td>
			<td></td>
			<td></td>
			<td>Any clear nailpolish can be used</td>
		</tr>
		<tr>
			<td>NanoDrop Microvolume UV-Vis Spectrophotometer</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td>any standard model</td>
		</tr>
		<tr>
			<td>NorthernMax 10X Denaturing Gel Buffer</td>
			<td>Life Technologies</td>
			<td>AM8676</td>
			<td></td>
		</tr>
		<tr>
			<td>NorthernMax 10X Running buffer</td>
			<td>Life Technologies</td>
			<td>AM8671</td>
			<td></td>
		</tr>
		<tr>
			<td>NuPAGE MOPS SDS Running buffer</td>
			<td>Thermo Scnentific</td>
			<td>NP0001</td>
			<td></td>
		</tr>
		<tr>
			<td>Organ Culture Dish 60x15mm</td>
			<td>Life Technologies</td>
			<td>08-772-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Polysciences, Inc.&#160;</td>
			<td>577773</td>
			<td></td>
		</tr>
		<tr>
			<td>PCR Thermal Cycler</td>
			<td>Thermo Fisher Scientific</td>
			<td>4484075</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri Dish 139 mm</td>
			<td>Thermo Fisher Scientifc</td>
			<td>501V</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri dish 35 mm</td>
			<td>Thermo Fisher Scientifc</td>
			<td>121V</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri Dish 60 mm</td>
			<td>Falcon BD</td>
			<td>351007</td>
			<td></td>
		</tr>
		<tr>
			<td>Picoinjector</td>
			<td>XenoWorks Digital Microinjector</td>
			<td></td>
			<td>any standard model</td>
		</tr>
		<tr>
			<td>Pipette puller</td>
			<td>Flaming-Brown Micropipette puller</td>
			<td>Model P-1000</td>
			<td></td>
		</tr>
		<tr>
			<td>pIVT plasmid</td>
			<td>AddGene</td>
			<td>32374</td>
			<td>Empty vector suitable for oocyte expression.</td>
		</tr>
		<tr>
			<td>Pregnant Mare Serum Gonadotropin</td>
			<td>Lee BioSolutions</td>
			<td>493-10</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAprep Spin Miniprep Kit</td>
			<td>Qiagen</td>
			<td>27104</td>
			<td>purification of up to 20 uL of plasmid DNA</td>
		</tr>
		<tr>
			<td>QIAquick PCR purification kit</td>
			<td>Qiagen</td>
			<td>28104</td>
			<td></td>
		</tr>
		<tr>
			<td>Quikchange II site directed mutagenesis kit</td>
			<td>Agilent&#160;</td>
			<td>200523</td>
			<td>mutagenesis kit for insertions and deletions</td>
		</tr>
		<tr>
			<td>Quikchange lightning multi-site directed mutagenesis kit</td>
			<td>Agilent&#160;</td>
			<td>210512</td>
			<td>mutagenesis kit for single site changes</td>
		</tr>
		<tr>
			<td>Scissors (Fine point)</td>
			<td>Fine science tools</td>
			<td>14393</td>
			<td></td>
		</tr>
		<tr>
			<td>Scissors (Medium point)</td>
			<td>Fine science tools</td>
			<td>WP114225</td>
			<td></td>
		</tr>
		<tr>
			<td>Seal-Rite 1.5 mL microcentrifuge tube</td>
			<td>USA Scientific</td>
			<td>1615-5500</td>
			<td></td>
		</tr>
		<tr>
			<td>Slide Warmer</td>
			<td></td>
			<td></td>
			<td>any standard model</td>
		</tr>
		<tr>
			<td>Spectrophotometer (Nanodrop)</td>
			<td>Thermo Fisher Scientific</td>
			<td>ND-ONE-W</td>
			<td></td>
		</tr>
		<tr>
			<td>Stereomicroscope</td>
			<td></td>
			<td></td>
			<td>any standard model</td>
		</tr>
		<tr>
			<td>Subcloning Efficiency DH5a Competent Cells</td>
			<td>Thermo Fisher Scientifc</td>
			<td>18265017</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe</td>
			<td>BD Bioscienes</td>
			<td>309623</td>
			<td>1 ml, 27G(1/2)</td>
		</tr>
		<tr>
			<td>T4 DNA Ligase</td>
			<td>New England Biolabs</td>
			<td>M0202L</td>
			<td></td>
		</tr>
		<tr>
			<td>T7 mMessage Machine high-yield capped RNA transcription kit</td>
			<td>Life Technologies</td>
			<td>AM1340</td>
			<td></td>
		</tr>
		<tr>
			<td>TritonX-100</td>
			<td>Sigma-Aldrich</td>
			<td>x-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Sigma-Aldrich</td>
			<td>274348</td>
			<td></td>
		</tr>
		<tr>
			<td>Tweezer (Fine point- Size 5)</td>
			<td>Fine science tools</td>
			<td>SN.743.12.1</td>
			<td></td>
		</tr>
		<tr>
			<td>UltraPure Dnase/Rnase-Free Distilled Water</td>
			<td>Thermo Fisher Scientifc</td>
			<td>10977015</td>
			<td></td>
		</tr>
		<tr>
			<td>UltraPure Ethidium Bromide 10mg/mL</td>
			<td>Thermo Fisher Scientifc</td>
			<td>15585011</td>
			<td></td>
		</tr>
		<tr>
			<td>UVP UV/White lite transilluminator</td>
			<td>Fisher Scientific</td>
			<td>UV95041501</td>
			<td></td>
		</tr>
		<tr>
			<td>Vectashield Mounting Medium</td>
			<td>Vector Laboratories</td>
			<td>H-1000</td>
			<td></td>
		</tr>
	</tbody>
</table>

using mouse oocytes to assess human gene function during meiosis i

Embryonic aneuploidy is the major genetic cause of infertility in humans. Most of these events originate during female meiosis, and albeit positively correlated with maternal age, age alone is not always predictive of the risk of generating an aneuploid embryo. Therefore, gene variants might account for incorrect chromosome segregation during oogenesis. Given that access to human oocytes is limited for research purposes, a series of assays were developed to study human gene function during meiosis I using mouse oocytes. First, messenger RNA (mRNA) of the gene and gene variant of interest are microinjected into prophase I-arrested mouse oocytes. After allowing time for expression, oocytes are synchronously released into meiotic maturation to complete meiosis I. By tagging the mRNA with a sequence of a fluorescent reporter, such as green fluorescent protein (Gfp), the localization of the human protein can be assessed in addition to the phenotypic alterations. For example, gain or loss of function can be investigated by establishing experimental conditions that challenge the gene product to fix meiotic errors. Although this system is advantageous in investigating human protein function during oogenesis, adequate interpretation of results should be undertaken given that protein expression is not at endogenous levels and, unless controlled for (i.e. knocked out or down), murine homologs are also present in the system.

After in vitro transcription high quality RNA will have an A260/A280 ratio of (1.8-2.2) and an A260/A230 ratio &#8805;1.7 when measured using a spectrophotometer. The picture in Figure 1 shows the migration of in vitro-produced RNA on a denaturing agarose gel after electrophoresis. A band that is smeared in pattern or a sample that has multiple sized bands can indicate contamination or degradation of the sample. Alternatively, multiple bands...

Watch this Scientific Journal Video about Using Mouse Oocytes to Assess Human Gene Function During Meiosis I at JoVE.com

Using Mouse Oocytes to Assess Human Gene Function During Meiosis I

As the genetic variants associated with human disease begin to become uncovered, it is becoming increasingly important to develop systems with which to rapidly evaluate the biological significance of those identified variants. This protocol describes methods for evaluating human gene function during female meiosis I using mouse oocytes.

Embryonic aneuploidy is the major genetic cause of infertility in humans. Most of these events originate during female meiosis, and albeit positively ...

The overall goal of this series of assays is to investigate human gene function during Meiosis I using mouse oocytes. These methods can help answer key questions in the human reproductive field, such as whether there's a genetic predisposition to maternal aneuploidy. The main advantage of this technique is that it uses mouse oocytes as a model for mammalian meiosis, which is useful given the inaccessibility of human eggs for gene function studies.We first had the idea for this method when we sequenced the exomes of women who had undergone in vitro fertilization treatments and who's embryonic aneuploidy rates could not be explained by their maternal age. Visual demonstration of this method is critical, as the image analysis steps are difficult to learn and defining strict analysis parameters is key to rigor and reproducibility. Using a validated cloning strategy, insert the full-length coding sequence of the gene of interest into the multiple cloning region of the in vitro transcription vector.Mutagenize the DNA if generating single nucleotide polymorphisms or insertions and deletions, as described in the text protocol. Next, transform the mutagenized DNA into a bacterial host. Use a kit to isolate and purify the plasmid, following the manufacturer's instructions.Then, linearize the final products using single restriction enzyme digestion of the purified DNA. Purify the digested product using a validated DNA cleanup protocol or a kit. And elute in 30 microliters of RNase/DNase-free water.In vitro, transcribe DNA using T7 polymerase following the manufacturer's protocol. Finally, purify and elute RNA in 30 microliters of RNase/DNase-free water using a silica matrix spin-column based nucleic acid purification kit following the manufacturer's protocol. Divide oocytes into equal groups for microinjection.Microinject one group with experimental mRNA and the other group with the wild-type control NPBs or GFP mRNA. Using a hand or mouth-operated pipetting apparatus where the glass pipette opening is slightly larger than the diameter of an oocyte, transfer oocytes into a 100 microliter drop of milrinone-free culture medium in a Petri dish covered in embryo-quality mineral oil. Then, incubate the oocytes for seven hours at 37 degrees Celsius in 5%CO2 to allow sufficient maturation to metaphase of Meiosis I.After incubation, use the same pipette apparatus to transfer the oocytes into a center-well organ culture dish containing 700 microliters of pre-chilled MEM collection medium in the center well and 500 microliters of water in the outside ring.Place the dish on ice for seven minutes. Fix the oocytes by transferring them into a well of a clear glass spot plate containing 400 microliters of 2%paraformaldehyde in 1x PBS. Incubate for 20 minutes at room temperature.Following immunostaining, as described in the text protocol, image the oocytes using a 40 to 63x objective on a confocal microscope. Capture small steps in the Z-plane optimized for the working objective, and image the entire region of the metaphase spindle. To identify the kinetochore microtubule attachment status, first open the image by dragging the file into the ImageJ toolbar.In the opened Z-series, navigate to the image drop down menu, and under the Color sub tab, click Merge Channels to make all channels visible. It is critical that the analyst be familiar with what type of attachments to kinetochores are possible in mouse oocytes. The quality of the image will greatly influence your ability to properly analyze these data.Using the toggle at the bottom of the image, move through each Z slice and determine kinetochore microtubule attachment. Using the same pipette apparatus, transfer the oocytes into a 100 microliter drop of milrinone-free culture medium under oil. Incubate the oocytes for seven hours to allow sufficient maturation to metaphase of Meiosis I as before.Then, transfer the oocytes to a center-well organ culture dish containing 700 microliters of culture medium containing monastrol in the center well and 400 microliters of water in the surrounding ring. Incubate at 37 degrees Celsius for two hours. Rinse out the monastrol by transferring oocytes through three drops of 100 microliters of CZB culture medium.Then transfer the oocytes to a new center-well organ culture dish containing 700 microliters of culture medium plus proteasome inhibitor in the center ring. Add 400 microliters of water to the outside ring and incubate for three hours. Next, fix the oocytes by transferring them into a well of a clear glass spot plate containing 400 microliters of 2%paraformaldehyde in PBS for 20 minutes at room temperature.Image the oocytes using a 40 to 63x objective on a confocal microscope, capturing less than one micron steps in the Z-plane and making sure to image the entire region of the metaphase spindle. To identify chromosome alignment status, open the image files using imaging software. Then drag the image into the ImageJ control panel.In the open Z-series, use the point tool to mark points at the end of each spindle pole in their respective Z slice by placing the tool over the spindle pole in the image and clicking on the image. Add these points to the ROI Manager by simultaneously pressing the command button and the T button on the keyboard. Determine the specific coordinates for each of the set positions by highlighting the specific point in the ROI Manager and clicking the Measure button.This will provide a Results table containing X and Y coordinates for each point, which are the X1, Y1 and X1, Y2 points, respectively. Next, determine the true Z coordinate. This is done by multiplying the slice number of the specific Z slice in the Z stack in which the spindle pole was identified by the stack thickness.These will be the Z1 and Z2 points, respectively. Determine the spindle length using the Pythagorean theorem equation with the previously defined X, Y, and Z coordinates. Next, determine the spindle midzone.This is calculated as 1/2 the length of the spindle. Click the line icon in the ImageJ toolbar and draw a line that is from one spindle pole to the spindle midzone. The length will be displayed on the ImageJ toolbar.Defining strict chromosome alignment parameters allows for a robust quantitative analysis, important in data reproducibility. Determine the chromosome alignment status by assessing chromosome distance from the spindle midzone using the line measurement tool. Click the line icon in the ImageJ toolbar, and draw a line from the spindle midzone to the chromosome.The length will be displayed on the ImageJ toolbar. Chromosomes greater than four microns from the spindle midzone are considered unaligned. After the oocytes have undergone immunostaining and imaging, correct microtubule kinetochore attachments can be assessed.In a normal attachment, each sister kinetochore pair of the bivalent is attached to spindle microtubules from opposite poles. Up to three different types of abnormal attachments may be observed. One example occurs when there are no microtubules contacting the kinetochore.Alternatively, microtubules can bind incorrectly, producing syntelic or merotelic attachments. Syntelic attachments form with both pairs of sister kinetochores attached to microtubules emanating from a single pole. Merotelic attachments occur when the sister kinetochores in a pair are attached to opposite poles.After oocytes recover from the induced misalignment, the ability for chromosomes to realign is assessed by imaging. In this example, one chromosome bivalent is considered misaligned since it is located at more than four microns from the spindle midzone. When choosing which assay is appropriate for assessing gene variant function, it's important to remember that the human gene variants under study are being overexpressed and that the endogenous mouse homologs may need to be depleted at the same time.Following this procedure, other methods like CRISPR-Cas9 to create humanized mouse's strains can be performed to answer additional questions, such as understanding how the gene variant influences egg and embryo quality and if it impacts reproductive health of the individual. After its development, this technique paved the way for researchers in the field of reproductive genetics to explore other causative factors to maternal aneuploidy in humans. Gene identification could provide powerful diagnostics and a basis for studies at correcting aneuploidies.Thank you for watching. Good luck with your experiments.

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Unit 2

Unit 1

Meiosis

SCIENTISTS IN ACTION

RNA Interference-based Investigation of the Function of Heat Shock Protein 27 during Corneal Epithelial Wound Healing

Small interfering RNA (siRNA) is among the most widely used RNA interference methods for the short-term silencing of protein-coding genes. siRNA is a synthetic RNA duplex created to specifically target a mRNA transcript to induce its degradation and it has been used to identify novel pathways in various cellular processes. Few reports exist regarding the role of phosphorylated heat shock protein 27 (HSP27) in corneal epithelial wound healing. Herein, cultured human corneal epithelial cells were divided into a scrambled control-siRNA transfected group and a HSP27-specific siRNA-transfected group. Scratch-induced directional wounding assays, and western blotting, and flow cytometry were then performed. We conclude that HSP27 has roles in corneal epithelial wound healing that may involve epithelial cell apoptosis and migration. Here, step-by-step descriptions of sample preparation and the study protocol are provided.

Herein, we present a protocol to use heat shock protein 27 (HSP27)-specific small interfering RNA to assess the function of HSP27 during corneal epithelial wound healing. RNA interference is the best method for effectively knocking-down gene expression to investigate protein function in various cell types.

Small interfering RNA (siRNA) is among the most widely used RNA interference methods for the short-term silencing of protein-coding genes. siRNA is a ...

Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell activation, stress, or stimulation. Single-cell multiplex gene expression enables the simultaneous assessment of tens of genes1,2,3. At the single-cell level, multiplex gene expression determines population heterogeneity4,5. It allows for the distinction of population heterogeneity by determining both the probable mix of diverse precursor stages among mature cells and also the diversity of cell responses to stimuli.
Innate lymphoid cells (ILC) have been recently described as a population of innate effectors of the immune response6,7. In this protocol, cell heterogeneity of the ILC hepatic compartment is investigated during homeostasis.
Currently, the most widely used technique to assess gene expression is RT-qPCR. This method measures gene expression only one gene at a time. Additionally, this method cannot estimate heterogeneity of gene expression, since multiple cells are needed for one test. This leads to the measurement of the average gene expression of the population. When assessing large numbers of genes, RT-qPCR becomes a time-, reagent-, and sample-consuming method. Hence, the trade-offs limit the number of genes or cell populations that can be evaluated, increasing the risk of missing the global picture.
This manuscript describes how single-cell multiplex RT-qPCR can be used to overcome these limitations. This technique has benefited from recent microfluidics technological advances1,2. Reactions occurring in multiplex RT-qPCR chips do not exceed the nanoliter-level. Hence, single-cell gene expression, as well as simultaneous multiple gene expression, can be performed in a reagent-, sample-, and cost-effective manner. It is possible to test cell gene signature heterogeneity at the clonal level between cell subsets within a population at different developmental stages or under different conditions4,5. Working on rare populations with large numbers of conditions at the single-cell level is no longer a restriction.

This protocol describes how to assess the expression of a large array of genes at the clonal level. Single-cell RT-qPCR produces highly reliable results with a strong sensitivity for hundreds of samples and genes.

Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell ...

Retroviral Scanning: Mapping MLV Integration Sites to Define Cell-specific Regulatory Regions

Moloney murine leukemia (MLV) virus-based retroviral vectors integrate predominantly in acetylated enhancers and promoters. For this reason, mLV integration sites can be used as functional markers of active regulatory elements. Here, we present a retroviral scanning tool, which allows the genome-wide identification of cell-specific enhancers and promoters. Briefly, the target cell population is transduced with an mLV-derived vector and genomic DNA is digested with a frequently cutting restriction enzyme. After ligation of genomic fragments with a compatible DNA linker, linker-mediated polymerase chain reaction (LM-PCR) allows the amplification of the virus-host genome junctions. Massive sequencing of the amplicons is used to define the mLV integration profile genome-wide. Finally, clusters of recurrent integrations are defined to identify cell-specific regulatory regions, responsible for the activation of cell-type specific transcriptional programs.
The retroviral scanning tool allows the genome-wide identification of cell-specific promoters and enhancers in prospectively isolated target cell populations. Notably, retroviral scanning represents an instrumental technique for the retrospective identification of rare populations (e.g. somatic stem cells) that lack robust markers for prospective isolation.

Here, we describe a protocol for genome-wide mapping of the integration sites of Moloney murine leukemia virus-based retroviral vectors in human cells.

Moloney murine leukemia (MLV) virus-based retroviral vectors integrate predominantly in acetylated enhancers and promoters. For this reason, mLV ...

A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells

Combinatorial gene editing using CRISPR/Cas9 and single-stranded oligonucleotides is an effective strategy for the correction of single-base point mutations, which often are responsible for a variety of human inherited disorders. Using a well-established cell-based model system, the point mutation of a single-copy mutant eGFP gene integrated into HCT116 cells has been repaired using this combinatorial approach. The analysis of corrected and uncorrected cells reveals both the precision of gene editing and the development of genetic lesions, when indels are created in uncorrected cells in the DNA sequence surrounding the target site. Here, the specific methodology used to analyze this combinatorial approach to the gene editing of a point mutation, coupled with a detailed experimental strategy to measuring indel formation at the target site, is outlined. This protocol outlines a foundational approach and workflow for investigations aimed at developing CRISPR/Cas9-based gene editing for human therapy. The conclusion of this work is that on-site mutagenesis takes place as a result of CRISPR/Cas9 activity during the process of point mutation repair. This work puts in place a standardized methodology to identify the degree of mutagenesis, which should be an important and critical aspect of any approach destined for clinical implementation.

This protocol outlines the workflow of a CRISPR/Cas9-based gene editing system for the repair of point mutations in mammalian cells. Here, we use a combinatorial approach to gene editing with a detailed follow-on experimental strategy for measuring indel formation at the target site&#8212;in essence, analyzing onsite mutagenesis.

Combinatorial gene editing using CRISPR/Cas9 and single-stranded oligonucleotides is an effective strategy for the correction of single-base point ...

Highly Efficient Gene Disruption of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9

Advances in the hematopoietic stem cell (HSCs) field have been aided by methods to genetically engineer primary progenitor cells as well as animal models. Complete gene ablation in HSCs required the generation of knockout mice from which HSCs could be isolated, and gene ablation in primary human HSCs was not possible. Viral transduction could be used for knock-down approaches, but these suffered from variable efficacy. In general, genetic manipulation of human and mouse hematopoietic cells was hampered by low efficiencies and extensive time and cost commitments. Recently, CRISPR/Cas9 has dramatically expanded the ability to engineer the DNA of mammalian cells. However, the application of CRISPR/Cas9 to hematopoietic cells has been challenging, mainly due to their low transfection efficiencies, the toxicity of plasmid-based approaches and the slow turnaround time of virus-based protocols.
A rapid method to perform CRISPR/Cas9-mediated gene editing in murine and human hematopoietic stem and progenitor cells with knockout efficiencies of up to 90% is provided in this article. This approach utilizes a ribonucleoprotein (RNP) delivery strategy with a streamlined three-day workflow. The use of Cas9-sgRNA RNP allows for a hit-and-run approach, introducing no exogenous DNA sequences in the genome of edited cells and reducing off-target effects. The RNP-based method is fast and straightforward: it does not require cloning of sgRNAs, virus preparation or specific sgRNA chemical modification. With this protocol, scientists should be able to successfully generate knockouts of a gene of interest in primary hematopoietic cells within a week, including downtimes for oligonucleotide synthesis. This approach will allow a much broader group of users to adapt this protocol for their needs.

A protocol for fast CRISPR/Cas9-mediated gene disruption in mouse and human primary hematopoietic cells is described in this article. Cas9-sgRNA ribonucleoproteins are introduced via electroporation with sgRNAs generated through in vitro transcription and commercial Cas9. High editing efficiencies are achieved with limited time and financial cost.

Advances in the hematopoietic stem cell (HSCs) field have been aided by methods to genetically engineer primary progenitor cells as well as animal models. ...

CRISPR/Cas9 Gene Editing to Make Conditional Mutants of Human Malaria Parasite P. falciparum

Malaria is a significant cause of morbidity and mortality worldwide. This disease, which primarily affects those living in tropical and subtropical regions, is caused by infection with Plasmodium parasites. The development of more effective drugs to combat malaria can be accelerated by improving our understanding of the biology of this complex parasite. Genetic manipulation of these parasites is key to understanding their biology; however, historically the genome of P. falciparum has been difficult to manipulate. Recently, CRISPR/Cas9 genome editing has been utilized in malaria parasites, allowing for easier protein tagging, generation of conditional protein knockdowns, and deletion of genes. CRISPR/Cas9 genome editing has proven to be a powerful tool for advancing the field of malaria research. Here, we describe a CRISPR/Cas9 method for generating glmS-based conditional knockdown mutants in P. falciparum. This method is highly adaptable to other types of genetic manipulations, including protein tagging and gene knockouts.

CRISPR/Cas9 Gene Editing to Make Conditional Mutants of Human Malaria Parasite P. falciparum

We describe a method for generating glmS-based conditional knockdown mutants in Plasmodium falciparum using CRISPR/Cas9 genome editing.

Malaria is a significant cause of morbidity and mortality worldwide. This disease, which primarily affects those living in tropical and subtropical ...

The Use of Mouse Splenocytes to Assess Pathogen-associated Molecular Pattern Influence on Clock Gene Expression

From behavior to gene expression, circadian rhythms regulate nearly all aspects of physiology. Here, we present a methodology to challenge mouse splenocytes with the pathogen-associated molecular patterns (PAMPs) lipopolysaccharide (LPS), ODN1826, and heat-killed Listeria monocytogenes and examine their effect on the molecular circadian clock. Previously, studies have focused on examining the influence of LPS on the molecular clock using a variety of in vivo and ex vivo approaches from an assortment of models (e.g., mouse, rat, and human). This protocol describes the isolation and challenge of splenocytes, as well as the methodology to assess clock gene expression post-challenge via quantitative PCR. This approach can be used to assess not only the influence of microbial components on the molecular clock but other molecules as well that may alter expression of the clock. This approach could be utilized to tease apart the molecular mechanism of how PAMP-Toll-like receptor interaction influences clock expression.

This protocol describes a technique using mouse splenocytes to discover pathogen-associated molecular patterns that alter molecular clock gene expression.

From behavior to gene expression, circadian rhythms regulate nearly all aspects of physiology. Here, we present a methodology to challenge mouse ...

Manipulation of Gene Function in Mexican Cavefish

Cave animals provide a compelling system for investigating the evolutionary mechanisms and genetic bases underlying changes in numerous complex traits, including eye degeneration, albinism, sleep loss, hyperphagia, and sensory processing. Species of cavefish from around the world display a convergent evolution of morphological and behavioral traits due to shared environmental pressures between different cave systems. Diverse cave species have been studied in the laboratory setting. The Mexican tetra, Astyanax mexicanus, with sighted and blind forms, has provided unique insights into biological and molecular processes underlying the evolution of complex traits and is well-poised as an emerging model system. While candidate genes regulating the evolution of diverse biological processes have been identified in A. mexicanus, the ability to validate a role for individual genes has been limited. The application of transgenesis and gene-editing technology has the potential to overcome this significant impediment and to investigate the mechanisms underlying the evolution of complex traits. Here, we describe a different methodology for manipulating gene expression in A. mexicanus. Approaches include the use of morpholinos, Tol2 transgenesis, and gene-editing systems, commonly used in zebrafish and other fish models, to manipulate gene function in A. mexicanus. These protocols include detailed descriptions of timed breeding procedures, the collection of fertilized eggs, injections, and the selection of genetically modified animals. These methodological approaches will allow for the investigation of the genetic and neural mechanisms underlying the evolution of diverse traits in A. mexicanus.&#160;

We describe approaches for the manipulation of genes in the evolutionary model system Astyanax mexicanus. Three different techniques are described: Tol2-mediated transgenesis, targeted manipulation of the genome using CRISPR/Cas9, and knockdown of expression using morpholinos. These tools should facilitate the direct investigation of genes underlying the variation between surface- and cave-dwelling forms.

Cave animals provide a compelling system for investigating the evolutionary mechanisms and genetic bases underlying changes in numerous complex traits, ...

Overexpressing Long Noncoding RNAs Using Gene-activating CRISPR

Long noncoding RNA (lncRNA) biology is a new and exciting field of research, with the number of publications from this field growing exponentially since 2007. These studies have confirmed that lncRNAs are altered in almost all diseases. However, studying the functional roles for lncRNAs in the context of disease remains difficult due to the lack of protein products, tissue-specific expression, low expression levels, complexities in splice forms, and lack of conservation among species. Given the species-specific expression, lncRNA studies are often restricted to human research contexts when studying disease processes. Since lncRNAs function at the molecular level, one way to dissect lncRNA biology is to either remove the lncRNA or overexpress the lncRNA and measure cellular effects. In this article, a written and visualized protocol to overexpress lncRNAs in vitro is presented. As a representative experiment, an lncRNA associated with inflammatory bowel disease, Interferon Gamma Antisense 1 (IFNG-AS1), is shown to be overexpressed in a Jurkat T-cell model. To accomplish this, the activating clustered regularly interspaced short palindromic repeats (CRISPR) technique is used to enable overexpression at the endogenous genomic loci. The activating CRISPR technique targets a set of transcription factors to the transcriptional start site of a gene, enabling a robust overexpression of multiple lncRNA splice forms. This procedure will be broken down into three steps, namely (i) guide RNA (gRNA) design and vector construction, (ii) virus generation and transduction, and (iii) colony screening for overexpression. For this representative experiment, a greater than 20-fold enhancement in IFNG-AS1 in Jurkat T cells was observed.

Traditional cDNA-based overexpression techniques have a limited applicability for the overexpression of long noncoding RNAs due to their multiple splice forms with potential functionality. This review reports a protocol using CRISPR technology to overexpress multiple splice variants of a long noncoding RNA.

Long noncoding RNA (lncRNA) biology is a new and exciting field of research, with the number of publications from this field growing exponentially since ...

Lentiviral Mediated Gene Silencing in Human Pseudoislet Prepared in Low Attachment Plates

Various genetic tools are available to modulate genes in pancreatic islets of rodents to dissect function of islet genes for diabetes research. However, the data obtained from rodent islets are often not fully reproduced in or applicable to human islets due to well-known differences in islet structure and function between the species. Currently, techniques that are available to manipulate gene expression of human islets are very limited. Introduction of transgene into intact islets by adenovirus, plasmid, and oligonucleotides often suffers from low efficiency and high toxicity. Low efficiency is especially problematic in gene downregulation studies in intact islets, which require high efficiency. It has been known that enzymatically-dispersed islet cells reaggregate in culture forming spheroids termed pseudoislets. Size-controlled reaggregation of human islet cells creates pseudoislets that maintain dynamic first phase insulin secretion after prolonged culture and provide a window to efficiently introduce lentiviral short hairpin RNA (shRNA) with low toxicity. Here, a detailed protocol for the creation of human pseudoislets after lentiviral transduction using two commercially available multiwell plates is described. The protocol can be easily performed and allows for efficient downregulation of genes and assessment of dynamism of insulin secretion using human islet cells. Thus, human pseudoislets with lentiviral mediated gene modulation provide a powerful and versatile model to assess gene function within human islet cells.

A protocol to create gene modified human pseudoislets from dispersed human islet cells that are transduced by lentivirus carrying short hairpin RNA (shRNA) is presented. This protocol utilizes readily available enzyme and culture vessels, can be performed easily, and produces genetically modified human pseudoislets suitable for functional and morphological studies.

Various genetic tools are available to modulate genes in pancreatic islets of rodents to dissect function of islet genes for diabetes research. However, ...