This work is supported in part by funds provided by The University of North Carolina at Charlotte, Wachovia foundation fund for faculty excellence, and a grant from NIGMS (R15GM101571).

1. LSE Preparation
<ol>
 <li>Female frogs (Xenopus laevis) are injected twice for egg collection. The first injection (priming) is 100 U PMSG (Pregnant Mare Serum Gonadotropin) per frog. Frogs must be primed at least two days before inducing egg laying and primed frogs are usable for up to two weeks. To prime frogs, inject PMSG subcutaneously in the dorsal lymph sacs using a 3 ml syringe and 27 G needle.</li>
 <li>To induce egg laying, inject 500 U hCG (human Chorionic Gonadotrophin) per primed frog subcutaneously in the dorsal lymph sacs using a 27 G needle. Incubate injected frogs in separate buckets containing 2 liters of 1x Marc's modified Ringer's solution (MMR). Allow frogs 14-20 hr to lay eggs before collection.</li>
 <li>Remove the frogs from the buckets and pour off the MMR solution until around 100 ml is left. Obtain eggs from the buckets by transferring eggs to a 250 ml beaker.</li>
 <li>Dejelly eggs by adding 100 ml of 2% cysteine (adjust pH to 7.8 with 10 M KOH). Gently swirl the eggs with an inverted glass Pasteur pipet (0.7 cm in diameter) approximately every 30 sec. Decant and replace with fresh cysteine twice during incubation. The dejellying process is complete in about 5-15 min when the eggs form a more condensed layer at the bottom of the beaker.</li>
 <li>Discard the cysteine solution and wash eggs three times with 0.25x MMR. Swirl the eggs in the solution by a glass pipet. "Bad" eggs are determined by simple visual inspection and are "puffy" white in appearance. The "bad" eggs will accumulate at the center of the beaker after swirling. Remove "bad" eggs by a Pasteur pipet.</li>
 <li>Wash eggs with Egg Lysis Buffer (ELB) three times. Remove any additional "bad" eggs by a Pasteur pipet. Pour eggs into a 14 ml Falcon tube.</li>
 <li>Spin the Falcon tube for 55 sec at 188 x g (1,100 rpm) using the CL2 IEC clinical table-top centrifuge with a swinging bucket rotor to compact the eggs. Remove excess buffer from the top of the egg layer. Add 0.5 &mu;l of Aprotinin/Leupeptin stock and 0.5 &mu;l of Cytochalasin B stock per ml of compacted eggs.</li>
 <li>Centrifuge eggs at 16,500 x g (10,000 rpm) for 15 min at 4 &deg;C using the Sorvall RC6 plus superspeed centrifuge with HB6 swinging bucket rotor. After centrifugation, eggs are fractionated into three layers in the tube: lipid, extract, and yolk/pigment from top to bottom, respectively. Puncture the side of the Falcon tube in the lower portion of the middle extract layer with a 21 G needle. Carefully remove the needle as the puncturing needle may be obstructed by plastic. Insert a fresh 21 G needle attached to a 1 ml syringe into the puncture site to collect the extract. Slowly aspirate the extract into syringe to avoid air bubbles and contamination with the lipid and yolk/pigment layers.</li>
 <li>Place the extracts into a chilled 1.5 ml microcentrifuge tube. For each milliliter of egg extract, add the following chemical stock solutions to the indicated final concentration (shown in parentheses): (1) 10 &mu;l Cycloheximide (100 &mu;g/ml); (2) 1 &mu;l Aprotinin/Leupeptin (10 &mu;g/ml each); (3) 1 &mu;l Cytochalasin B (5 &mu;g/ml); (4) 1 &mu;l Dithiothreitol (1 mM); and (5) 0.33 &mu;l Nocodazole (3 &mu;g/ml). Invert the egg extract at least 10 times gently. This is the LSE, which must be made fresh and used within 4 hr. The quality of LSE is compromised after 4 hr or freeze-thaw.</li>
</ol>
2. Treatment of Sperm Chromatin with DNA Damaging Approaches
<ol>
 <li>Prepare normal sperm chromatin according to the method described previously 13.</li>
 <li>Prepare MMS-treated sperm chromatin
 <ol>
 <li>Resuspend normal sperm chromatin in 0.5 ml Buffer X.</li>
 <li>Add ~ 5.5 &mu;l of MMS (9.1 M in stock) to 500 &mu;l resuspended chromatin to a final concentration of 100 mM.</li>
 <li>Incubate sperm chromatin in microcentrifuge tube at room temperature for 30 min with rotation.</li>
 <li>Spin the microcentrifuge tube at 686 x g (2,100 rpm) for 10 min at room temperature using the IEC CL2 clinical centrifuge with swinging bucket rotor and tube adaptors.</li>
 <li>Discard supernatant and resuspend the pellet in 0.5 ml of Buffer X plus BSA (3%), DTT (0.1 mM) and Aprotinin/Leupeptin (10 &mu;g/ml each).</li>
 <li>Repeat steps (4) and (5) twice to wash the sperm chromatin.</li>
 <li>Determine the concentration of sperm chromatin with a hemocytometer and dilute to 100,000 sperm/&mu;l. Save 5 &mu;l aliquots in -80 &deg;C freezer for further use.</li>
 </ol>
 </li>
 <li>Prepare UV-treated sperm chromatin
 <ol>
 <li>Add desired amount (e.g. 10 &mu;l) of normal sperm chromatin on the surface of a piece of Parafilm.</li>
 <li>Place the Parafilm into a UV crosslinker. Set desired energy parameter, depending on your experiment, and start to damage the sperm chromatin via UV light. For example, it takes approximately 21 sec to reach 1,000 J/m2.</li>
 <li>After UV irradiation, UV-treated sperm chromatin should be added to egg extracts immediately.</li>
 </ol>
 </li>
</ol>
3. Preparation of a DNA Damage-mimicking Structure (AT70)
<ol>
 <li>Dissolve two synthetic oligonucleotides poly-(dA)70 (designated as A70) and poly-(dT)70 (designated as T70) in water to a concentration of 2 &mu;g/&mu;l, respectively.</li>
 <li>Add 100 &mu;l of A70 and 100 &mu;l of T70 to one 1.5 ml microcentrifuge tube. Boil mixed synthetic oligo solution for 5 min at 95 &deg;C in a heatblock.</li>
 <li>Take the dry bath block out (with the tube containing AT mixture in it), and let it cool down to room temperature on a lab bench. This temperature adjustment takes around 45-60 min.</li>
 <li>The cooled mixture is AT70 with a final concentration of 2 &mu;g/&mu;l. Store 10 &mu;l of AT70 aliquots in -20 &deg;C freezer for further use.</li>
</ol>
4. Triggering the DNA Damage Checkpoint in LSE with Damaged Sperm Chromatin or a DNA Damage-mimicking Structure
<ol>
 <li>Induce DNA damage checkpoint in LSE with damaged sperm chromatin
 <ol>
 <li>Add 50 &mu;l of LSE to a 1.5 ml microcentrifuge tube and complement it with 1 &mu;l of Energy Mixture and 2 &mu;l of damaged sperm chromatin (final concentration ~4,000 sperm/&mu;l reaction).</li>
 <li>Incubate the reaction tube at room temperature for 90 min and flick the tube every 10 min.</li>
 <li>Dispense 1 &mu;l of reaction mixture onto a microscope slide supplemented with 1 &mu;l of nuclear dye solution after 30-min incubation. Place a cover slip over the reaction mixture and check for nuclei formation via fluorescence microscope. Typically, round nuclei will form after 30 min of incubation, indicating DNA replication has initiated.</li>
 <li>Take 10 &mu;l of the reaction mixture into 90 &mu;l of sample buffer. Samples are analyzed via immunoblotting using anti-Chk1 P-S344 or anti-Chk1 antibodies.</li>
 </ol>
 </li>
 <li>Induce DNA damage checkpoint in LSE with the AT70
 <ol>
 <li>Add 50 &mu;l of LSE to a 1.5 ml microcentrifuge tube supplemented with 1 &mu;l of Energy Mixture and 1.6 &mu;l of Tautomycin stock.</li>
 <li>Add 1.25 &mu;l of pre-made AT70 (2 &mu;g/&mu;l) or water (as negative control) to each reaction. Incubate the reactions at room temperature for 90 min. Flick the reaction tubes every 10 min.</li>
 <li>Add 10 &mu;l of the reaction mixture into 90 &mu;l of sample buffer. Samples are examined via immunoblotting using anti-Chk1 P-S344 or anti-Chk1 antibodies.</li>
 </ol>
 </li>
</ol>
5. Representative Results
The damaged sperm chromatin or DNA damage-mimicking structure can trigger the ATR/Chk1-mediated DNA damage checkpoint in the Xenopus egg extract system. Figure 2A shows that MMS induces Chk1 phosphorylation at Ser344 (Chk1 P-S344), which is an indicator of ATR kinase activation. Figure 2B shows that AT70, as a DNA damage-mimicking structure, also triggers Chk1 phosphorylation. Total Chk1 samples are used as loading controls in both examples.
<img alt="Figure 1" src="/files/ftp_upload/4449/4449fig1.jpg" /> 
Figure 1. A diagram of the DNA damage checkpoint signaling.
<img alt="Figure 2" src="/files/ftp_upload/4449/4449fig2.jpg" /> 
Figure 2. Chk1 phosphorylation is induced by either MMS or AT70 treatments in Xenopus egg extracts. (A) MMS-damaged sperm chromatin (MMS) or normal sperm chromatin (Con) are incubated in egg extracts for 90 min. Chk1 phosphorylation at Ser344 (Chk1 P-S344) and total Chk1 in egg extracts are examined via immunoblotting. (B) AT70 or water (Con) are added into egg extracts, respectively. Samples are also analyzed via immunoblotting as in (A).

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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+the+ATR-mediated+checkpoint+using+Xenopus+egg+extracts.">Analyzing the ATR-mediated checkpoint using Xenopus egg extracts.</a> Methods. 41 (2), 222-231 (2007).</li><li>Lupardus, P. J., Byun, T., Yee, M. C., Hekmat-Nejad, M., Cimprich, K. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+requirement+for+replication+in+activation+of+the+ATR-dependent+DNA+damage+checkpoint.">A requirement for replication in activation of the ATR-dependent DNA damage checkpoint.</a> Genes Dev. 16 (18), 2327-2332 (2002).</li><li>Stokes, M. P., Van Hatten, R., Lindsay, H. D., Michael, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+replication+is+required+for+the+checkpoint+response+to+damaged+DNA+in+Xenopus+egg+extracts.">DNA replication is required for the checkpoint response to damaged DNA in Xenopus egg extracts.</a> J. Cell Biol. 158 (5), 863-872 (2002).</li><li>Kato, K., Strauss, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Accumulation+of+an+intermediate+in+DNA+synthesis+by+HEp.2+cells+treated+with+methyl+methanesulfonate.">Accumulation of an intermediate in DNA synthesis by HEp.2 cells treated with methyl methanesulfonate.</a> Proc. Natl. Acad. Sci. U.S.A. 71 (5), 1969-1973 (1974).</li><li>Paulovich, A. G., Hartwell, L. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+checkpoint+regulates+the+rate+of+progression+through+S+phase+in+S.+cerevisiae+in+response+to+DNA+damage.">A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage.</a> Cell. 82 (5), 841-847 (1995).</li><li>Guo, Z., Kumagai, A., Wang, S. X., Dunphy, W. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Requirement+for+Atr+in+phosphorylation+of+Chk1+and+cell+cycle+regulation+in+response+to+DNA+replication+blocks+and+UV-damaged+DNA+in+Xenopus+egg+extracts.">Requirement for Atr in phosphorylation of Chk1 and cell cycle regulation in response to DNA replication blocks and UV-damaged DNA in Xenopus egg extracts.</a> Genes Dev. 14 (21), 2745-2756 (2000).</li><li>Jazayeri, A., Balestrini, A., Garner, E., Haber, J. E., Costanzo, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mre11-Rad50-Nbs1-dependent+processing+of+DNA+breaks+generates+oligonucleotides+that+stimulate+ATM+activity.">Mre11-Rad50-Nbs1-dependent processing of DNA breaks generates oligonucleotides that stimulate ATM activity.</a> EMBO. J. 27 (14), 1953-1962 (2008).</li><li>Kumagai, A., Dunphy, W. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Claspin,+a+novel+protein+required+for+the+activation+of+Chk1+during+a+DNA+replication+checkpoint+response+in+Xenopus+egg+extracts.">Claspin, a novel protein required for the activation of Chk1 during a DNA replication checkpoint response in Xenopus egg extracts.</a> Mol. Cell. 6 (4), 839-849 (2000).</li><li>Yan, S., Lindsay, H. D., Michael, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+requirement+for+Xmus101+in+ATR-mediated+phosphorylation+of+Claspin+bound+Chk1+during+checkpoint+signaling.">Direct requirement for Xmus101 in ATR-mediated phosphorylation of Claspin bound Chk1 during checkpoint signaling.</a> J. Cell Biol. 173 (2), 181-186 (2006).</li><li>Shiotani, B., Zou, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-stranded+DNA+orchestrates+an+ATM-to-ATR+switch+at+DNA+breaks.">Single-stranded DNA orchestrates an ATM-to-ATR switch at DNA breaks.</a> Mol. Cell. 33 (5), 547-558 (2009).</li><li>Tutter, A. V., Walter, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromosomal+DNA+replication+in+a+soluble+cell-free+system+derived+from+Xenopus+eggs.">Chromosomal DNA replication in a soluble cell-free system derived from Xenopus eggs.</a> Methods Mol. Biol. 322, 121-137 (2006).</li><li>Cross, M. K., Powers, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+and+Fractionation+of+Xenopus+laevis+Egg+Extracts.">Preparation and Fractionation of Xenopus laevis Egg Extracts.</a> J. Vis. Exp. (18), e891 (2008).</li></ol>

No conflicts of interest declared.

There are several advantages in studying the DNA damage checkpoint using Xenopus egg extracts. The use of egg extracts provides a large quantity of cell-free extracts synchronized at interphase of the cell cycle. The egg extracts can be easily and inexpensively made. It is relatively easy to damage DNA or chromatin and to reveal a defect in the DNA damage checkpoint after immunodepleting a target protein from egg extract. Subsequently, a potential function defect can be "rescued" by addback of wild type or muta...

<table border="1">
 <tbody>
 <tr>
 <td></td>
 <td></td>
 <td></td>
 <td>Reagents</td>
 </tr>
 <tr>
 <td>Anti-Chk1 P-S344 antibody</td>
 <td>Cell Signaling</td>
 <td>2348L</td>
 <td></td>
 </tr>
 <tr>
 <td>Anti-Chk1 antibody</td>
 <td>Santa Cruz</td>
 <td>SC7898</td>
 <td></td>
 </tr>
 <tr>
 <td>Aprotinin</td>
 <td>MP Biomedicals</td>
 <td>0219115880</td>
 <td></td>
 </tr>
 <tr>
 <td>Cycloheximide</td>
 <td>Sigma</td>
 <td>C7698-5G</td>
 <td></td>
 </tr>
 <tr>
 <td>Cytochalasin B</td>
 <td>EMD</td>
 <td>250233</td>
 <td></td>
 </tr>
 <tr>
 <td>Dithiothreitol (DTT)</td>
 <td>VWR</td>
 <td>JTF780-2</td>
 <td></td>
 </tr>
 <tr>
 <td>hCG</td>
 <td>Sigma</td>
 <td>CG10-10VL</td>
 <td></td>
 </tr>
 <tr>
 <td>L-Cysteine</td>
 <td>Sigma</td>
 <td>C7352-1KG</td>
 <td></td>
 </tr>
 <tr>
 <td>Leupeptin</td>
 <td>VWR</td>
 <td>97063-922</td>
 <td></td>
 </tr>
 <tr>
 <td>Methyl methanesulfonate (MMS)</td>
 <td>Sigma</td>
 <td>129925-5G</td>
 <td></td>
 </tr>
 <tr>
 <td>Nocodazole</td>
 <td>Sigma</td>
 <td>M1404-2MG</td>
 <td></td>
 </tr>
 <tr>
 <td>PMSG</td>
 <td>Calbiochem</td>
 <td>367222</td>
 <td></td>
 </tr>
 <tr>
 <td>Sample buffer</td>
 <td>Sigma </td>
 <td>S3401</td>
 <td></td>
 </tr>
 <tr>
 <td>Tautomycin</td>
 <td>Wako Chemicals USA</td>
 <td>209-12041</td>
 <td></td>
 </tr>
 <tr>
 <td></td>
 <td></td>
 <td></td>
 <td>Equipment </td>
 </tr>
 <tr>
 <td>Bucket for egg laying</td>
 <td>Rubbermaid commercial products</td>
 <td>6308</td>
 <td></td>
 </tr>
 <tr>
 <td>CL2 IEC centrifuge with swinging bucket rotor</td>
 <td>Thermo Scientific</td>
 <td>004260F</td>
 <td></td>
 </tr>
 <tr>
 <td>HB6 swinging bucket rotor</td>
 <td>Thermo Scientific</td>
 <td>11860</td>
 <td></td>
 </tr>
 <tr>
 <td>Sorvall RC6 plus superspeed centrifuge </td>
 <td>Thermo Scientific </td>
 <td>46910</td>
 <td></td>
 </tr>
 <tr>
 <td>UV crosslinker</td>
 <td>UVP</td>
 <td>95-0174-01</td>
 <td></td>
 </tr>
 <tr>
 <td></td>
 <td></td>
 <td></td>
 <td>Solutions</td>
 </tr>
 <tr>
 <td>1x MMR</td>
 <td></td>
 <td></td>
 <td>100 mM NaCl, 2 mM KCl, 0.5 mM MgSO4, 2.5 mM CaCl2, 5 mM HEPES, adjust pH to 7.8 with 10 M NaOH</td>
 </tr>
 <tr>
 <td>Aprotinin/Leupeptin stock</td>
 <td></td>
 <td></td>
 <td>10 mg/ml each in water. Store 20 &mu;l aliquots at -80 &deg;C. </td>
 </tr>
 <tr>
 <td>Buffer X</td>
 <td></td>
 <td></td>
 <td>0.2 M sucrose, 80 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM EDTA, 10 mM HEPES, adjust pH to 7.5 by HCl</td>
 </tr>
 <tr>
 <td>Cycloheximide stock</td>
 <td></td>
 <td></td>
 <td>10 mg/ml in water. Store 1 ml aliquots at -20 &deg;C. </td>
 </tr>
 <tr>
 <td>Cytochalasin B stock</td>
 <td></td>
 <td></td>
 <td>5 mg/ml in DMSO. Store 20 &mu;l aliquots at -20 &deg;C. </td>
 </tr>
 <tr>
 <td>Dithiothreitol (DTT) stock</td>
 <td></td>
 <td></td>
 <td>1 M in water. Store 1 ml aliquots at -20 &deg;C. </td>
 </tr>
 <tr>
 <td>ELB</td>
 <td></td>
 <td></td>
 <td>0.25 M sucrose, 1 mM DTT, 50 &mu;g/ml cycloheximide, 2.5 mM MgCl2, 50 mM KCl, 10 mM HEPES, pH7.7</td>
 </tr>
 <tr>
 <td>Nocodazole stock</td>
 <td></td>
 <td></td>
 <td>10 mg/ml in DMSO. Store 5 &mu;l aliquots at -80 &deg;C. </td>
 </tr>
 <tr>
 <td>Energy Mixture</td>
 <td></td>
 <td></td>
 <td>375 mM creatine phosphate, 50 mM ATP, and 25 mM MgCl2. Aliquots are saved at -80 &deg;C.</td>
 </tr>
 <tr>
 <td>Nuclear dye solution</td>
 <td></td>
 <td></td>
 <td>0.4 &mu;g/ml Hoechst 33258, 25% glycerol (v/v), in 1x PBS </td>
 </tr>
 <tr>
 <td>Tautomycin stock</td>
 <td></td>
 <td></td>
 <td>100 &mu;M in DMSO. Store 10 &mu;l aliquots at -80 &deg;C. </td>
 </tr>
 </tbody>
 </table>

study of the dna damage checkpoint using xenopus egg extracts

On a daily basis, cells are subjected to a variety of endogenous and environmental insults. To combat these insults, cells have evolved DNA damage checkpoint signaling as a surveillance mechanism to sense DNA damage and direct cellular responses to DNA damage. There are several groups of proteins called sensors, transducers and effectors involved in DNA damage checkpoint signaling (Figure 1). In this complex signaling pathway, ATR (ATM and Rad3-related) is one of the major kinases that can respond to DNA damage and replication stress. Activated ATR can phosphorylate its downstream substrates such as Chk1 (Checkpoint kinase 1). Consequently, phosphorylated and activated Chk1 leads to many downstream effects in the DNA damage checkpoint including cell cycle arrest, transcription activation, DNA damage repair, and apoptosis or senescence (Figure 1). When DNA is damaged, failing to activate the DNA damage checkpoint results in unrepaired damage and, subsequently, genomic instability. The study of the DNA damage checkpoint will elucidate how cells maintain genomic integrity and provide a better understanding of how human diseases, such as cancer, develop.
Xenopus laevis egg extracts are emerging as a powerful cell-free extract model system in DNA damage checkpoint research. Low-speed extract (LSE) was initially described by the Masui group1. The addition of demembranated sperm chromatin to LSE results in nuclei formation where DNA is replicated in a semiconservative fashion once per cell cycle.
The ATR/Chk1-mediated checkpoint signaling pathway is triggered by DNA damage or replication stress 2. Two methods are currently used to induce the DNA damage checkpoint: DNA damaging approaches and DNA damage-mimicking structures 3. DNA damage can be induced by ultraviolet (UV) irradiation, &gamma;-irradiation, methyl methanesulfonate (MMS), mitomycin C (MMC), 4-nitroquinoline-1-oxide (4-NQO), or aphidicolin3, 4. MMS is an alkylating agent that inhibits DNA replication and activates the ATR/Chk1-mediated DNA damage checkpoint 4-7. UV irradiation also triggers the ATR/Chk1-dependent DNA damage checkpoint 8. The DNA damage-mimicking structure AT70 is an annealed complex of two oligonucleotides poly-(dA)70 and poly-(dT)70. The AT70 system was developed in Bill Dunphy's laboratory and is widely used to induce ATR/Chk1 checkpoint signaling 9-12.
Here, we describe protocols (1) to prepare cell-free egg extracts (LSE), (2) to treat Xenopus sperm chromatin with two different DNA damaging approaches (MMS and UV), (3) to prepare the DNA damage-mimicking structure AT70, and (4) to trigger the ATR/Chk1-mediated DNA damage checkpoint in LSE with damaged sperm chromatin or a DNA damage-mimicking structure.

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Study of the DNA Damage Checkpoint using Xenopus Egg Extracts

Xenopus egg extract is a useful model system to investigate the DNA damage checkpoint. This protocol is for the preparation of Xenopus egg extracts and DNA damage checkpoint inducing reagents. These techniques are adaptable to a variety of DNA damaging approaches in the study of the DNA damage checkpoint signaling.

Study of the DNA Damage Checkpoint using Xenopus Egg Extracts

On a daily basis, cells are subjected to a variety of endogenous and environmental insults. To combat these insults, cells have evolved DNA damage ...

study-of-the-dna-damage-checkpoint-using-xenopus-egg-extracts

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16.5K Views.  University of North Carolina at Charlotte. Xenopus egg extract is a useful model system to investigate the DNA damage checkpoint. This protocol is for the preparation of Xenopus egg extracts and DNA damage checkpoint inducing reagents. These techniques are adaptable to a variety of DNA damaging approaches in the study of the DNA damage checkpoint signaling.

Video: Study of the DNA Damage Checkpoint using Xenopus Egg Extracts

Preparation and Fractionation of Xenopus laevis Egg Extracts

Crude and fractionated Xenopus egg extracts can be used to provide ingredients for reconstituting cellular processes for morphological and biochemical analysis. Egg lysis and differential centrifugation are used to prepare the crude extract which in turn in used to prepare fractionated extracts and light membrane preparations.

Crude and fractionated Xenopus egg extracts can be used to provide ingredients for reconstituting cellular processes for morphological and biochemical analysis. Egg lysis and differential centrifugation are used to prepare the crude extract which in turn in used to prepare fractionated extracts and light membrane preparations.

Crude and fractionated Xenopus egg extracts can be used to provide ingredients for reconstituting cellular processes for morphological and biochemical ...

In Vitro Nuclear Assembly Using Fractionated Xenopus Egg Extracts

Nuclear membrane assembly is an essential step in the cell division cycle; this process can be replicated in the test tube by combining Xenopus sperm chromatin, cytosol, and light membrane fractions. Complete nuclei are formed, including nuclear membranes with pore complexes, and these reconstituted nuclei are capable of normal nuclear processes.

Nuclear membrane assembly is an essential step in the cell division cycle; this process can be replicated in the test tube by combining Xenopus sperm chromatin, cytosol, and light membrane fractions. Complete nuclei are formed, including nuclear membranes with pore complexes, and these reconstituted nuclei are capable of normal nuclear processes.

Nuclear membrane assembly is an essential step in the cell division cycle; this process can be replicated in the test tube by combining Xenopus sperm ...

Production of Xenopus tropicalis Egg Extracts to Identify Microtubule-associated RNAs

Many organisms localize mRNAs to specific subcellular destinations to spatially and temporally control gene expression. Recent studies have demonstrated that the majority of the transcriptome is localized to a nonrandom position in cells and embryos. One approach to identify localized mRNAs is to biochemically purify a cellular structure of interest and to identify all associated transcripts. Using recently developed high-throughput sequencing technologies it is now straightforward to identify all RNAs associated with a subcellular structure. To facilitate transcript identification it is necessary to work with an organism with a fully sequenced genome. One attractive system for the biochemical purification of subcellular structures are egg extracts produced from the frog Xenopus laevis. However, X. laevis currently does not have a fully sequenced genome, which hampers transcript identification. In this article we describe a method to produce egg extracts from a related frog, X. tropicalis, that has a fully sequenced genome. We provide details for microtubule polymerization, purification and transcript isolation. While this article describes a specific method for identification of microtubule-associated transcripts, we believe that it will be easily applied to other subcellular structures and will provide a powerful method for identification of localized RNAs.

Production of Xenopus tropicalis Egg Extracts to Identify Microtubule-associated RNAs

We describe the collection of unfertilized Xenopus tropicalis eggs and production of a meiosis II-arrested egg extract. This egg extract can be used to purify microtubules and microtubule-associated RNAs.

Many  organisms localize mRNAs to specific subcellular destinations to spatially and  temporally control gene expression. Recent studies have demonstrated ...

Reconstitution Of &#946;-catenin Degradation In Xenopus Egg Extract

Xenopus laevis egg extract is a well-characterized, robust system for studying the biochemistry of diverse cellular processes. Xenopus egg extract has been used to study protein turnover in many cellular contexts, including the cell cycle and signal transduction pathways1-3. Herein, a method is described for isolating Xenopus egg extract that has been optimized to promote the degradation of the critical Wnt pathway component, &beta;-catenin. Two different methods are described to assess &beta;-catenin protein degradation in Xenopus egg extract. One method is visually informative ([35S]-radiolabeled proteins), while the other is more readily scaled for high-throughput assays (firefly luciferase-tagged fusion proteins). The techniques described can be used to, but are not limited to, assess &beta;-catenin protein turnover and identify molecular components contributing to its turnover. Additionally, the ability to purify large volumes of homogenous Xenopus egg extract combined with the quantitative and facile readout of luciferase-tagged proteins allows this system to be easily adapted for high-throughput screening for modulators of &beta;-catenin degradation.

Reconstitution Of &amp;#946;-catenin Degradation In Xenopus Egg Extract

A method is described for analyzing protein degradation using radiolabeled and luciferase-fusion proteins in Xenopus egg extract and its adaptation for high-throughput screening for small molecule modulators of protein degradation.

Xenopus laevis egg extract is a well-characterized, robust system for studying the biochemistry of diverse cellular processes. Xenopus egg extract has ...

Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method

Terminal deoxynucleotidyl transferase (TdT) deoxyuridine triphosphate (dUTP) nick end labeling (TUNEL) is the method of using the TdT enzyme to covalently attach a tagged form of dUTP to 3&#8217; ends of double- and single-stranded DNA breaks in cells. It is a reliable and useful method to detect DNA damage and cell death in situ. This video describes dissection, tissue processing, sectioning, and fluorescence-based TUNEL labeling of mouse skeletal muscle. It also describes a method of semi-automated TUNEL signal quantitation. Inherent normal tissue features and tissue processing conditions affect the ability of the TdT enzyme to efficiently label DNA. Tissue processing may also add undesirable autofluorescence that will interfere with TUNEL signal detection. Therefore, it is important to empirically determine tissue processing and TUNEL labeling methods that will yield the optimal signal-to-noise ratio for subsequent quantitation. The fluorescence-based assay described here provides a way to exclude autofluorescent signal by digital channel subtraction. The TUNEL assay, used with appropriate tissue processing techniques and controls, is a relatively fast, reproducible, quantitative method for detecting apoptosis in tissue. It can be used to confirm DNA damage and apoptosis as pathological mechanisms, to identify affected cell types, and to assess the efficacy of therapeutic treatments in vivo.

Detection and Analysis of DNA Damage in Mouse Skeletal Muscle In Situ Using the TUNEL Method

This video describes dissection, tissue processing, sectioning, and fluorescence-based TUNEL labeling of mouse skeletal muscle. It also describes a method for semi-automated analysis of TUNEL labeling.

Terminal deoxynucleotidyl transferase (TdT) deoxyuridine triphosphate (dUTP) nick end labeling (TUNEL) is the method of using the TdT enzyme to covalently ...

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients.

We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of ...

A Cell-Free Assay Using Xenopus laevis Embryo Extracts to Study Mechanisms of Nuclear Size Regulation

A fundamental question in cell biology is how cell and organelle sizes are regulated. It has long been recognized that the size of the nucleus generally scales with the size of the cell, notably during embryogenesis when dramatic reductions in both cell and nuclear sizes occur. Mechanisms of nuclear size regulation are largely unknown and may be relevant to cancer where altered nuclear size is a key diagnostic and prognostic parameter. In vivo approaches to identifying nuclear size regulators are complicated by the essential and complex nature of nuclear function. The in vitro approach described here to study nuclear size control takes advantage of the normal reductions in nuclear size that occur during Xenopus laevis development. First, nuclei are assembled in X. laevis egg extract. Then, these nuclei are isolated and resuspended in cytoplasm from late stage embryos. After a 30 - 90 min incubation period, nuclear surface area decreases by 20 - 60%, providing a useful assay to identify cytoplasmic components present in late stage embryos that contribute to developmental nuclear size scaling. A major advantage of this approach is the relative facility with which the egg and embryo extracts can be biochemically manipulated, allowing for the identification of novel proteins and activities that regulate nuclear size. As with any in vitro approach, validation of results in an in vivo system is important, and microinjection of X. laevis embryos is particularly appropriate for these studies.

A Cell-Free Assay Using Xenopus laevis Embryo Extracts to Study Mechanisms of Nuclear Size Regulation

Mechanisms of cellular and intra-cellular scaling remain elusive. The use of Xenopus embryo extracts has become increasingly common to elucidate mechanisms of organelle size regulation. This method describes embryo extract preparation and a novel nuclear scaling assay through which mechanisms of nuclear size regulation can be identified.

A fundamental question in cell biology is how cell and organelle sizes are regulated. It has long been recognized that the size of the nucleus generally ...

Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization

Traditionally used for bulk biochemical assays, Xenopus laevis egg extracts have emerged as a powerful imaging-based tool for studying cytoplasmic phenomena, such as cytokinesis, mitotic spindle formation and assembly of the nucleus. Building upon early methods that imaged fixed extracts sampled at sparse time points, recent approaches image live extracts using time-lapse microscopy, revealing more dynamical features with enhanced temporal resolution. These methods usually require sophisticated surface treatments of the imaging vessel. Here we introduce an alternative method for live imaging of egg extracts that require no chemical surface treatment. It is simple to implement and utilizes mass-produced laboratory consumables for imaging. We describe a system that can be used for both wide-field and confocal microscopy. It is designed for imaging extracts in a 2-dimensional (2D) field, but can be easily extended to imaging in 3D. It is well-suited for studying spatial pattern formation within the cytoplasm. With representative data, we demonstrate the typical dynamic organization of microtubules, nuclei and mitochondria in interphase extracts prepared using this method. These image data can provide quantitative information on cytoplasmic dynamics and spatial organization.

Xenopus laevis Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization

We describe a method for the preparation and live imaging of undiluted cytoplasmic extracts from Xenopus laevis eggs.

Traditionally used for bulk biochemical assays, Xenopus laevis egg extracts have emerged as a powerful imaging-based tool for studying cytoplasmic ...

Demonstration of the DNA Fiber Assay for Investigating DNA Damage and Repair Dynamics Induced by Nanoparticles

Nanomaterial exposure can cause replication stress and genomic instability in cells. The degree of instability depends on the chemistry, size, and concentration of the nanomaterials, the time of exposure, and the exposed cell type. Several established methods have been used to elucidate how endogenous/exogenous agents impact global replication. However, replicon-level assays, such as the DNA fiber assay, are imperative to understand how these agents influence replication initiation, terminations, and replication fork progression. Knowing this allows one to understand better how nanomaterials increase the chances of mutation fixation and genomic instability. We used RAW 264.7 macrophages as model cells to study the replication dynamics under graphene oxide nanoparticle exposure. Here, we demonstrate the basic protocol for the DNA fiber assay, which includes pulse labeling with nucleotide analogs, cell lysis, spreading the pulse-labeled DNA fibers onto slides, fluorescent immunostaining of the nucleotide analogs within the DNA fibers, imaging of the replication intermediates within the DNA fibers using confocal microscopy, and replication intermediate analysis utilizing a computer-assisted scoring and analysis (CASA) software.

The methodology assists in the analysis of variation in DNA replication dynamics in the presence of nanoparticles. Different methodologies can be adopted based on the cytotoxicity level of the material of interest. In addition, a description of the image analysis is provided to help in DNA fiber analysis.

Nanomaterial exposure can cause replication stress and genomic instability in cells. The degree of instability depends on the chemistry, size, and ...

Assessing Protein Interaction and Localization in DNA Damage

Proximity Ligand Assay to Localize Proteins in DNA Damage Sites

The DNA damage response is a genetic information safeguard that protects cells from perpetuating damaged DNA. The characterization of the proteins that cooperate in this process allows the identification of alternative targets for therapeutic intervention in several diseases, such as cancer, aging-related diseases, and chronic inflammation. The Proximity Ligand Assay (PLA) emerged as a tool for estimating interaction between proteins as well as spatial proximity among organelles or cellular structures and allows the temporal localization and co-localization analysis under stress conditions, for instance. The method is simple because it is similar to conventional immunofluorescence and allows the staining of an organelle, cellular structure, or a specific marker such as mitochondria, endoplasmic reticulum, PML bodies, or DNA double-strand marker, yH2AX simultaneously. The phosphorylation of the S139 at Histone 2A variant, H2AX, then referred to as yH2AX, is widely used as a very sensitive and specific marker of DNA double-strand breaks. Each focus of yH2AX staining corresponds to one break in DNA that occurs a few minutes after the damage. The analysis of changes in yH2AX foci is the most common assay for studying if the protein of interest is implicated in DNA damage response (DDR). Whether a direct role in the DNA damage site is expected, fluorescence microscopy is used to verify the colocalization of the protein of interest with yH2AX foci. However, except for the new super-resolution fluorescence methods, to conclude, the local interaction with DNA damage sites can be a little subjective. Here, we show an assay to evaluate the localization of proteins in the DDR pathway using yH2AX as a marker of the damage site. This assay can be used to characterize the temporal localization under different insults that cause DNA damage.

Author Spotlight: Combining Proximity Ligand Assay with Gamma-H2AX Staining to Characterize Protein Interactions in DNA Damage Response

Here, we present a simple and rapid protocol for the detection of protein interaction at DNA damage sites.

The DNA damage response is a genetic information safeguard that protects cells from perpetuating damaged DNA. The characterization of the proteins that ...