The work in this manuscript was supported by funds from Dept. of Radiation Oncology and Huntsman Cancer Institute and the National Institute of Health grant (R01-CA188520) to SB. I thank Danielle Johnson and Steven Bennett in my lab for demonstrating the protocol and explaining its benefits. I am grateful to Dr. Mahesh Chandrasekharan (Huntsman Cancer Institute) for critical comments on the manuscript.

1. Chromatin immunoprecipitation (ChIP) following BrdU Labeling
<ol>
	<li>Culture NIH3T3 cells in the presence of either DMSO or HDAC1,2-selective inhibitors as described previously6.</li>
	<li>Following treatment with DMSO or HDAC1,2 selective inhibitors, add BrdU to the cells in a sterile tissue culture hood. Incubate 2 x 106 NIH3T3 cells plated in 10 ml NIH3T3 media with a 20 &#181;M final concentration of bromodeoxyuridine (BrdU) for 60 min in a sterile 37 &#176;C tissue culture incubator.</li...

<ol>
	<li>Podhorecka, M., Skladanowski, A., Bozko, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=H2AX+Phosphorylation:+Its+Role+in+DNA+Damage+Response+and+Cancer+Therapy.">H2AX Phosphorylation: Its Role in DNA Damage Response and Cancer Therapy.</a> J nucleic acids. , (2010).</li><li>Groth, A., Rocha, W., Verreault, A., Almouzni, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+challenges+during+DNA+replication+and+repair.">Chromatin challenges during DNA replication and repair.</a> 128, 721-733 (2007).</li><li>Demeret, C., Vassetzky, Y., Mechali, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+remodelling+and+DNA+replication:+from+nucleosomes+to+loop+domains.">Chromatin remodelling and DNA replication: from nucleosomes to loop domains.</a> Oncogene. 20, 3086-3093 (2001).</li><li>Bhaskara, 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=Deletion+of+histone+deacetylase+3+reveals+critical+roles+in+S+phase+progression+and+DNA+damage+control.">Deletion of histone deacetylase 3 reveals critical roles in S phase progression and DNA damage control.</a> Mol Cell. 30, 61-72 (2008).</li><li>Bhaskara, S., Hiebert, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+for+histone+deacetylase+3+in+maintenance+of+genome+stability.">Role for histone deacetylase 3 in maintenance of genome stability.</a> Cell Cycle. 10, 727-728 (2011).</li><li>Bhaskara, 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=Histone+deacetylases+1+and+2+maintain+S-phase+chromatin+and+DNA+replication+fork+progression.">Histone deacetylases 1 and 2 maintain S-phase chromatin and DNA replication fork progression.</a> Epigenetics Chromatin. 6, 27 (2013).</li><li>Bhaskara, 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=Hdac3+is+essential+for+the+maintenance+of+chromatin+structure+and+genome+stability.">Hdac3 is essential for the maintenance of chromatin structure and genome stability.</a> Cancer Cell. 18, 436-447 (2010).</li><li>Johnson, D. P., 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=HDAC1,2+inhibition+impairs+EZH2-+and+BBAP-mediated+DNA+repair+to+overcome+chemoresistance+in+EZH2+gain-of-function+mutant+diffuse+large+B-cell+lymphoma.">HDAC1,2 inhibition impairs EZH2- and BBAP-mediated DNA repair to overcome chemoresistance in EZH2 gain-of-function mutant diffuse large B-cell lymphoma.</a> Oncotarget. 6, 4863-4887 (2015).</li><li>Bhaskara, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histone+deacetylases+1+and+2+regulate+DNA+replication+and+DNA+repair:+potential+targets+for+genome+stability-mechanism-based+therapeutics+for+a+subset+of+cancers.">Histone deacetylases 1 and 2 regulate DNA replication and DNA repair: potential targets for genome stability-mechanism-based therapeutics for a subset of cancers.</a> Cell Cycle. 14, 1779-1785 (2015).</li><li>Taddei, A., Roche, D., Sibarita, J. B., Turner, B. M., Almouzni, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Duplication+and+maintenance+of+heterochromatin+domains.">Duplication and maintenance of heterochromatin domains.</a> J Cell Biol. 147, 1153-1166 (1999).</li><li>Alabert, C., Groth, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+replication+and+epigenome+maintenance.">Chromatin replication and epigenome maintenance.</a> Nat Rev Mol Cell Biol. 13, 153-167 (2012).</li><li>Clapier, C. R., Cairns, B. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+ISWI+involves+inhibitory+modules+antagonized+by+nucleosomal+epitopes.">Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes.</a> Nature. 492, 280-284 (2012).</li><li>Sirbu, B. 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=Analysis+of+protein+dynamics+at+active,+stalled,+and+collapsed+replication+forks.">Analysis of protein dynamics at active, stalled, and collapsed replication forks.</a> Genes Dev. 25, 1320-1327 (2011).</li></ol>

The protocol described in this manuscript is a relatively quick method to demonstrate the presence of proteins or their post-translationally modified forms on newly replicated or nascent DNA. Additionally, this technique permits one to measure the association-dissociation kinetics of a protein or its modified form with nascent DNA. This technique is complementary to the elegant iPOND technology13. In the iPOND technology, newly synthesized DNA is labeled with ethyl deoxyuridine (EdU). A biotin conjugate is the...

Defective DNA repair and/or DNA replication are a major cause of genome instability, which can trigger cell death. A single unrepaired double strand break is sufficient to cause cell death1. Chromatin organization is transiently altered during both replication and repair2,3, and failure to maintain epigenetic information during these processes will result in a threat to genome integrity. Loss of HDAC3 or HDAC1,2 function impedes S-phase progression,&#160;DNA replication and repair leading to genotoxic stress (DNA damage) and cell&#160;death4-9. It is therefore a practical strategy to use selective HDAC inhibitors to disrupt replication, repair and chromatin in cancer cells and cause DNA damage, which in turn can stop growth and induce cell death selectively in rapidly growing cancer cells.
During DNA replication, chromatin is rapidly disassembled and then reassembled following DNA duplication. Newly synthesized histone H4 is acetylated at K5 and K12 residues (H4K5K12ac) and following deposition onto chromatin, they are rapidly deacetylated by histone deacetylases (HDACs)10,11. Failure of cells to maintain nascent chromatin integrity by histone deacetylation can lead to fork collapse, which in turn can result in DNA damage and cell death. We recently showed that selective inhibition of HDAC1,2 increases histone acetylation (H4K5ac, H4K12ac and H4K16ac) and inhibits SMARCA5 chromatin remodeler activity on nascent chromatin, which correlates with reduced replication fork progression, increased fork collapse and increased replication stress-induced DNA damage6. Thus, HDAC inhibitor treatment can alter nascent chromatin structure to trigger DNA damage and death very quickly in cancer cells, as these cells cycle rapidly and pass many times through the S-phase. It is therefore important to understand how HDACs function to regulate histone acetylation and protein binding to maintain DNA replication in mammalian cells.
To quantitatively measure the amount of histone acetylation and SMARCA5 chromatin remodeler associated with nascent DNA during DNA replication, we devised a modified ChIP assay called the BrdU-ChIP-Slot-Western technique. Following chromatin immunoprecipitation (ChIP) of a desired protein or histone modification, the amount of nascent DNA (labeled using thymidine analog, BrdU) in the ChIP sample can be detected using western analysis of BrdU-labeled ChIP DNA transferred onto a membrane using a Slot Blot apparatus. Using this technique, we showed that H4K16ac (a mark involved in chromatin packaging) and the ISWI family member SMARCA5 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin) chromatin remodeler are associated with nascent DNA in S-phase cells6. We also found that the nascent H4K16ac mark is deacetylated by HDAC1,2 during DNA replication6. H4K16ac inhibits chromatin remodeler activity of the ISWI family member SMARCA512. Hence, using the BrdU-CHIP-Slot-Western technique, we could connect the functions for HDAC1,2 in regulating chromatin remodeling during DNA replication. Hence, the BrdU-ChIP-Slot-Western Blot technique is a powerful approach to quantitatively measure the association and dissociation dynamics of proteins or their post-translational modifications that are bound to nascent DNA.

<table border="0" cellpadding="0" cellspacing="0" width="608">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Anti-BrdU (westerns)</td>
			<td style="width:107px;">BD Biosciences</td>
			<td style="width:119px;">B555627</td>
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			<td height="21" style="height:21px;">Anti-SMARCA5</td>
			<td>Abcam</td>
			<td style="width:119px;">ab3749</td>
			<td></td>
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			<td height="21" style="height:21px;width:216px;">Anti-H4K16ac</td>
			<td style="width:107px;">Active Motif</td>
			<td>39167</td>
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			<td height="21" style="height:21px;width:216px;">Zeta-Probe GT Membrane</td>
			<td style="width:107px;">Bio-Rad</td>
			<td style="width:119px;">162-0197</td>
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			<td height="21" style="height:21px;width:216px;">Formaldehyde</td>
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			<td style="width:119px;">BP531-500</td>
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			<td height="21" style="height:21px;width:216px;">Protein A agarose</td>
			<td style="width:107px;">Millipore</td>
			<td style="width:119px;">16-156</td>
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			<td height="21" style="height:21px;width:216px;">Rnase A</td>
			<td style="width:107px;">Qiagen</td>
			<td style="width:119px;">19101</td>
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			<td height="21" style="height:21px;width:216px;">Proteinase K</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">P4850</td>
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			<td height="21" style="height:21px;width:216px;">PCR Purification Kit</td>
			<td style="width:107px;">Qiagen</td>
			<td style="width:119px;">28106</td>
			<td></td>
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			<td height="21" style="height:21px;width:216px;">Glycine</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">G7403</td>
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			<td height="21" style="height:21px;width:216px;">Protease inhibitor cocktail</td>
			<td style="width:107px;">Roche</td>
			<td style="width:119px;">11836170001</td>
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			<td height="21" style="height:21px;width:216px;">BrdU</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">B9285</td>
			<td></td>
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			<td height="21" style="height:21px;width:216px;">Rabbit IgG&#160;</td>
			<td style="width:107px;">Millipore</td>
			<td style="width:119px;">12-370</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">HEPES</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">H3375</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">NaCl</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">S-3014</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Triton-X-100</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">93443</td>
			<td></td>
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			<td height="42" style="height:42px;width:216px;">NP40</td>
			<td style="width:107px;">USB Corporation</td>
			<td style="width:119px;">19628</td>
			<td></td>
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			<td height="21" style="height:21px;width:216px;">Sodium deoxycholate</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">D6750</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:216px;">Sodium bicarbonate</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">S-4019</td>
			<td></td>
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			<td height="42" style="height:42px;width:216px;">Ethanol</td>
			<td style="width:107px;">Decon Laboratories</td>
			<td style="width:119px;">04-355-222</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:216px;">DEPC-treated water</td>
			<td style="width:107px;">Sigma</td>
			<td style="width:119px;">95284</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Tris</td>
			<td style="width:107px;">Fisher</td>
			<td style="width:119px;">BP-152-5</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">EDTA</td>
			<td style="width:107px;">Invitrogen</td>
			<td style="width:119px;">15575-020</td>
			<td></td>
		</tr>
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			<td height="21" style="height:21px;width:216px;">SDS</td>
			<td style="width:107px;">Ambion</td>
			<td style="width:119px;">AM9820</td>
			<td></td>
		</tr>
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			<td height="42" style="height:42px;width:216px;">Sodium hydroxide</td>
			<td style="width:107px;">Mallinckrodt GenAR&#160;</td>
			<td style="width:119px;">MAL7772-06</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">20X SSC</td>
			<td style="width:107px;">Life Technologies</td>
			<td style="width:119px;">15557-036</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Non-fat dry milk</td>
			<td style="width:107px;">Lab Scientific Inc</td>
			<td style="width:119px;">M0841</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ECL</td>
			<td style="width:107px;">Thermo Fisher</td>
			<td style="width:119px;">80196</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">X-ray film</td>
			<td style="width:107px;">Genesee Sci</td>
			<td style="width:119px;">30-101</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Developer</td>
			<td style="width:107px;">Konica Minolta</td>
			<td style="width:119px;">SRX-101A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">UV Crosslinker</td>
			<td style="width:107px;">Stratagene</td>
			<td style="width:119px;">XLE-1000</td>
			<td></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">Sonicator</td>
			<td style="width:107px;">Branson Sonifier&#160; Digital Ultrasonic Cell Disruptor</td>
			<td style="width:119px;">Model: 450</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Centrifuge</td>
			<td style="width:107px;">Eppendorf</td>
			<td style="width:119px;">Model: 5810R</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Water bath</td>
			<td style="width:107px;">Fisher Scientific Isotemp</td>
			<td style="width:119px;">Model: 2322</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">NanoDrop 1000 spectrophotometer</td>
			<td style="width:107px;">ThermoScientific</td>
			<td style="width:119px;">Model: 1000</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Slot Blot apparatus&#160;</td>
			<td style="width:107px;">Schleicher and Schuell Minifold II</td>
			<td style="width:119px;">44-27570</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Tissue Culture Incubator</td>
			<td style="width:107px;">Thermo Scientific</td>
			<td style="width:119px;">Series II 3110 Water-Jacketed CO2 Incubators</td>
			<td></td>
		</tr>
	</tbody>
</table>

examination of proteins bound to nascent dna in mammalian cells using  brdu-chip-slot-western technique

Histone deacetylases 1 and 2 (HDAC1,2) localize to the sites of DNA replication. In the previous study, using a selective inhibitor and a genetic knockdown system, we showed novel functions for HDAC1,2 in replication fork progression and nascent chromatin maintenance in mammalian cells. Additionally, we used a BrdU-ChIP-Slot-Western technique that combines chromatin immunoprecipitation (ChIP) of bromo-deoxyuridine (BrdU)-labeled DNA with slot blot and Western analyses to quantitatively measure proteins or histone modification associated with nascent DNA.
Actively dividing cells were treated with HDAC1,2 selective inhibitor or transfected with siRNAs against Hdac1 and Hdac2 and then newly synthesized DNA was labeled with the thymidine analog bromodeoxyuridine (BrdU). The BrdU labeling was done at a time point when there was no significant cell cycle arrest or apoptosis due to the loss of HDAC1,2 functions. Following labeling of cells with BrdU, chromatin immunoprecipitation (ChIP) of histone acetylation marks or the chromatin-remodeler was performed with specific antibodies. BrdU-labeled input DNA and the immunoprecipitated (or ChIPed) DNA was then spotted onto a membrane using the slot blot technique and immobilized using UV. The amount of nascent DNA in each slot was then quantitatively assessed using Western analysis with an anti-BrdU antibody. The effect of loss of HDAC1,2 functions on the levels of newly synthesized DNA-associated histone acetylation marks and chromatin remodeler was then determined by normalizing the BrdU-ChIP signal obtained from the treated samples to the control samples.

To determine the specificity of HDAC1,2-selective inhibitors, Hdac1,2FL/FL and Hdac3FL/FL fibrosarcoma cells were used. Adenovirus-containing Cre recombinase (Ad-Cre) was used to delete Hdac1,2 and Hdac3 in these cells. Following Ad-Cre infection of Hdac1,2FL/FL cells, a robust increase in H4K5ac was observed. Treatment of Hdac1,2&#160;knockout cells with 233 or 898 did not result in...

Watch this Scientific Journal Video about Examination of Proteins Bound to Nascent DNA in Mammalian Cells Using  BrdU-ChIP-Slot-Western Technique at JoVE.com

Examination of Proteins Bound to Nascent DNA in Mammalian Cells Using  BrdU-ChIP-Slot-Western Technique

In this protocol, we describe a novel BrdU-ChIP-Slot-Western technique to examine proteins and histone modifications associated with newly synthesized or nascent DNA.

Histone deacetylases 1 and 2 (HDAC1,2) localize to the sites of DNA replication. In the previous study, using a selective inhibitor and a genetic ...

The overall goal of this procedure is to rapidly examine proteins bound to nascent DNA with accuracy using BrdU labeling and chromatin precipitation. This method can answer key questions in the replication, repair in chromatin field, such as, what proteins are bound to nascent DNA during DNA replication and what repair proteins are bound to nascent DNA during replication stress. The main advantage of this technique is that it is a relatively quick method to detect proteins bound to nascent DNA in a highly quantitative manner.To begin, set up cultures of two million NIH 3T3 cells in 10 milliliters of media with either DMSO or inhibitors. Also, add BrdU to a final concentration of 20 micromolar. Once plated, incubate the cells for 60 minutes.After an hour, crosslink the intracellular proteins to the DNA by adding formaldehyde directly to the culture medium to a concentration of 1%by volume. Then, let the cells incubate at room temperature for 10 minutes with agitation. After 10 minutes, quench the reaction by adding glycine to the media to 125 millimolar and continue the incubation for five more minutes.Next, collect the cells in PBS and wash them twice with PBS using centrifugation. The pellet can be frozen at 80 degrees Celsius per storage if desired. Now, prepare the lysate from the crosslinked cells, add 500 microliters of FA140 buffer supplemented with the protease inhibitor cocktail to the pellet and shear the chromatin using five 15-second pulses of sonication.Keep the cells chilled between the pulses. Then, run 10 microliters of sample out on a 1.5%gel to diagnose the efficiency of the shearing. Once sheared, centrifuge the samples for 10 minutes, and transfer the supernatant to a new tube.Then, estimate the protein concentration in the supernatant using a kit. Next, prepare a 50%slurry of Protein A Agarose beads with FA140 buffer containing protease inhibitor. Add 50 microliters of the slurry to each sample and incubate the samples at 4 degrees Celsius with constant end-over-end rotation for 30 minutes.After half an hour, spin down the samples for a minute around 1000 G's in a refrigerated centrifuge. Then, collect the supernatant containing the labelled chromatin. Before proceeding, save 1/10th of the extract at 20 degrees Celsius to later serve as the input control.To immunoprecipitate the chromatin, add either eight microliters of H4K16ac antibody or five micrograms of SMARCA5 antibody to the supernatants. Also, add five micrograms of rapid IgG to the extract that serves as the negative control sample. Incubate the chromatin at 4 degrees Celsius overnight on a rotisserie mixer.The next day, add 50 microliters of the prepared 50%Protein A Agarose slurry to the immunoprecipitations and incubate the mixtures for an hour at 4 degrees Celsius with rotation. After an hour, pellet the Agarose beads and carefully discard the supernatant. Now, wash the beads using end-over-end rotations at 4 degrees Celsius in three sequential buffers.First, use freshly prepared, low-salt immune complex wash buffer for five minutes. Second, use freshly prepared, high-salt immune complex wash buffer for five minutes. Third, use freshly prepared, Lithium chloride immune complex wash buffer for five minutes.Following washes, add elution solution to the samples as described in the text. Spin the samples and transfer the eluate to a new 1.5 milliliter tube. Now, incubate the samples at 65 degrees Celsius for 5 hours to reverse the crosslinking.Later, precipitate the DNA. Add one milliliter of 100%ethanol to the samples and mix well. Then, incubate them at 80 degrees Celsius for two to three hours or overnight at 20 degrees Celsius.After the precipitation, remove the ethanol with a 15-minute ceintrifugation at 18000 G's. Then, following the text protocol, wash the pellet, treat the samples with RNase, then Proteinase K, purify DNA as described in the text, and finally, store at 20 degrees Celsius. To begin, measure the yield of input and ChIP DNA on a spectrophotometer.Then, denature the samples. Add 2.5 volumes of 0.4 normal sodium hydroxide, briefly vortex and centrifuge and incubate the samples at room temperature for 30 minutes. Next, neutralize the denatured DNA by adding 175 microliters of one molar Tris hydochloride pH 6.8.Vortex, centrifuge, and place the samples on ice. Now, prepare serial dilutions of the input and immunoprecipitated DNA and proceed with the slot-blot assay as described in the text protocol. After the DNA on the blot has been UV immobilized, detect the BrdU on the slot blot using western blotting.First, block the membrane with 5%nonfat dry milk in PBST for an hour at room temperature to prevent nonspecific binding. Next, prepare a bath of 1%nonfat dry milk in PBST with added 1:500 diluted anti-BrdU antibody. Incubate the blot in this bath for three hours at room temperature on a shaker.Afterwards, wash the membrane with PBST three times. Then, submerge the blot in a 1:5000 dilution of HRP conjugated anti-mouse secondary antibody in PBST. Incubate at room temperature for an hour with shaking.Use three washes with PBST to remove the secondary and analyse the result. The BrdU H4K16ac ChIP slot western technique was used to determine the amount of H4K16ac associated with nascent DNA. A robust enrichment in H4K16ac associated with nascent DNA was observed when compared to the rapid IgG control.Following inhibition of HDAC1/2 with compound 233, an increase in nascent-DNA-associated H4K16ac was observed. The same result was obtained using compound 898. Finally, the level of SMARCA5 chromatin remodeler on nascent DNA was determined using the BrdU SMARCA5 ChIP slot western technique.Indeed, SMARCA5 associated with nascent DNA and compound 898 did not change the levels of SMARCA5. After watching this video, you should have a good understanding of the changes that occur in chromatin and chromatin-modifying enzymes during DNA replication in mammalian cells. After its development, this technique paved the way for researchers in the field of replication to explore chromatin changes on nascent DNA as well as dynamics of DNA repair proteins on nascent DNA.In the future, this technique could also be used to study the dynamics of the DNA damage response and DNA repair proteins at the stalled fork in addition to studying the histone modifications and chromatin modifying enzymes at the fork.

Research

JoVE Journal

Biology

Long-term Imaging Mammalian Cells using Wide-Field Microscopy

DNA Transfection of Mammalian Skeletal Muscles using In Vivo Electroporation

DNA Transfection of Mammalian Skeletal Muscles using In Vivo Electroporation

 A growing interest in cell biology is to express transgenically modified forms of essential proteins (e.g. fluorescently tagged constructs and/or mutant ...

Intranuclear Microinjection of DNA into Dissociated Adult Mammalian Neurons

Primary neuronal cell cultures are valuable tools to study protein function since they represent a more biologically relevant system compared to ...

Analysis of DNA Double-strand Break (DSB) Repair in Mammalian Cells

Analysis of DNA Double-strand Break DSB Repair in Mammalian Cells

DNA double-strand breaks are the most dangerous DNA lesions that may lead to massive loss of genetic information and cell death.  Cells repair DSBs using ...

Visualization of DNA Replication in the Vertebrate Model System DT40 using the DNA Fiber Technique

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not ...

Analysis of Cell Cycle Position in Mammalian Cells

The regulation of cell proliferation is central to tissue morphogenesis during the development of multicellular organisms. Furthermore, loss of control of ...

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the ...

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides

Extensive research has provided ample evidences suggesting that protein folding in the cell is a co-translational process1-5. However, the exact pathway ...

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the ...

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel ...