Name: adaptation of hybridization capture of chromatin-associated proteins for proteomics to mammalian cells
Uploaded: 2018-06-01T13:30:00
Description: Watch this Scientific Journal Video about Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells at JoVE.com

This work was supported by NIH Grants P50HG004952 and R01GM109099 to MO.

1. Capture Oligonucleotide Design
<ol>
	<li>Design a panel of oligonucleotides to be used during the hybridization capture of the target region/s.
	<ol>
		<li>Aim to design 4&#8211;8 oligonucleotides per target region, but as a minimum, design at least one oligonucleotide targeting each end of the target region.</li>
		<li>If the target sequence is long (&#62;500 base pairs), design the oligonucleotides as spread out as possible to assure effective enrichment of chromatin across the entire target regio...

<ol>
	<li>Consortium, E. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+integrated+encyclopedia+of+DNA+elements+in+the+human+genome.">An integrated encyclopedia of DNA elements in the human genome.</a> Nature. 489 (7414), 57-74 (2013).</li><li>Galas, D. J., Schmitz, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNAse+footprinting:+a+simple+method+for+the+detection+of+protein-DNA+binding+specificity.">DNAse footprinting: a simple method for the detection of protein-DNA binding specificity.</a> Nucleic Acids Res. 5 (9), 3157-3170 (1978).</li><li>Simon, J. M., Giresi, P. G., Davis, I. J., Lieb, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+formaldehyde-assisted+isolation+of+regulatory+elements+(FAIRE)+to+isolate+active+regulatory+DNA.">Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.</a> Nat. Protoc. 7 (2), 256-267 (2012).</li><li>Dai, Y., Kennedy-Darling, J., Shortreed, M. R., Scalf, M., Gasch, A. P., Smith, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+Sequence-Specific+Capture+of+Chromatin+and+Mass+Spectrometric+Discovery+of+Associated+Proteins.">Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins.</a> Anal. Chem. 89 (15), 7841-7846 (2017).</li><li>Guillen-Ahlers, H., 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=HyCCAPP+as+a+tool+to+characterize+promoter+DNA-protein+interactions+in+Saccharomyces+cerevisiae.">HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.</a> Genomics. 107 (6), (2016).</li><li>Kennedy-Darling, 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=Discovery+of+Chromatin-Associated+Proteins+via+Sequence-Specific+Capture+and+Mass+Spectrometric+Protein+Identification+in+Saccharomyces+cerevisiae.">Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.</a> J Proteome Res. 13 (8), 3810-3825 (2014).</li><li>Guillen-Ahlers, H., Shortreed, M. R. R., Smith, L. M. M., Olivier, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advanced+methods+for+the+analysis+of+chromatin-associated+proteins.">Advanced methods for the analysis of chromatin-associated proteins.</a> Physiol Genomics. 46 (13), 441-447 (2014).</li><li>Lambert, J. -. P., Fillingham, J., Siahbazi, M., Greenblatt, J., Baetz, K., Figeys, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Defining+the+budding+yeast+chromatin-associated+interactome.">Defining the budding yeast chromatin-associated interactome.</a> Mol Syst Biol. 6, 448 (2010).</li><li>Soldi, M., Bonaldi, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Proteomic+Investigation+of+Chromatin+Functional+Domains+Reveals+Novel+Synergisms+among+Distinct+Heterochromatin+Components.">The Proteomic Investigation of Chromatin Functional Domains Reveals Novel Synergisms among Distinct Heterochromatin Components.</a> Mol Cell Proteomics. 12 (3), 764-780 (2013).</li><li>Wang, C. I., 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=Chromatin+proteins+captured+by+ChIP-mass+spectrometry+are+linked+to+dosage+compensation+in+Drosophila.">Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila.</a> Nat Struct Mol Biol. 20 (2), 202-209 (2013).</li><li>Byrum, S. D., Raman, A., Taverna, S. D., Tackett, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChAP-MS:+A+Method+for+Identification+of+Proteins+and+Histone+Posttranslational+Modifications+at+a+Single+Genomic+Locus.">ChAP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic Locus.</a> Cell Rep. 2 (1), 198-205 (2012).</li><li>Fujita, T., Fujii, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+isolation+of+specific+genomic+regions+and+identification+of+associated+immunoprecipitation+(+eChIP+)+using+CRISPR.">Efficient isolation of specific genomic regions and identification of associated immunoprecipitation ( eChIP ) using CRISPR.</a> Biochem. Bioph. Res. Co. 439 (1), 132-136 (2013).</li><li>Liu, X., 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+Situ+Capture+of+Chromatin+Interactions+by+Biotinylated+dCas9.">In Situ Capture of Chromatin Interactions by Biotinylated dCas9.</a> Cell. 170 (5), 1028-1043 (2017).</li><li>Myers, S. A., Wright, J., Zhang, F., Carr, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CRISPR/Cas9-APEX-mediated+proximity+labeling+enables+discovery+of+proteins+associated+with+a+predefined+genomic+locus+in+living+cells.">CRISPR/Cas9-APEX-mediated proximity labeling enables discovery of proteins associated with a predefined genomic locus in living cells.</a> bioRxiv. , (2017).</li><li>D&#233;jardin, J., Kingston, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+of+Proteins+Associated+with+Specific+Genomic+Loci.">Purification of Proteins Associated with Specific Genomic Loci.</a> Cell. 136 (1), 175-186 (2009).</li><li>Buxton, K. 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=Elucidating+Protein-DNA+Interactions+in+Human+Alphoid+Chromatin+via+Hybridization+Capture+and+Mass+Spectrometry.">Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry.</a> J. Proteome Res. 16 (9), 3433-3442 (2017).</li><li>Kennedy-Darling, J., Holden, M. T., Shortreed, M. R., Smith, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+programmable+release+of+captured+DNA.">Multiplexed programmable release of captured DNA.</a> Chembiochem. 15 (16), 2353-2356 (2014).</li><li>Fujita, T., Fujii, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+specific+genomic+regions+and+identification+of+associated+molecules+by+engineered+DNA-binding+molecule-mediated+chromatin+immunoprecipitation+(enChIP)+using+CRISPR.">Isolation of specific genomic regions and identification of associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR.</a> Chromatin Protoc. Third Ed. , 43-52 (2015).</li><li>Lambert, J. -. P., Mitchell, L., Rudner, A., Baetz, K., Figeys, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Novel+Proteomics+Approach+for+the+Discovery+of+Chromatin-associated+Protein+Networks.">A Novel Proteomics Approach for the Discovery of Chromatin-associated Protein Networks.</a> Mol Cell Proteomics. 8 (4), 870-882 (2009).</li></ol>

The HyCCAPP method described here has many unique features that make it a powerful approach to uncover DNA-interactions that otherwise would remain elusive. The nature of the process gives HyCCAPP the flexibility to work in different organisms and regions of the genome. It is a method, however, that has several limitations to be considered.
HyCCAPP is a method that avoids any cell modifications so that it can potentially be applied in primary cells, cell culture systems, or even tissue samples...

During the past decade, there has seen a dramatic improvement in sequencing technologies, allowing the study of a wide range of genomes in large numbers of samples, and with astonishing resolution. The Encyclopedia of DNA Elements (ENCODE) Consortium, a large-scale multi-institutional effort spearheaded by the National Human Genome Research Institute of the National Institutes of Health, has provided insights into how individual transcription factors and other regulatory proteins bind to and interact with the genome. The initial effort characterized specific DNA-protein interactions, as assessed by Chromatin immunoprecipitation (ChIP) for over 100 known DNA-binding proteins1. Alternative methods such as DNase footprinting2 and formaldehyde assisted isolation of regulatory elements (FAIRE)3 have also been used to locate specific regions of the genome interacting with proteins, but with the obvious limitation that these experimental approaches do not identify the interacting proteins. Despite the extensive efforts over the past years, no technology has emerged that efficiently allows the comprehensive characterization of protein-DNA interactions in chromatin, and the identification and quantification of chromatin-associated proteins.
To address this need, we developed a novel approach which we termed as Hybridization Capture of Chromatin-Associated Proteins for Proteomics (HyCCAPP). Initially developed in yeast4,5,6, the approach isolates crosslinked chromatin regions of interest (with bound proteins) using sequence-specific hybridization capture. After isolation of the protein-DNA complexes, approaches such as mass spectrometry can be used to characterize the set of proteins bound to the sequence of interest. Thus, HyCCAPP can be considered as a non-biased approach to uncover novel DNA-protein interactions, in the sense that it does not rely on antibodies and it is completely agnostic about the proteins that might be found. There are other approaches capable to uncover novel DNA-interacting proteins7, but most rely on ChIP-like methods8,9,10, plasmid insertions11,12,13,14, or regions with high copy numbers15. In contrast, HyCCAPP can be applied to multi- and single-copy regions, and it does not require any prior information about the proteins in the region. In addition, while some of the methods mentioned above have valuable features, notably avoiding the need for DNA-protein crosslinking reactions, the unique feature of HyCCAPP is that it can be applied to single-copy regions in unmodified cells, and without any prior knowledge about putative binding proteins, or available antibodies.
At this point, HyCCAPP has predominantly been applied to the analysis of various genomic regions in yeast4,5,6, and was recently used to analyze protein-DNA interactions in alpha-satellite DNA, a repeat region in the human genome16. As part of our ongoing work, we have adapted the hybridization capture approach initially developed for yeast chromatin to be applicable to the analysis of human cells, and present here a modified protocol that allows the selective capture of single-copy target regions in the human genome with efficiencies similar to our initial studies in yeast. This new optimized protocol now allows the adaptation and utilization of the technology to interrogate protein-DNA interactions across the human genome, using mass spectrometry or other analytical approaches.
It is important to emphasize that the HyCCAPP method is meant for the analysis of specific target regions and is not yet suitable for genome-wide analyses. The technology is especially useful when dealing with regions for which there is scarce information about interacting proteins, or when a more comprehensive in-depth analysis of interacting proteins at a specific genome locus is desired. HyCCAPP is meant to uncover DNA-binding proteins but not characterize accurately the specific protein binding sites in genomic DNA. In its current implementation, the methodology does not provide information about the DNA binding sequences or motifs for individual proteins. Therefore, it nicely complements existing technologies such as FAIRE, and may allow the identification of novel binding proteins in genomic regions identified by an initial FAIRE analysis.

<table>
	<tbody>
		<tr>
			<td>PrimerQuest tool</td>
			<td>IDT</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>OligoAnalyzer 3.1</td>
			<td>IDT</td>
			<td></td>
			<td>Analyze capture oligonucleotids</td>
		</tr>
		<tr>
			<td>PairFold</td>
			<td>UBC</td>
			<td></td>
			<td>Analyze interactions</td>
		</tr>
		<tr>
			<td>RPMI 1640 media</td>
			<td>Thermo Fisher</td>
			<td>11875093</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-streptomycin</td>
			<td>Thermo Fisher</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>L-Glutamine&#160;</td>
			<td>Thermo Fisher</td>
			<td>25030081</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Thermo Fisher</td>
			<td>26140079</td>
			<td></td>
		</tr>
		<tr>
			<td>Countess automated cell counter</td>
			<td>Thermo Fisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>850 cm2 roller bottle&#160;</td>
			<td>Greiner Bio-one</td>
			<td>680058</td>
			<td></td>
		</tr>
		<tr>
			<td>Roller system</td>
			<td>Wheaton</td>
			<td>22-288-525</td>
			<td></td>
		</tr>
		<tr>
			<td>37 % formaldehyde&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>F8775</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Igepal CA-630</td>
			<td>Sigma-Aldrich</td>
			<td>I3021</td>
			<td></td>
		</tr>
		<tr>
			<td>Protease inhibitor cocktail</td>
			<td>Sigma-Aldrich</td>
			<td>P4380</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Thermo Fisher</td>
			<td>15630080</td>
			<td></td>
		</tr>
		<tr>
			<td>Branson digital sonifier SFX 150</td>
			<td>Emerson</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit 3.0 fluorometer</td>
			<td>Thermo Fisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit dsDNA BR assay kit</td>
			<td>Thermo Fisher</td>
			<td>Q32850</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioanalyzer 2100</td>
			<td>Agilent</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent DNA 1000 kit</td>
			<td>Agilent</td>
			<td>5067-1504</td>
			<td></td>
		</tr>
		<tr>
			<td>MES sodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>M3885</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl 5M</td>
			<td>Thermo Fisher</td>
			<td>AM9760G</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DynaMag-2 magnet</td>
			<td>Thermo Fisher</td>
			<td>12321D</td>
			<td></td>
		</tr>
		<tr>
			<td>DynaMag-15 magnet</td>
			<td>Thermo Fisher</td>
			<td>12301D</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynabeads M-280 atreptavidin</td>
			<td>Thermo Fisher</td>
			<td>60210</td>
			<td></td>
		</tr>
		<tr>
			<td>Low binding tubes</td>
			<td>Eppendorf</td>
			<td>22431081</td>
			<td></td>
		</tr>
		<tr>
			<td>Hybridization oven</td>
			<td>SciGene</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Tube shaker and rotator</td>
			<td>Thermo Fisher</td>
			<td>415110Q</td>
			<td></td>
		</tr>
		<tr>
			<td>DNase I (RNase-free)</td>
			<td>New England BioLabs</td>
			<td>M0303</td>
			<td></td>
		</tr>
		<tr>
			<td>SSC buffer 20&#215; concentrate</td>
			<td>Sigma-Aldrich</td>
			<td>S6639</td>
			<td></td>
		</tr>
	</tbody>
</table>

adaptation of hybridization capture of chromatin-associated proteins for proteomics to mammalian cells

The hybridization capture of chromatin-associated proteins for proteomics (HyCCAPP) technology was initially developed to uncover novel DNA-protein interactions in yeast. It allows analysis of a target region of interest without the need for prior knowledge about likely proteins bound to the target region. This, in theory, allows HyCCAPP to be used to analyze any genomic region of interest, and it provides sufficient flexibility to work in different cell systems. This method is not meant to study binding sites of known transcription factors, a task better suited for Chromatin Immunoprecipitation (ChIP) and ChIP-like methods. The strength of HyCCAPP lies in its ability to explore DNA regions for which there is limited or no knowledge about the proteins bound to it. It can also be a convenient method to avoid biases (present in ChIP-like methods) introduced by protein-based chromatin enrichment using antibodies. Potentially, HyCCAPP can be a powerful tool to uncover truly novel DNA-protein interactions. To date, the technology has been predominantly applied to yeast cells or to high copy repeat sequences in mammalian cells. In order to become the powerful tool we envision, HyCCAPP approaches need to be optimized to efficiently capture single-copy loci in mammalian cells. Here, we present our adaptation of the initial yeast HyCCAPP capture protocol to human cell lines, and show that single-copy chromatin regions can be efficiently isolated with this modified protocol.

Due to the need for large input amounts of chromatin for HyCCAPP to succeed, cells are grown to relatively high levels of confluency. Trypan blue staining is used to confirm that cell death rates are moderate (&#60;10 %). In single copy experiments, chromatin content prior to hybridization capture needs to be in the femtomolar range, which usually requires at least 109 cells as starting material. Prior to full scale experiments, it is recommended to test capture oligonucleotide...

Watch this Scientific Journal Video about Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells at JoVE.com

Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells

This is a method to identify novel DNA-interacting proteins at specific target loci, relying on sequence-specific capture of crosslinked chromatin for subsequent proteomic analyses. No prior knowledge about potential binding proteins, nor cell modifications are required. Initially developed for yeast, the technology has now been adapted for mammalian cells.

The hybridization capture of chromatin-associated proteins for proteomics (HyCCAPP) technology was initially developed to uncover novel DNA-protein ...

This method can help answer key questions in our understanding of genome regulation, such as how disease associated sequence variants in non-coding regions affect gene expression and regulation by altering protein binding, and it can help identify those proteins. The main advantage of this technique is that it does not require any sort of genetic manipulation of cells or tissues, nor antibodies, and no prior knowledge of DNA binding proteins that might interact with DNA at that locus. Demonstrating this procedure will be Danu Perumalla, a technician from my laboratory.After designing oligonucleotides according to the text protocol, plate 2 to 5 times 10 to the 5th lymphoblastoid cells, or other cell lines, in a T25 flask with 6 milliliters of RPMI 1640 medium, supplemented with 1%Pen Strep, 2 mil or more L-glutamine, and 5%FBS. Incubate the cells at 37 degrees Celsius, and 5%carbon dioxide. Use a hemocytometer, or an automated cell counter, to measure the cell density.Before the cells reach 1 times 10 to the 6 cells per milliliter, spin them down at 100 times G for five minutes, and transfer them to a T75 flask with 25 milliliters of the RPMI 1640 medium prepared earlier in this video. Grow the cells until the reach a cell density of 1 times 10 to the 6 cells per milliliter, then transfer the cells to a T150 flask in 38 milliliters of the same medium, and grow them for an additional two days. Next, spin down the cells at 100 times G for five minutes, and resuspend them in 10 milliliters of RPMI 1640 medium.Then pour the suspension into an 1850 square centimeter roller bottle containing 500 milliliters of medium, and incubate the cells under the same conditions as before, except with constant rotation. Once the desired cell count is reached, spin down the culture at 100 times G for five minutes, and resuspend the cells in 36 milliliters of RPMI 1640 medium. Then transfer the cell suspension to a 50 milliliter conical tube, and remove small aliquots for cell counting and DNA extraction.To cross-link the cells, add 1 milliliter of 37%formaldehyde to reach a final concentration of 1%Then incubate the cells at 10 to 30 RPM in room temperature for 10 minutes. Quench the cross-linking reaction by adding 2 milliliters of a 2.5 molar glycine solution for a final concentration of 125 millimolar. Then incubate the cells with rotation for five minutes.After pelleting the cells by centrifugation, use ice-cold 1X PBS to wash the cells twice. Continue with lysis and sheering of the cells, or resuspend the pellet in 5 milliliters of cell lysis buffer, and snap-freeze the suspension drop-by-drop in liquid nitrogen. Then store the samples at minus 80 degrees Celsius.To carry out lysis and sheering, resuspend the pellet in 20 milliliters of cell lysis buffer. The centrifuge the cells at 400 times G, in 4 degrees Celsius for five minutes. Discard the supernatant, and resuspend the cells in 6 milliliters of nuclei lysis buffer with protease inhibitors.In preparation for sonication, divide the sample evenly into six to eight Microfuge tubes. Place the samples on ice or a cold rack, and use a sonicator with a microtip to sonicate them at 65%amplitude with five 20-second constant bursts, allowing the suspension to cool down for at least 40 seconds between pulses. Centrifuge the cells at 12, 000 times G, and 4 degrees Celsius for 10 minutes, then transfer the supernatant to a new tube, and discard the pellets.After estimating the total recovery using fluorometry, snap freeze the samples. Following the preparation of hybridization and wash buffers according to the text protocol, use 1, 200 microliters of 1X hybridization buffer to wash 600 microliters of beads three times. Then use 1, 200 microliters of 2X hybridization buffer to resuspend the beads.In 1.5 milliliter microcentrifuge tubes, add 600 microliters of sample, 120 microliters of washed beads suspended in 2X hybridization buffer, and 480 microliters of 2X hybridization buffer. Incubate the tubes at 31 degrees Celsius, and 30 to 60 RPM for 10 minutes. Then place the tubes on a magnet, until the beads are immobilized, and transfer the samples to new tubes before discarding the beads.Resuspend the capture oligonucleotides to a working solution of 10 picomoles per microliter, and add 4 microliters of this solution to each tube. Incubate the tubes at 42 degrees Celsius in 30 to 60 RPM for 40 minutes. During the incubation, set aside the beads needed, wash the beads three times as before, but this time use 1X hybridization buffer to resuspend them.Add the washed beads to the tubes, and incubate the samples at 30 to 60 RPM in room temperature for 30 minutes. Place the tubes on the magnet, and remove the supernatant once the beads have been immobilized. After washing the beads, elute the sample by adding 40 microliters of molecular grade water, and incubate the tubes at 94 degrees Celsius for five minutes.Place the tubes on the magnet, and wait a couple of minutes until the solution clears, then transfer the supernatant into a new tube, and discard the beads. Store the sample at minus 80 degrees Celsius, or proceed to the proteomic analysis according to the text protocol. To evaluate the capture yield, use molecular grade water to dilute an aliquot of the eluate, one to ten.After extracting the DNA from an aliquot taken earlier in the video, use the DNA sample and molecular grade water to prepare a standard curve, with five serial one to ten dilutions. Prepare a qPCR master mix adding primers and probes, and dispense the appropriate amount in each well of the reaction. To each well, add 5 microliters of either the diluted sample, the standard curve, or molecular grade water to serve as no template control.Seal the plate and spin it at 100 times G for one minute. Then run the samples in a qPCR system using the parameters found in the text protocol. Finally, use the standard curve to assess yields, and scrambled capture to assess capture specificity.Shown here are hybridization captures using a titration of oligonucleotides. The number of oligonucleotides is gradually increased, while the total concentration is kept constant. This experiment helps to determine how many different oligonucleotides are needed to reach optimal hybridization efficiencies.It also reveals any obvious detrimental hybridization interactions between a particular set of oligonucleotides, and if there are any oligos with poor specificity, resulting in high background. A large proportion of fragments in the cross linked chromatin will not be amenable for hybridization capture. If the hybridization capture is successfully run, a subsequent capture experiment of the same chromatin material, using a different set of capture oligonucleotides, will result in comparable yields as when using fresh chromatin.However, in a second capture experiment using the original oligos and leftover chromatin from the first experiment, the yield will decrease approximately 90%if most of the hybridization amenable material had been captured in the first experiment. This figure shows the hybridization capture of different chromosomal target regions, with each region serving as a negative control for the other. A scrambled sequence also serves as a true negative control.Once mastered, this technique can be done in two days, if it is performed properly. While attempting this procedure, it's important to remember to test the capture oligonucleotides first, to assure that the desired region is amenable to hybridization capture. Following this procedure, other methods, like chromatin immunoprecipitation, can be performed to answer additional questions, like where else in the genome the identified DNA interacting proteins bind.After watching this video, you should have a good understanding of how to perform HyCCAPP in order to enrich genomic regions of interest with the purpose of de novo identification of local protein interactions.

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Genetics

Methyl-binding DNA capture Sequencing for Patient Tissues

Methylation is one of the essential epigenetic modifications to the DNA, which is responsible for the precise regulation of genes required for stable ...

Analysis of Cap-binding Proteins in Human Cells Exposed to Physiological Oxygen Conditions

Translational control is a focal point of gene regulation, especially during periods of cellular stress. Cap-dependent translation via the eIF4F complex ...

Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells

The CRISPR/Cas9 genome engineering system has revolutionized biology by allowing for precise genome editing with little effort. Guided by a single guide ...

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

Investigating the three-dimensional architecture of chromatin offers invaluable insight into the mechanisms of gene regulation. Here, we describe a ...

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

Appropriate gene expression in response to extracellular cues, that is, tissue- and lineage-specific gene transcription, critically depends on highly ...

A Simple, Rapid, and Quantitative Assay to Measure Repair of DNA-protein Crosslinks on Plasmids Transfected into Mammalian Cells

The purpose of this method is to provide a flexible, rapid, and quantitative technique to examine the kinetics of DNA-protein crosslink (DPC) repair in ...

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Cross-talk between genes, transcripts, and proteins is the key to cellular responses; hence, analysis of molecular levels as distinct entities is slowly ...

CRISPR Guide RNA Cloning for Mammalian Systems

The outlined protocol describes streamlined methods for the efficient and cost-effective generation of Cas9-associated guide RNAs. Two alternative ...

Chromatin Immunoprecipitation Assay Using Micrococcal Nucleases in Mammalian Cells

To express cellular phenotypes in organisms, living cells execute gene expression accordingly, and transcriptional programs play a central role in gene ...

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Genome annotation is central to today's proteomic research as it draws the outlines of the proteomic landscape. Traditional models of open reading frame ...