Name: detection of post-translational modifications on native intact nucleosomes by elisa
Uploaded: 2011-04-26T14:00:00
Duration: 7 min 13 s
Description: Watch this Scientific Journal Video about Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA at JoVE.com

Development of the NU-ELISA method was supported by NIH grant RO1AG023687.

1. Mammalian Cell Culture 
NU-ELISA can be performed on any mammalian cell type that can be grown in culture. We prefer to prepare moderate to large batches of cells so that nucleosomes can be isolated in sufficient quantity to prepare several identically loaded ELISA plates, thus allowing assays with several different antibodies (Abs). The following culture scales provide ample material:
For mouse embyronic stem cells, grow one or two 15 cm plates of cells without feeder cells.
For fibroblasts, grow 5 to 10 15 cm plates to confluence.
2. Isolation of Nuclei
Note: All the steps are on ice with pre-chilled buffers, except as indicated.
<ol>
	<li>Trypsinize cells with 3 ml trypsin per plate, combine, and add 20 ml of ice-cold PBS/butyrate. Centrifuge at 1000 rpm for 5 min.</li>
 <li>Resuspend the cells in 10 ml PBS/butyrate and centrifuge at 1000 rpm for 5 min.</li>
 <li>Resuspend in 4 ml lysis buffer with protease inhibitors (Sigma-Aldrich P-8340). Dounce homogenize 20 strokes with type B pestle on ice.</li>
 <li>Centrifuge at 2000g for 10 min at 4&deg;C. (The supernatant contains cytoplasm, which is not needed for this protocol, but it can be saved for other uses if desired).</li>
 <li>Resuspend the pellet in 2 ml ice cold wash buffer C (with protease inhibitors). </li>
 <li>Layer the resuspended material over 5 ml 30% sucrose cushion, then centrifuge at 2400g for 5 min in a swinging bucket rotor. Nuclei will migrate through cushion, and debris remains at the interface.</li>
 <li>Remove all liquid volume carefully and resuspend the nuclei in 250 &mu;l ice cold wash buffer C + protease inhibitors.</li>
</ol>
3. Isolation of Nucleosomes by in situ Micrococcal Nuclease (MNase) Digestion
We use a procedure in which chromatin is digested in situ within nuclei by infusing them with MNase, followed by a hypotonic treatment to drive free intact nucleosomes into the supernatant. 
<ol>
	<li>Add 3 &mu;l 0.1 M CaCl2 to the sample. Put in 37&deg;C heat block. Allow to assume 37&deg;C temperature.</li>
 <li>Add 2 units MNase (Micrococcal Nuclease, Sigma-Aldrich, dissolved at 2 units/10&mu;l in MNase buffer), then incubate for at 37&deg;C for 12 min, with frequent mixing using a pipet tip.</li>
 <li>Add 6 &mu;l of 0.5 M Na-EDTA, pH 8.0 to stop the reaction. Put on ice.</li>
 <li>Centrifuge at 2000g for 4 min, discard supernatant. Resuspend the pellet in 300 &mu;l 0.2 mM Na-EDTA. Store on ice for 1 h with occasional gentle pipeting. (These hypotonic conditions liberate free nucleosomes from nuclei).</li>
 <li>Centrifuge at 3000 g for 4 min at 4&deg;C. Save the supernatant, which contains free nucleosomes, on ice. </li>
 <li>Resuspend the pellet again with 300 &mu;l 0.2 mM Na-EDTA. Store on ice for 1 h with occasional gentle pipeting.</li>
 <li>Centrifuge at 3000g for 4min at 4&deg;C. Retain the supernatant and combine with the first supernatant from step 5. The resulting mononucleosome preparations can be aliquoted and stored at -80&deg;C. </li> 
</ol>
Note: The amount of chromatin can be crudely quantitated by measuring absorbance at 260 nm of a 10 &mu;l sample added to 990 &mu;l of water. A260=10 (after adjusting for the 1/100 dilution) corresponds to about 1mg/ml of chromatin. Also, during the above procedure, small samples may be retained and later analyzed for their DNA content to monitor the quality and extent of MNase digestions, which should predominantly contain DNA of 146 bp in length. Laddering is indicative of incomplete MNase digestion.
Note: Fig.1 contains a diagrammed summary of nuclear isolation and MNase digestions steps. 
4. Nucleosome-ELISA (NU-ELISA)
We detect PTMs on fractions containing native intact nuclesosomes that have been immobilized on 96 well ELISA microtiter plates. For each sample, we make a series of 2-fold dilutions, and these are coated onto wells in triplicate. 
<ol>
	<li>Coat MaxiSorp plates overnight at 4&deg;C with 50 &mu;l/well of nucleosomes diluted in coating buffer. Suggested serial twofold dilutions of nucleosomes are prepared from top row to the bottom row by adding 0.1 &mu;g, 0.05 &mu;g, 0.025 &mu;g, 0.0125 &mu;g, 0.00625 &mu;g, 0.00313 &mu;g, 0.00156 &mu;g, with coating buffer only (0 &mu;g chromatin) in the bottom row. (Note: plate covers are needed for this step.)</li>
 <li>In the morning, wash the plates 4 times with 200 &mu;l/well PBS/0.5% Tween-20 at room temperature (RT) for a combined total of 10 min with a plate washer. </li>
 <li>Block 1 hr at RT with 100 &mu;l/well PBS/0.05% Tween-20/5% BSA.</li>
 <li>Remove the blocking buffer by shaking the inverted plate briskly over a sink. Cover and store the plates at -20&deg;C, or go directly to the next step.</li>
 <li>Add 1&deg; Abs in a volume of 50 &mu;l/well diluted 1:1000 (or as needed) in PBS/0.05% Tween-20/5% BSA, incubate at RT for 1 hour on a rotator.</li>
 <li>Wash plates 4 times with 200 &mu;l/well PBS/0.5% Tween-20 at RT and for a combined total of 10 min in a plate washer.</li>
 <li>Add horse radish peroxidase (HRP)-conjugated 2&deg; Abs, diluted 1:5000 (or as needed) in PBS/0.05% Tween-20/5% BSA at RT for an hour on a rotator.</li>
 <li>Wash plates 4 times with 200 &mu;l/well PBS/0.5% Tween-20. Each wash is at RT and for a total of 10 minutes with a plate washer.</li>
 <li>Develop the plates by adding 50 &mu;l of TMB substrate to each well for 10 min at RT. Stop the reaction by adding 50 &mu;l/well of 2N H2SO4 and read the plates 450 nm. (Tip: Centrifuge at 1500 rpm for 2 min using a plate rotor to dissipate any air bubbles in the wells prior to reading absorbances). </li>
 <li>Export the readings to spreadsheet files for quantitative and statistical analyses.</li> 
</ol>
Reagents
<table border="1">
 <tbody>	
 	<tr>
 	<td>PBS/butyrate</td>
 </tr>
 <tr>
 	<td>135 mM NaCl</td>
 </tr>

	<tr>
 	<td>2.5 mM KCl</td>
 </tr>
 <tr>
 	<td>8 mM Na2HPO4</td>
 </tr>
 <tr>
 	<td>1.5 mM KH2PO4</td>
 </tr>
 <tr>
 	<td>10 mM Na-butyrate</td>
 </tr> 
 </tbody>
</table>
<table border="1">
	<tbody>
 	<tr>
 	<td>Lysis Buffer</td>
 </tr>
 <tr>
 	<td>250 mM sucrose</td>
 </tr>
 <tr>
 	<td>10 mM Tris-HCl, pH 7.4</td>
 </tr>
 <tr>
 	<td>10 mM Na-butyrate</td>
 </tr>
 <tr>
 	<td>4 mM MgCl2</td>
 </tr>
 <tr>
 	<td>0.1% Triton X-100</td>
 </tr>
 </tbody>
</table>


<table border="1">
	<tbody>
 	<tr>
 	<td>Wash buffer C</td>
 </tr>
 <tr>
 	<td>250 mM sucrose</td>
 </tr>
 <tr>
 	<td>10 mM Tris-HCl, pH 7.4</td>
 </tr>
 <tr>
 	<td>10 mM Na-butyrate</td>
 </tr>
 <tr>
 	<td>4 mM MgCl2</td>
 </tr>
 
 </tbody>
</table>
<table border="1">
	<tbody>
 	<tr>
 	<td>Sucrose Cushion</td>
 </tr>
 <tr>
 	<td>30% (w/v) sucrose in wash buffer C</td>
 </tr>
 </tbody>
</table>
<table border="1">
	<tbody>
 <tr>
 	<td>Microccocal Nuclease Buffer</td>
 </tr>
 <tr>
 	<td>5 mM NaPO4 Buffer, pH 7.0 </td>
 </tr>
 <tr>
 	<td>0.025 mM CaCl2</td>
 </tr>
 </tbody>
</table>
<table border="1">
	<tbody>

 <tr>
 	<td>Coating buffer </td>
 </tr>
 <tr>
 	<td>80ml Solution A + 170ml Solution B + 250ml dH2O</td>
 </tr>
 <tr>
 	<td>Solution A: 0.2 M Na2CO3 </td>
 </tr>
 <tr>
 	<td>Solution B: 0.2 M NaHCO3</td>
 </tr>
 </tbody>
</table> 
5. Representative Results
Using the NU-ELISA method, a series of several identical plates are prepared which can be loaded with chromatin prepared in the form of mononucleosomes. We typically prepare series of identically-loaded plates so that each can be probed with different anti-PTM specific antibodies (Abs). We also always prepare a plate that can be probed with an Ab that detects histones without regard to their modification state total chromatin loading control. This control is essential in order to later quantitatively compare PTM content of nucleosomes prepared from different samples. To quantitate the levels of PTMs within a given chromatin sample we correct the raw absorbance values using this approach: First, we subtract any background signal using values obtained from control wells containing no chromatin (background is usually negligible). We then standardize PTM-specific signals to NU-ELISA results obtained from an identically loaded plate that was assayed with an Ab that detects nucleosomes independent of their modification state. (We have used polyclonal Abs specific for histones H2A or H2B for this purpose). We then determine means and variances for each dilution of chromatin, and use data obtained from the linear portion of the ELISA assay. Detailed examples of NU-ELISA mathematical and statistical analyses have been reported previously4 
<img src="/files/ftp_upload/2593/2593fig1.jpg" alt="Figure 1"/> 
Figure 1. Schematic diagam of NU-ELISA steps. A. Mammalian Cells are harvested; B. Nuclei are separated from cells by Dounce homogenization, C. Disrupted cells are loaded on top of a 30% w/v sucrose cushion, D. After centrifugation, nuclei are deposited in the pellet; E, F. Chromatin are digested in situ to predominantly mononucleomes by MNase; G, H, I. Soluble mononucleosomes are extracted by hypotonic treatment and repeated centrifugation of residual nuclear material. J. Mononucleosomes from different samples (labeled samp. 1 and 2 in this case) are coated on microtiter wells in series of identically-loaded plates and interrogated with PTM-specific Abs and PTM-independent Abs to determine total chromatin loading. K. Depiction of differential signal detection levels in two samples that differ in their PTM content, yet have similar overall chromatin content, as judged by anti-H2B immunoreactivity.

<ol>
	<li>Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., Richmond, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crystal+structure+of+the+nucleosome+core+particle+at+2.8+A+resolution.">Crystal structure of the nucleosome core particle at 2.8 A resolution.</a> Nature. 389, 251-260 (1997).</li><li>Jenuwein, T., Allis, C. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Translating+the+histone+code.">Translating the histone code.</a> Science. 293, 1074-1080 (2001).</li><li>Turner, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histone+acetylation+and+an+epigenetic+code.">Histone acetylation and an epigenetic code.</a> Bioessays. 22, 836-845 (2000).</li><li>Dai, B., Rasmussen, T. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+epiproteomic+signatures+distinguish+embryonic+stem+cells+from+differentiated+cells.">Global epiproteomic signatures distinguish embryonic stem cells from differentiated cells.</a> Stem Cells. 25, 2567-2574 (2007).</li><li>Tanasijevic, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Progressive+accumulation+of+epigen+etic+heterogeneity+during+human+ES+cell+culture.">Progressive accumulation of epigen etic heterogeneity during human ES cell culture.</a> Epigenetics. 4, 330-338 (2009).</li><li>Thomas, J. O., Gould, 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+and+fractionation+of+chromatin+and+linker+histones.">Isolation and fractionation of chromatin and linker histones.</a> Chromatin: a practical approach. , 12-14 (1998).</li><li>Thorne, A. W., Cary, P. D., Crane-Robinson, C., Gould, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extraction+and+separation+of+core+histones+and+non-histone+chromosomal+proteins.">Extraction and separation of core histones and non-histone chromosomal proteins.</a> Chromatin: a practical approach. , 38-39 (1998).</li></ol>

No conflicts of interest declared.

NU-ELISA provides a method to ascertain the global status of nucleosome PTMs present within a particular cell type. NU-ELISA studies have shown that global nucleosome modification states differ in comparisons of divergent cell types 4. In addition, NU-ELISA PTM profiles change when cells are exposed to epigenetic modulatory agents such as trichostatin-A or when mouse embyronic stem cells are differentiated 4. The method has also been applied successfully to study the chromatin of human ES cells5. It is important to note the NU-ELISA, in its present form, can detect only the composite signature of PTMs present within the sum total of the cellular epigenome. This differs markedly from genome-wide chromatin immunoprecipitation, which can determine the distribution of a specific PTM across specific genetic loci. 

The initial steps of the NU-ELISA procedures are adapted from previous methods to isolate mononucleosomes from mammalian nuclei6,7. These adapted methods provide an expedient way to obtain high-quality intact mononucleosomes from mammalian cells, and the resulting fractions are comprehensive in their chromatin content, but contain a great deal of additional nuclear material. Since specific Abs are used, contaminating non-nucleosomal material is tolerated well in the NU-ELISA assay, unlike mass-spec approaches that require greater purity. However, NU-ELISA is more sensitive and quantitative than western blotting 4, thus providing good alternatives to westerns and mass spec for the detection of nucleosomal PTMs.

<table border="1">
	<tbody>
 <tr>
 	<th>Name of the reagent</th>
 <th>Company</th>
 <th>Catalogue number</th>
 <th>Comments</th>
 </tr>
 <tr>
 	<td>Micrococcal Nucleae</td>
 <td>Sigma</td>
 <td>N3755</td>
 <td>Make aliquots of 2 U/10&mu;l buffer, stored at -20&deg;C</td>
 </tr>
 <tr>
 	<td>Nunc MaxiSorp Microtiter Plates</td>
 <td>Fisher</td>
 <td>12-565-135</td>
 <td>Adhesive plate covers can also be ordered through Fisher</td>
 </tr>
		<tr>
 	<td>Automated Plate Washer</td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 </tr>
 <tr>
 	<td>1-Step TMB-ELISA
substrate
</td>
 <td>Pierce</td>
 <td>34028</td>
 <td>Store at 4&deg;C pre-warm to RT before use or as directed on the specification sheet</td>
 </tr>
 <tr>
 	<td>Microtiter Plate Reader </td>
 <td>Bio-Rad microplate reader (model: 680)</td>
 <td>&nbsp;</td>
 <td>Most colorimetric plate reader models are suitable </td>
 </tr>
 </tbody>
</table>

detection of post-translational modifications on native intact nucleosomes by elisa

The genome of eukaryotes exists as chromatin which contains both DNA and proteins. The fundamental unit of chromatin is the nucleosome, which contains 146 base pairs of DNA associated with two each of histones H2A, H2B, H3, and H41. The N-terminal tails of histones are rich in lysine and arginine and are modified post-transcriptionally by acetylation, methylation, and other post-translational modifications (PTMs). The PTM configuration of nucleosomes can affect the transcriptional activity of associated DNA, thus providing a mode of gene regulation that is epigenetic in nature 2,3. We developed a method called nucleosome ELISA (NU-ELISA) to quantitatively determine global PTM signatures of nucleosomes extracted from cells. NU-ELISA is more sensitive and quantitative than western blotting, and is useful to interrogate the epiproteomic state of specific cell types. This video journal article shows detailed procedures to perform NU-ELISA analysis.

Watch this Scientific Journal Video about Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA at JoVE.com

Detection of Post-translational Modifications on Native Intact Nucleosomes by ELISA

Nucleosome ELISA (NU-ELISA) is a sensitive and quantitative method to detect global patterns of post-translational modifications in preparations of native, intact nucleosomes. These modifications include methylations, acetylations, and phosphorylations at specific histone amino acid residues, and hence NU-ELISA provides a global proteomic assay of the overall chromatin modification states of specific cell types.

The genome of eukaryotes exists as chromatin which contains both DNA and proteins. The fundamental unit of chromatin is the nucleosome, which contains 146 ...

Research

JoVE Journal

Biology

Detection of Functional Matrix Metalloproteinases by Zymography

Matrix metalloproteinases (MMPs) are zinc-containing endopeptidases. They degrade proteins by cleavage of peptide bonds. More than twenty MMPs have been ...

Analyzing the Function of Small GTPases by Microinjection of Plasmids into Polarized Epithelial Cells

Epithelial cells polarize their plasma membrane into biochemically and functionally distinct apical and basolateral domains where the apical domain faces ...

Detection of Histone Modifications in Plant Leaves

Chromatin structure is important for the regulation of gene expression in eukaryotes. In this process, chromatin remodeling, DNA methylation, and covalent ...

Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously ...

Identification of Post-translational Modifications of Plant Protein Complexes

Plants adapt quickly to changing environments due to elaborate perception and signaling systems. During pathogen attack, plants rapidly respond to ...

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP

The identification of molecules associated with specific genomic regions of interest is required to understand the mechanisms of regulation of the ...

En Face Detection of Nitric Oxide and Superoxide in Endothelial Layer of Intact Arteries

En Face Detection of Nitric Oxide and Superoxide in Endothelial Layer of Intact Arteries

Endothelium-derived nitric oxide (NO) produced from endothelial NO-synthase (eNOS) is one of the most important vasoprotective molecules in cardiovascular ...

High-throughput CRISPR Vector Construction and Characterization of DNA Modifications by Generation of Tomato Hairy Roots

Targeted DNA mutations generated by vectors with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology have proven useful for ...

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone ...

Comparison of Tobacco Host Cell Protein Removal Methods by Blanching Intact Plants or by Heat Treatment of Extracts

Plants not only provide food, feed and raw materials for humans, but have also been developed as an economical production system for biopharmaceutical ...