Name: the chrop approach combines chip and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin
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Description: Watch this Scientific Journal Video about The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin at JoVE.com

This research was originally published in Mol Cell Proteomics. Soldi M. and Bonaldi T. The Proteomic Investigation of Chromatin Functional Domains Reveals Novel Synergisms among Distinct Heterochromatin Components MCP. 2013; 12: 64-80. &#169; the American Society for Biochemistry and Molecular Biology. We thank Roberta Noberini (Italian Institute of Technology and IEO, Italy) for critical reading of the manuscript. TB work is supported by grants from the Giovanni Armenise-Harvard Foundation Career Development Program, the Italian Association for Cancer Research and the Italian Ministry of Health. MS work was supported by a FIRC fellowship.

1. Cell Culture
<ol>
	<li>Standard medium for native ChIP
	<ol>
		<li>Grow HeLa cells in Dulbecco&#39;s modified Eagle&#39;s medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% Glutamine, 1% Pen/Strep and 10 mM HEPES pH 7.5.</li>
	</ol>
	</li>
	<li>SILAC labelling for crosslinking ChIP
	<ol>
		<li>Grow HeLa cells in SILAC DMEM medium, depleted of lysine and arginine, supplemented with 10% dialyzed FBS, 1% Glutamine, 1% Pen/Strep, 10 mM HEPES pH 7.5 and either the light L-l...

<ol>
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We have recently described ChroP, a quantitative strategy for the large-scale characterization of the protein components of chromatin. ChroP combines two complementary approaches used in the epigenetic field, ChIP and MS, profiting from their strengths and overcoming their respective limitations. ChIP coupled to deep sequencing (ChIP-Seq) allows the genome-wide mapping of histone modifications at the resolution of few nucleosomes35. Although advantageous for their sensitivity, antibody-based assays are limited...

Chromatin is a highly dynamic nucleoprotein complex that is involved as primary template for all DNA-mediated processes. The nucleosome is the basic repeated unit of chromatin and consists of a proteinaceous octameric core containing two molecules of each canonical histone H2A, H2B, H3 and H4, around which 147 bp of DNA are wrapped1,2. All core histones are structured as a globular domain and a flexible N-terminal &#8220;tail&#8221; that protrudes outside the nucleosome. One of the major mechanisms for regulating chromatin structure and dynamics is based on covalent post-translational modifications (PTMs), which mainly occur on the N-termini of histones3,4. Histone modifications can function either by altering the higher order chromatin structure, by changing contacts between histones-DNA or between nucleosomes, and thus controlling the accessibility of DNA-binding proteins (cis mechanisms), or by acting as docking sites for regulatory proteins, either as single units, or embedded in multimeric complexes. Such regulating proteins can exert their function in different ways: by modulating directly gene expression (i.e. TAF proteins), or by altering the nucleosome positioning (i.e. chromatin remodeling complexes) or by modifying other histone residues (i.e. proteins with methyl-transferase or acetyl-transferase activity) (trans mechanisms)5. The observation that distinct PTM patterns cluster at specific chromatin loci led to the elaboration of the hypothesis that different modifications at distinct sites may synergize to generate a molecular code mediating the functional state of the underlying DNA. The &#34;histone code hypothesis&#34; has gained large consensus in the years but its experimental verification has been held back by technical limitations6,7.
Mass spectrometry (MS)-based proteomics has emerged as a powerful tool to map histone modification patterns and to characterize chromatin-binding proteins8. MS detects a modification as a specific &#916;mass between the experimental and theoretical mass of a peptide. At the level of individual histones, MS provides an unbiased and comprehensive method to map PTMs, allowing the detection of new modifications and revealing interplays among them9-14.
In recent years, a number of strategies have been developed to dissect the proteomic composition of chromatin, including the characterization of intact mitotic chromosomes15, the identification of soluble hPTM-binding proteins16-18 and the isolation and analysis of specific chromatin regions (i.e. telomeres)19,20. However, the investigation of the locus-specific synergies between histone PTMs, variants, and chromatin-associated proteins is still incomplete. Here, we describe a new approach, named ChroP (Chromatin Proteomics)21, that we have developed to efficiently characterize functionally distinct chromatin domains. This approach adapts chromatin immunoprecipitation (ChIP), a well-established protocol used in epigenetic research, for the efficient MS-based proteomic analysis of the enriched sample. We have developed two different protocols, depending on the type of chromatin used as input and the question addressed by MS; in particular: 1) ChIP of unfixed native chromatin digested with MNase is employed to purify mono-nucleosomes and to dissect the co-associating hPTMs (N-ChroP); 2) ChIP of crosslinked chromatin fragmented by sonication is used in combination with a SILAC-based interactomics strategy to characterize all co-enriching chromatin binding proteins (X-ChroP). We illustrate here the combination of N- and X-ChroP for enriching and studying heterochromatin, using H3K9me3 as bait for the immunoprecipitation steps. The use of ChroP can be extended to study either distinct regions on chromatin, or changes in the chromatin composition within the same region during the transition to a different functional state, thus paving the way to various applications in epigenetics.

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	<tbody>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">DMEM&#160;</td>
			<td style="width:145px;">Lonza</td>
			<td style="width:119px;">BE12-614F</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">FBS</td>
			<td style="width:145px;">Invitrogen</td>
			<td style="width:119px;">10270-106</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">SILAC DMEM</td>
			<td style="width:145px;">M-Medical</td>
			<td style="width:119px;">FA30E15086</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Dialyzed FBS</td>
			<td style="width:145px;">Invitrogen</td>
			<td style="width:119px;">26400-044</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Lysine 0 (12C6 14N2 L-lysine)</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td style="width:119px;">L8662</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Arginine 0 (12C6 14N4 L-arginine)</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td style="width:119px;">A6969</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Lysine 8 (13C6 15N2 L-lysine)</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td>68041</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Arginine 10 (13C6 15N4 L-arginine)</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td>608033</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Micrococcal Nuclease</td>
			<td style="width:145px;">Roche</td>
			<td style="width:119px;">10 107 921 001</td>
			<td></td>
		</tr>
		<tr height="53">
			<td height="53" style="height:53px;width:271px;">Complete, EDTA-free Protease Inhibitor Cocktail Tablets</td>
			<td style="width:145px;">Roche</td>
			<td style="width:119px;">04 693 132 001</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:271px;">Spectra/Por 3 dialysis tubing, 3.5K MWCO, 18mm flat width, 50 foot length</td>
			<td style="width:145px;">Spectrumlabs</td>
			<td style="width:119px;">132720</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:271px;">QIAquick PCR purification kit</td>
			<td style="width:145px;">QIAGEN</td>
			<td style="width:119px;">28104</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:271px;">Anti-Histone H3 tri-methylated K9-ChIP grade</td>
			<td>Abcam</td>
			<td>ab8898</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Histone H3 peptide tri-methyl K9&#160;</td>
			<td>Abcam</td>
			<td style="width:119px;">ab1773</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Dynabeads Protein G</td>
			<td>Invitrogen</td>
			<td style="width:119px;">100.04D</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:271px;">NuPAGE Novex 4-12%&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Bis-Tris Gel&#160;</td>
			<td>Invitrogen&#160;</td>
			<td>NP0335BOX</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Colloidal Blue Staining Kit</td>
			<td>Invitrogen&#160;</td>
			<td>LC6025</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">LDS Sample Buffer</td>
			<td>Invitrogen&#160;</td>
			<td>NP0007</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Formaldheyde</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td style="width:119px;">F8775</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Aceti anhydride-d6</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td style="width:119px;">175641-1G</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Formic Acid</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td style="width:119px;">94318-50ML-F</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:271px;">Iodoacetamide &#8805;99% (HPLC), crystalline</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td style="width:119px;">I6125</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">DL-Dithiothreitol</td>
			<td style="width:145px;">Sigma Aldrich</td>
			<td style="width:119px;">43815</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:271px;">Sequencing Grade Modified Trypsin, Frozen 100ug (5 &#215; 20&#956;g)</td>
			<td>Promega</td>
			<td style="width:119px;">V5113</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Nanospray OD 360&#956;m x ID 75&#956;m, tips ID 8&#956;m uncoated Pk 5</td>
			<td style="width:145px;">Microcolumn Srl</td>
			<td style="width:119px;">FS360-75-8-N-5-C15</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:271px;">&#160; ReproSil-Pur 120 C18-AQ, 3 &#181;m&#160;&#160; 15 % C</td>
			<td style="width:145px;">Dr. Maisch GmbH</td>
			<td style="width:119px;">r13.aq.</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">C18 extraction disk, 47 mm</td>
			<td style="width:145px;">Agilent Technologies</td>
			<td style="width:119px;">1&#8203;2&#8203;1&#8203;4&#8203;5&#8203;0&#8203;0&#8203;4</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Carbon extraction disk, 47 mm</td>
			<td style="width:145px;">Agilent Technologies</td>
			<td style="width:119px;">12145040</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:271px;">Cation extraction disk</td>
			<td style="width:145px;">Agilent Technologies</td>
			<td style="width:119px;">66889-U</td>
			<td></td>
		</tr>
	</tbody>
</table>

the chrop approach combines chip and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin

Chromatin is a highly dynamic nucleoprotein complex made of DNA and proteins that controls various DNA-dependent processes. Chromatin structure and function at specific regions is regulated by the local enrichment of histone post-translational modifications (hPTMs) and variants, chromatin-binding proteins, including transcription factors, and DNA methylation. The proteomic characterization of chromatin composition at distinct functional regions has been so far hampered by the lack of efficient protocols to enrich such domains at the appropriate purity and amount for the subsequent in-depth analysis by Mass Spectrometry (MS). We describe here a newly designed chromatin proteomics strategy, named ChroP (Chromatin Proteomics), whereby a preparative chromatin immunoprecipitation is used to isolate distinct chromatin regions whose features, in terms of hPTMs, variants and co-associated non-histonic proteins, are analyzed by MS. We illustrate here the setting up of ChroP for the enrichment and analysis of transcriptionally silent heterochromatic regions, marked by the presence of tri-methylation of lysine 9 on histone H3. The results achieved demonstrate the potential of ChroP in thoroughly characterizing the heterochromatin proteome and prove it as a powerful analytical strategy for understanding how the distinct protein determinants of chromatin interact and synergize to establish locus-specific structural and functional configurations.

Chromatin immunoprecipitation is a powerful technique used to profile the localization of a protein or a histone modification along the genome. In a proteomics equivalent, ChIP is followed by MS-based proteomics to identify qualitatively and quantitatively the hPTMs, histone variants and chromatin-binding proteins that are immunoprecipitated together with the modification or protein of interest, used as &#8220;bait&#8221;. In the N-ChroP approach, outlined in Figure 1A, native ChIP, in which chromatin is...

Watch this Scientific Journal Video about The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin at JoVE.com

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

By combining native and crosslinking chromatin immunoprecipitation with high-resolution Mass Spectrometry, ChroP approach enables to dissect the composite proteomic architecture of histone modifications, variants and non-histonic proteins synergizing at functionally distinct chromatin domains.

Chromatin is a highly dynamic nucleoprotein complex made of DNA and proteins that controls various DNA-dependent processes. Chromatin structure and ...

Research

JoVE Journal

Biology

MALDI Sample Preparation: the Ultra Thin Layer Method

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption ...

Electrophoretic Separation of Proteins

Electrophoresis is used to separate complex mixtures of proteins (e.g., from cells, subcellular fractions, column fractions, or immunoprecipitates), to ...

A Quantitative Assessment of The Yeast Lipidome using Electrospray Ionization Mass Spectrometry

Lipids are one of the major classes of biomolecules and play important roles membrane dynamics, energy storage, and signalling1-4. The budding yeast ...

Chromatin Immunoprecipitation (ChIP) to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells

Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells

In response to a variety of extracellular ligands, the STAT (signal transducer and activator of transcription) transcription factors are rapidly recruited ...

Chromatin Immunoprecipitation (ChIP) using Drosophila tissue

Chromatin Immunoprecipitation ChIP using Drosophila tissue

Epigenetics remains a rapidly developing field that studies how the chromatin state contributes to differential gene expression in distinct cell types at ...

Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry

Pseudomonas syringae pv. tomato strain DC3000 not only causes bacterial speck disease in Solanum lycopersicum but also on Brassica species, as well as on ...

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

The introduced protocol provides a tool for the analysis of multiprotein complexes in the thylakoid membrane, by revealing insights into complex ...

Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins

Considerable progress has been made during the last decade towards the identification and characterization of enzymes involved in the synthesis ...

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 ...

Identification of MyoD Interactome Using Tandem Affinity Purification Coupled to Mass Spectrometry

Skeletal muscle terminal differentiation starts with the commitment of pluripotent mesodermal precursor cells to myoblasts. These cells have still the ...