Name: chromatin immunoprecipitation of murine brown adipose tissue
Uploaded: 2018-11-21T15:00:00
Description: Watch this Scientific Journal Video about Chromatin Immunoprecipitation of Murine Brown Adipose Tissue at JoVE.com

The animal handling steps of the protocol have been approved by Boston University&#8217;s Institutional Animal Care and Use Committee (IACUC).
1. Day 1: Dissection and Preparation of BAT for Chromatin Immunoprecipitation (ChIP)
<ol>
	<li>Euthanize mice using a carbon dioxide (CO2) chamber, and perform the dissection immediately afterwards. Spray mouse fur with 70% ethanol before incision. Place the mouse with its back facing up, then cut open the skin along the neck. Locate the BA...

<ol>
	<li>Cannon, B., Nedergaard, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Brown+adipose+tissue:+function+and+physiological+significance.">Brown adipose tissue: function and physiological significance.</a> Physiological Reviews. , (2004).</li><li>Cardamone, M. D., 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=Mitochondrial+Retrograde+Signaling+in+Mammals+Is+Mediated+by+the+Transcriptional+Cofactor+GPS2+via+Direct+Mitochondria-to-Nucleus+Translocation.">Mitochondrial Retrograde Signaling in Mammals Is Mediated by the Transcriptional Cofactor GPS2 via Direct Mitochondria-to-Nucleus Translocation.</a> Molecular Cell. 69, (2018).</li><li>Emmett, M. 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=Histone+deacetylase+3+prepares+brown+adipose+tissue+for+acute+thermogenic+challenge.">Histone deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge.</a> Nature. , (2017).</li><li>Harms, M. 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=PRDM16+binds+MED1+and+controls+chromatin+architecture+to+determine+a+brown+fat+transcriptional+program.">PRDM16 binds MED1 and controls chromatin architecture to determine a brown fat transcriptional program.</a> Genes &amp; Development. , (2015).</li><li>Shapira, S. N., 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=EBF2+transcriptionally+regulates+brown+adipogenesis+via+the+histone+reader+DPF3+and+the+BAF+chromatin+remodeling+complex.">EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex.</a> Genes &amp; Development. , (2017).</li><li>Landt, S. G., 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=ChIP-seq+guidelines+and+practices+of+the+ENCODE+and+modENCODE+consortia.">ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.</a> Genome Research. 22, 1813-1831 (2012).</li><li>Liisberg Aune, U., Ruiz, L., Kajimura, S. <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+Differentiation+of+Stromal+Vascular+Cells+to+Beige/Brite+Cells.">Isolation and Differentiation of Stromal Vascular Cells to Beige/Brite Cells.</a> Journal of Visualized Experiments. , e50191 (2013).</li><li>Bolger, A. M., Lohse, M., Usadel, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trimmomatic:+a+flexible+trimmer+for+Illumina+sequence+data.">Trimmomatic: a flexible trimmer for Illumina sequence data.</a> Bioinformatics. 30, 2114-2120 (2014).</li><li>. Genome Browser Gateway Available from: <a target="_blank" href="https://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10">https://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10</a> (2018)</li><li>Langmead, B., Salzberg, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fast+gapped-read+alignment+with+Bowtie+2.">Fast gapped-read alignment with Bowtie 2.</a> Nature Methods. , 357-359 (2012).</li><li>Li, 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=The+Sequence+alignment/map+(SAM)+format+and+SAMtools.">The Sequence alignment/map (SAM) format and SAMtools.</a> Bioinformatics. 25 (16), 2078-2079 (2009).</li><li>Kharchenko, P. V., Tolstorukov, M. Y., Park, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+analysis+of+ChIP-seq+experiments+for+DNA-binding+proteins.">Design and analysis of ChIP-seq experiments for DNA-binding proteins.</a> Nature Biotechnology. 26, 1351-1359 (2008).</li><li>Carroll, T. S., Liang, Z., Salama, R., Stark, R., de Santiago, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+artifact+removal+on+ChIP+quality+metrics+in+ChIP-seq+and+ChIP-exo+data.">Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.</a> Frontiers in Genetics. 5, 75 (2014).</li><li>Ram&#237;rez, F., 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=deepTools2:+A+next+Generation+Web+Server+for+Deep-Sequencing+Data+Analysis.">deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis.</a> Nucleic Acids Research. , (2016).</li><li>Zhang, Y., 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=Model-based+Analysis+of+ChIP-Seq+(MACS).">Model-based Analysis of ChIP-Seq (MACS).</a> Genome Biology. 9, R137 (2008).</li><li>ENCODE Project Consortium. <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 (2012).</li><li>Quinlan, A. R., Hall, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BEDTools:+a+flexible+suite+of+utilities+for+comparing+genomic+features.">BEDTools: a flexible suite of utilities for comparing genomic features.</a> Bioinformatics. 26, 841-842 (2010).</li><li>Li, Q., Brown, J. B., Huang, H., Bickel, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+reproducibility+of+high-throughput+experiments.">Measuring reproducibility of high-throughput experiments.</a> Annals of Applied Statistics. 5 (3), 1752-1779 (2011).</li><li>. Irreproducible Discovery Rate (IDR) Available from: <a target="_blank" href="https://github.com/nboley/idr">https://github.com/nboley/idr</a> (2018)</li><li>The Gene Ontology Consortium. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expansion+of+the+Gene+Ontology+Knowledgebase+and+Resources.">Expansion of the Gene Ontology Knowledgebase and Resources.</a> Nucleic Acids Research. 45, D331-D338 (2017).</li><li>Ashburner, 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=Gene+Ontology:+tool+for+the+unification+of+biology.">Gene Ontology: tool for the unification of biology.</a> Nature Genetics. 25, 25-29 (2000).</li><li>Boeva, V. <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+Genomic+Sequence+Motifs+for+Deciphering+Transcription+Factor+Binding+and+Transcriptional+Regulation+in+Eukaryotic+Cells.">Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells.</a> Frontiers in Genetics. 7, 24 (2016).</li></ol>

The protocol described here represents a valuable tool for performing ChIP from murine tissues, specifically optimized for brown adipose tissue. One of the greater challenges in performing ChIP from tissue is recovering a sufficient number of cells during sample preparation. Shearing the BAT using a tissue homogenizer blender coupled with stainless steel beads instead of a canonical glass pestle significantly reduces the number of cells lost due to unbroken tissue. Moreover, homogenizing the tissue directly in a hypotoni...

While white adipose tissue (WAT) is specialized for energy storage, brown adipose tissue (BAT) dissipates energy in the form of heat due to its ability to convert carbohydrates and lipids into thermal energy via mitochondrial uncoupling1. Because of this specialized function, the BAT depot is required for maintenance of body temperature in physiological conditions and in response to cold exposure. While gene expression changes during BAT differentiation and upon thermogenic stress have been extensively studied in vivo and in vitro, the molecular mechanisms underlying these changes have been mostly dissected in immortalized cell lines and primary pre-adipocytes, with the exception of several in vivo studies2,3,4,5.
Regulation of specific gene expression programs through transcriptional regulation is achieved by coordinated changes in chromatin structure via various transcription factors and co-factors actions. Chromatin immunoprecipitation (ChIP) is a valuable molecular biology approach for investigating the recruitment of these factors to DNA and for profiling the associated changes in the chromatin landscape. Key factors for the success of ChIP experiments include optimizations of crosslinking conditions and chromatin shearing consistency throughout different samples, availability of adequate starting material, and, most notably, quality of the antibodies. When performing ChIP from whole tissues, it is also important to consider heterogeneity of the samples and optimize the protocol to improve efficiency of nuclei isolation, with the latter being a particularly sensitive step when working with adipose tissue due to the elevated lipid content. In fact, molecular isolation techniques from whole adipose depots are complicated by the presence of high levels of triglycerides, and protocols must be optimized to increase the amount of chromatin isolation. Finally, when high-throughput sequencing is performed after ChIP-DNA isolation, the sequencing depth is critical for determining the number of peaks that are confidently detected.
Here, we refer to the working standards and general guidelines for ChIP-seq experiments recommended by the ENCODE and modENCODE consortia6 for best practices, and we focus on a step-by-step description of a protocol optimized for ChIP-seq from BAT. The described protocol allows for efficient isolation of chromatin from adipose tissue to perform genome-wide sequencing for DNA-binding factors with well-defined peaks as well as histone marks with more diffuse signals.

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			<td height="42" style="height:42px;width:239px;">Bullet Blender Tissue Homogenizer&#160;</td>
			<td style="width:113px;">Next Advence&#160;</td>
			<td style="width:119px;">BBX24</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Stainless Steel Beads 3.2mm Diameter</td>
			<td style="width:113px;">Next Advence&#160;</td>
			<td>SSB32</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bioruptor Sonicator</td>
			<td>Diagenode</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1.5 ml Micro Tube TPX Plastic&#160;</td>
			<td>Diagenode</td>
			<td style="width:119px;">C30010010-5</td>
			<td></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:239px;">Complete-Protease inhibitor</td>
			<td style="width:113px;">Roche&#160;</td>
			<td>11836145001</td>
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			<td height="21" style="height:21px;">Protein A Agarose Slurry&#160;</td>
			<td style="width:113px;">Invitrogen&#160;</td>
			<td style="width:119px;">101041</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:239px;">GPS2 antibody</td>
			<td style="width:113px;">In house</td>
			<td style="width:119px;"></td>
			<td>Rabbit polyclonal, Ct antibody (Cardamone et al., Mol Cell 2018)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:239px;">Pol2 antibody&#160;</td>
			<td>Diagenode</td>
			<td style="width:119px;">C15100055</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:239px;">h3K9me3 antibody</td>
			<td style="width:113px;">Millipore&#160;</td>
			<td style="width:119px;">05-1242</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:239px;">Fast Syber Green Master Mix</td>
			<td style="width:113px;">Aplied Biosytem</td>
			<td style="width:119px;">4385612</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:239px;">ViiA7</td>
			<td style="width:113px;">Aplied Biosytem</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TruSeq ChIP Library Preparation Kit</td>
			<td style="width:113px;">Illumina&#160;</td>
			<td>IP-202-1012</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:239px;">HiSeq 2000&#160;</td>
			<td style="width:113px;">Illumina&#160;</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
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chromatin immunoprecipitation of murine brown adipose tissue

Most cellular processes are regulated by transcriptional modulation of specific gene programs. Such modulation is achieved through the combined actions of a wide range of transcription factors (TFs) and cofactors mediating transcriptional activation or repression via changes in chromatin structure. Chromatin immunoprecipitation (ChIP) is a useful molecular biology approach for mapping histone modifications and profiling transcription factors/cofactors binding to DNA, thus providing a snapshot of the dynamic nuclear changes occurring during different biological processes.
To study transcriptional regulation in adipose tissue, samples derived from in vitro cell cultures of immortalized or primary cell lines are often favored in ChIP assays because of the abundance of starting material and reduced biological variability. However, these models represent a limited snapshot of the actual chromatin state in living organisms. Thus, there is a critical need for optimized protocols to perform ChIP on adipose tissue samples derived from animal models.
Here we describe a protocol for efficient ChIP-seq of both histone modifications and non-histone proteins in brown adipose tissue (BAT) isolated from a mouse. The protocol is optimized for investigating genome-wide localization of proteins of interest and epigenetic markers in the BAT, which is a morphologically and physiologically distinct tissue amongst fat depots.

<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/58682/58682fig1.jpg" /> 
Figure 1: ChIP validation by qPCR. ChIP-qPCR analysis of representative GPS2 target genes NDUFV1 (left) and TOMM20 (right) in the BAT of WT and GPS2-AKO mice, showing relative changes in the level of H3K9 methylation and GPS2 and Pol2 binding. The bar graphs represent the sample mean of 3 replicates with *p &#60; 0.05 and **p &#60; 0.01 as calculated with Student&#39...

Watch this Scientific Journal Video about Chromatin Immunoprecipitation of Murine Brown Adipose Tissue at JoVE.com

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Here we describe a protocol for efficient chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) of brown adipose tissue (BAT) isolated from a mouse. This protocol is suitable for both mapping histone modifications and investigating genome-wide localization of non-histone proteins of interest in vivo.

Most cellular processes are regulated by transcriptional modulation of specific gene programs. Such modulation is achieved through the combined actions of ...

The metered it's used for to perform efficient ChIP sequencing of both ester and non-ester proteins in brown lipid tissue isolated from mouse. The main advantage of the technique is that the protocol has been optimized for efficient immunoprecipitation of chromatin-associated complex from the lipid tissue. Before incision, spray the euthanized mouse with 70%ethanol.Place the mouse with its back facing up, then make an incision along the neck. Next, located BAT directly under the skin between the shoulders and carefully remove the thin layer of white fat. Cross-link each BAT pad in 10 milliliters of PBS containing 1%formaldehyde for 15 minutes at 150 RPM at room temperature.After 15 minutes, quench cross-linking by adding 2.5 molar glycine to the BAT, resulting in a final concentration of 125 millimolar. Place it on a shaker for five minutes, rotating at 150 RPM at room temperature. Subsequently, transfer the BAT pad to 500 microliters of hypotonic lysis buffer and add two stainless steel beads for each BAT pad.Then, use a bead-based tissue homogenizer to shred the tissue. Start with five minutes at max power. If needed, extend the time until the tissue is homogenized and single cells are separated.Transfer the sample into a new tube, and centrifuge at four degrees Celsius at 16, 000 G for 10 minutes. After 10 minutes, transfer the supernatant into a new tube and keep the cell pellet on ice. Centrifuge the supernatant at four degrees Celsius at 16, 000 G for 10 minutes to prevent loss of floating cells.Then, discard the final supernatant and re-suspend both cell pellets together in 300 microliters of SDS lysis buffer with one times protease inhibitor. Incubate on ice for 10 minutes. Next, sonicate the lysates to generate DNA fragments 200 to 500 base pairs long.After sonication, remove debris by centrifugation for 10 minutes at 16, 000 G at four degrees celsius. To perform immunoprecipitation, keep 1%of the chromatin solution aside as the ChIP input and keep the inputs overnight at four degrees Celsius. Next, add the ChIP antibody to one milliliter of chromatin solution and perform parallel immunoprecipitation with corresponding pre-immune IgG or normal IgG of the same species.Alternatively, save one milliliter of chromatin solution for a no antibody control. Incubate overnight at four degrees Celsius with rotation. To collect the immune complexes, add 50 microliters of protein A agarose 50%slurry to the immune complexes and incubate for one hour at four degrees Celsius with rotation at 150 RPM.After an hour, pellet the beads by centrifugation for one minute at 1000 times G at four degrees Celsius. Perform sequential washes of the beads on 0.45 micrometer PVDF centrifugal filter columns with buffers of increasing stringency by first transferring the beads in the columns with 500 microliters of low salt wash buffer. Then, pellet the beads in the columns for three minutes at 2500 G.Discard the flow-through.Repeat the wash with high salt wash buffer according to the low salt wash procedures. Then, repeat the procedures with lithium chloride and finally with one times TE.After the washes are completed, elute the immune complexes by adding 300 microliters of elution buffer to the pelleted beads in the columns. Incubate them at room temperature for 30 minutes on a shaker at 400 RPM.Subsequently, collect the elute by spinning down the columns for three minutes at 2500 G in a fresh tube. Reverse the cross-links by incubating the elute and inputs collected at 65 degrees Celsius overnight. To recover DNA, add 300 microliters of phenol chloroform IAA to the elute and inputs at a one-to-one ratio and vortex for 10 seconds.Next, spin down at 21, 000 G at four degrees Celsius for 20 minutes. Keep the pellet and discard the supernatant. Wash the pellet with one milliliter of cold 70%ethanol.Then spin down at 21, 000 G at four degrees Celsius for five minutes. Discard the supernatant and air dry the pellet. Re-suspend the pellet in 70 microliters of DNAse-free water for further procedures.Here is an example of ChIP Q PCR using BAT isolated from wildtype or GPS2-A knockout mice. Since GPS2 has been found to be required for the expression of nuclear encoded mitochondrial genes in different cell lines, the recruitment of GPS2 was tested on two specific nuclear encoded mitochondrial genes. NDUFV1 and TOMM20 in BAT from mice as the examples of a tissue highly enriched in mitochondria.GPS2 promoter occupancy was compared in GPS2-A knockout mice and wild type letter mates. An expected decrease was observed in GPS2 binding on selective target genes in the BAT from GPS2-A knockout mice. Using the protocol described here, an increased binding of RNA polymerase two and the repressive histone mark, H3K9ME3, was recorded in the BAT from GPS2-A knockout mice as compared to wild type letter mates.These results confirm the recruitment of GPS2 on selected nuclear encoded mitochondrial genes and show that GPS2 is required for preventing the accumulation of H3K9ME3 and thus required for stalling of pole two transcriptional activity on target promoters. The protocol described here, even if specifically optimized for the brown adipose tissue, represents a valued tool for performing ChIP from other murine and human tissue. Don't forget that working with phenochloroform can be extremely hazardous.Therefore, it's extremely important to always operate under the fume hood while using this reagent.

chromatin-immunoprecipitation-of-murine-brown-adipose-tissue

Research

JoVE Journal

Genetics

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Elucidation of the binding properties of chromatin-targeting proteins can be very challenging due to the complex nature of chromatin and the heterogeneous nature of most mammalian chromatin-modifying complexes. In order to overcome these hurdles, we have adapted a sequential salt extraction (SSE) assay for evaluating the relative binding affinities of chromatin-bound complexes. This easy and straightforward assay can be used by non-experts to evaluate the relative difference in binding affinity of two related complexes, the changes in affinity of a complex when a subunit is lost or an individual domain is inactivated, and the change in binding affinity after alterations to the chromatin landscape. By sequentially re-suspending bulk chromatin in increasing amounts of salt, we are able to profile the elution of a particular protein from chromatin. Using these profiles, we are able to determine how alterations in a chromatin-modifying complex or alterations to the chromatin environment affect binding interactions. Coupling SSE with other in vitro and in vivo assays, we can determine the roles of individual domains and proteins on the functionality of a complex in a variety of chromatin environments.

Sequential salt extraction of chromatin bound proteins is a useful tool for determining the binding properties of large protein complexes. This method can be employed to evaluate the role of individual subunits or domains in the overall affinity of a protein complex to bulk chromatin.

Elucidation of the binding properties of chromatin-targeting proteins can be very challenging due to the complex nature of chromatin and the heterogeneous ...

Analysis of the c-KIT Ligand Promoter Using Chromatin Immunoprecipitation

Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. Therefore, DNA-protein interactions regulate multiple physiological, pathophysiological, and biological functions, such as cell differentiation, cell proliferation, cell cycle control, chromosome stability, epigenetic gene regulation, and cell transformation. In eukaryotic cells, the DNA interacts with histone and nonhistone proteins and is condensed into chromatin. Several technical tools can be used to analyze DNA-protein interactions, such as the Electrophoresis (gel) Mobility Shift Assay (EMSA) and DNase I footprinting. However, these techniques analyze the protein-DNA interaction in vitro, not within the cellular context. Chromatin immunoprecipitation (ChIP) is a technique that captures proteins at their specific DNA binding sites, thereby allowing for the identification of DNA-protein interactions within their chromatin context. It is done by fixation&#160;of the DNA-protein interaction, followed by&#160;immunoprecipitation of the protein of interest. Subsequently, the genomic site that the protein was bound to is characterized. Here, we describe and discuss ChIP and demonstrate its analytical value for the identification of the Transforming Growth Factor-&#946; (TGF-&#946;)-induced binding of the transcription factor SMAD2 to SMAD Binding Elements (SBE) within the promoter region of the tyrosine-protein kinase Kit (c-KIT) receptor ligand Stem Cell Factor (SCF).

DNA-protein interactions are essential for multiple biological processes. During the evaluation of cellular functions, the analysis of DNA-protein interactions is indispensable for understanding gene regulation. Chromatin immunoprecipitation (ChIP) is a powerful tool to analyze such interactions in vivo.

Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. ...

Chromatin Immunoprecipitation (ChIP) in Mouse T-cell Lines

Signaling pathways regulate gene expression programs via the modulation of the chromatin structure at different levels, such as by post-translational modifications (PTMs) of histone tails, the exchange of canonical histones with histone variants, and nucleosome eviction. Such regulation requires the binding of signal-sensitive transcription factors (TFs) that recruit chromatin-modifying enzymes at regulatory elements defined as enhancers. Understanding how signaling cascades regulate enhancer activity requires a comprehensive analysis of the binding of TFs, chromatin modifying enzymes, and the occupancy of specific histone marks and histone variants. Chromatin immunoprecipitation (ChIP) assays utilize highly specific antibodies to immunoprecipitate specific protein/DNA complexes. The subsequent analysis of the purified DNA allows for the identification the region occupied by the protein recognized by the antibody. This work describes a protocol to efficiently perform ChIP of histone proteins in a mature mouse T-cell line. The presented protocol allows for the performance of ChIP assays in a reasonable timeframe and with high reproducibility.

Chromatin Immunoprecipitation ChIP in Mouse T-cell Lines

This work describes a protocol for chromatin immunoprecipitation (ChIP) using a mature mouse T-cell line. This protocol is suitable to investigate the distribution of specific histone marks at specific promoter sites or genome-wide.

Signaling pathways regulate gene expression programs via the modulation of the chromatin structure at different levels, such as by post-translational ...

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution based analysis methodology (nucleosome density ChIP-seq; ndChIP-seq) that enables the generation of combined measurements of micrococcal nuclease (MNase) accessibility with histone modification genome-wide. Nucleosome position and local density, and the posttranslational modification of their histone subunits, act in concert to regulate local transcription states. Combinatorial measurements of nucleosome accessibility with histone modification generated by ndChIP-seq allows for the simultaneous interrogation of these features. The ndChIP-seq methodology is applicable to small numbers of primary cells inaccessible to cross-linking based ChIP-seq protocols. Taken together, ndChIP-seq enables the measurement of histone modification in combination with local nucleosome density to obtain new insights into shared mechanisms that regulate RNA transcription within rare primary cell populations.

We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) methodology for the generation of sequence datasets suitable for a nucleosome density ChIP-seq analytical framework integrating micrococcal nuclease (MNase) accessibility with histone modification measurements.

We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) experimental protocol compatible with a Gaussian mixture distribution ...

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, transcription factors, or chromatin-modifying enzymes at a given locus or on a genome-wide scale. The combination of ChIP assays with next-generation sequencing (i.e., ChIP-Seq) is a powerful approach to globally uncover gene regulatory networks and to improve the functional annotation of genomes, especially of non-coding regulatory sequences. ChIP protocols normally require large amounts of cellular material, thus precluding the applicability of this method to investigating rare cell types or small tissue biopsies. In order to make the ChIP assay compatible with the amount of biological material that can typically be obtained in vivo during early vertebrate embryogenesis, we describe here a simplified ChIP protocol in which the number of steps required to complete the assay were reduced to minimize sample loss. This ChIP protocol has been successfully used to investigate different histone modifications in various embryonic chicken and adult mouse tissues using low to medium cell numbers (5 x 104 - 5 x 105 cells). Importantly, this protocol is compatible with ChIP-seq technology using standard library preparation methods, thus providing global epigenomic maps in highly relevant embryonic tissues.

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

Here, we describe a chromatin immunoprecipitation (ChIP) and ChIP-seq library preparation protocol to generate global epigenomic profiles from low-abundance chicken embryonic samples.

Chromatin immunoprecipitation (ChIP) is a widely-used technique for mapping the localization of post-translationally modified histones, histone variants, ...

Chromatin Immunoprecipitation (ChIP) of Histone Modifications from Saccharomyces cerevisiae

Histone post-translational modifications (PTMs), such as acetylation, methylation and phosphorylation, are dynamically regulated by a series of enzymes that add or remove these marks in response to signals received by the cell. These PTMS are key contributors to the regulation of processes such as gene expression control and DNA repair. Chromatin immunoprecipitation (chIP) has been an instrumental approach for dissecting the abundance and localization of many histone PTMs throughout the genome in response to diverse perturbations to the cell. Here, a versatile method for performing chIP of post-translationally modified histones from the budding yeast Saccharomyces cerevisiae (S. cerevisiae) is described. This method relies on crosslinking of proteins and DNA using formaldehyde treatment of yeast cultures, generation of yeast lysates by bead beating, solubilization of chromatin fragments by micrococcal nuclease, and immunoprecipitation of histone-DNA complexes. DNA associated with the histone mark of interest is purified and subjected to quantitative PCR analysis to evaluate its enrichment at multiple loci throughout the genome. Representative experiments probing the localization of the histone marks H3K4me2 and H4K16ac in wildtype and mutant yeast are discussed to demonstrate data analysis and interpretation. This method is suitable for a variety of histone PTMs and can be performed with different mutant strains or in the presence of diverse environmental stresses, making it an excellent tool for investigating changes in chromatin dynamics under different conditions.

Chromatin Immunoprecipitation ChIP of Histone Modifications from Saccharomyces cerevisiae

Here, we describe a protocol for chromatin immunoprecipitation of modified histones from the budding yeast Saccharomyces cerevisiae. Immunoprecipitated DNA is subsequently used for quantitative PCR to interrogate the abundance and localization of histone post-translational modifications throughout the genome.

Histone post-translational modifications (PTMs), such as acetylation, methylation and phosphorylation, are dynamically regulated by a series of enzymes ...

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 expression. The cellular transcriptional machinery and its chromatin modification proteins coordinate to regulate transcription. To analyze transcriptional regulation at the molecular level, several experimental methods such as electrophoretic mobility shift, transient reporter and chromatin immunoprecipitation (ChIP) assays are available. We describe a modified ChIP assay in detail in this article because of its advantages in directly showing histone modifications and the interactions between proteins and DNA in cells. One of the key steps in a successful ChIP assay is chromatin shearing. Although sonication is commonly used for shearing chromatin, it is difficult to identify reproducible conditions. Instead of shearing chromatin by sonication, we utilized enzymatic digestion with micrococcal nuclease (MNase) to obtain more reproducible results. In this article, we provide a straightforward ChIP assay protocol using MNase.

Chromatin immunoprecipitation (ChIP) is a powerful tool for understanding the molecular mechanisms of gene regulation. However, the method involves difficulties in obtaining reproducible chromatin fragmentation by mechanical shearing. Here, we provide an improved protocol for a ChIP assay using enzymatic digestion.

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

Discovering CsgD Regulatory Targets in Salmonella Biofilm Using Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-seq)

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique that can be used to discover the regulatory targets of transcription factors, histone modifications, and other DNA-associated proteins. ChIP-seq data can also be used to find differential binding of transcription factors in different environmental conditions or cell types. Initially, ChIP was performed through hybridization on a microarray (ChIP-chip); however, ChIP-seq has become the preferred method through technological advancements, decreasing financial barriers to sequencing, and massive amounts of high-quality data output. Techniques of performing ChIP-seq with bacterial biofilms, a major source of persistent and chronic infections, are described in this protocol. ChIP-seq is performed on Salmonella enterica serovar Typhimurium biofilm and planktonic cells, targeting the master biofilm regulator, CsgD, to determine differential binding in the two cell types. Here, we demonstrate the appropriate amount of biofilm to harvest, normalizing to a planktonic control sample, homogenizing biofilm for cross-linker access, and performing routine ChIP-seq steps to obtain high quality sequencing results.

Discovering CsgD Regulatory Targets in Salmonella Biofilm Using Chromatin Immunoprecipitation and High-Throughput Sequencing ChIP-seq

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) is a method used to establish interactions between transcription factors and the genomic sequences they control. This protocol outlines techniques for performing ChIP-seq with bacterial biofilms, using Salmonella enterica serovar Typhimurium bacterial biofilm as an example.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a technique that can be used to discover the regulatory targets of transcription ...

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease (ChIP-Exo)

Identification of specific protein-DNA interactions on the genome is important for understanding gene regulation. Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) is widely used to identify genome-wide binding locations of DNA-binding proteins. However, the ChIP-seq method is limited by its heterogeneity in length of sonicated DNA fragments and non-specific background DNA, resulting in low mapping resolution and uncertainty in DNA-binding sites. To overcome these limitations, the combination of ChIP with exonuclease digestion (ChIP-exo) utilizes 5&#8217; to 3&#8217; exonuclease digestion to trim the heterogeneously sized immunoprecipitated DNA to the protein-DNA crosslinking site. Exonuclease treatment also eliminates non-specific background DNA. The library-prepared and exonuclease-digested DNA can be sent for high-throughput sequencing. The ChIP-exo method allows for near base-pair mapping resolution with greater detection sensitivity and reduced background signal. An optimized ChIP-exo protocol for mammalian cells and next-generation sequencing is described below.

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

Precise determination of protein-binding locations across the genome is important for understanding gene regulation. Here we describe a&#160;genomic mapping method that treats chromatin-immunoprecipitated DNA with exonuclease digestion (ChIP-exo) followed by high-throughput sequencing. This method detects protein-DNA interactions with near base-pair mapping resolution and high signal-to-noise ratio in mammalian neurons.

Identification of specific protein-DNA interactions on the genome is important for understanding gene regulation. Chromatin immunoprecipitation coupled ...

Isolation of Adipose Tissue Nuclei for Single-Cell Genomic Applications

Brown and beige fat are specialized adipose tissues that dissipate energy for thermogenesis by UCP1 (Uncoupling Protein-1)-dependent and independent pathways. Until recently, thermogenic adipocytes were considered a homogeneous population. However, recent studies have indicated that there are multiple subtypes or subpopulations that are distinct in developmental origin, substrate use, and transcriptome. Despite advances in single-cell genomics, unbiased decomposition of adipose tissues into cellular subtypes has been challenging because of the fragile nature of lipid-filled adipocytes. The protocol presented was developed to circumvent these obstacles by effective isolation of single nuclei from adipose tissue for downstream applications, including RNA sequencing. Cellular heterogeneity can then be analyzed by RNA sequencing and bioinformatic analyses.

This publication describes a protocol for the isolation of nuclei from mature adipocytes, purification by fluorescence-activated sorting, and single-cell level transcriptomics.

Brown and beige fat are specialized adipose tissues that dissipate energy for thermogenesis by UCP1 (Uncoupling Protein-1)-dependent and independent ...