Name: the chip-exo method: identifying protein-dna interactions with near base pair precision
Uploaded: 2016-12-23T15:00:00
Description: Watch this Scientific Journal Video about The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision at JoVE.com

We thank the Venters Lab and members of the Molecular Physiology and Biophysics Department for helpful discussions. Special thanks to Frank Pugh for his guidance, mentoring, and many insightful discussions on the nuances of ChIP-exo while I was a post-doctoral fellow in his laboratory.

Note: Double distilled H2O or molecular grade equivalent is recommended for all buffers and reactions mixes.
Day 0: Material Preparation and Cell Harvest
1. Buffer Preparation
<ol>
	<li>Prepare Lysis Buffers 1 - 3 (Tables 1 - 3) and add 100 &#181;l complete protease inhibitor stock (CPI) to 50 ml of each buffer just prior to use. Prepare CPI stock by dissolving one tablet in 1 ml molecular grade H2O.</li>
	<li>Prepare ChIP Buff...

<ol>
	<li>Venters, B. J., Pugh, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+eukaryotic+genes+are+transcribed.">How eukaryotic genes are transcribed.</a> Crit Rev Biochem Mol Biol. 44, 117-141 (2009).</li><li>Rhee, H. S., Pugh, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+genome-wide+protein-DNA+interactions+detected+at+single-nucleotide+resolution.">Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.</a> Cell. 147, 1408-1419 (2011).</li><li>Chen, 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=Single-molecule+dynamics+of+enhanceosome+assembly+in+embryonic+stem+cells.">Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.</a> Cell. 156, 1274-1285 (2014).</li><li>Wales, S., Hashemi, S., Blais, A., McDermott, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+MEF2+target+gene+analysis+in+cardiac+and+skeletal+muscle+reveals+novel+regulation+of+DUSP6+by+p38MAPK-MEF2+signaling.">Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPK-MEF2 signaling.</a> Nucleic acids research. 42, 11349-11362 (2014).</li><li>Cho, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+architecture+of+ArgR-DNA+complexes+at+the+genome-scale+in+Escherichia+coli.">The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.</a> Nucleic Acids Res. 43, 3079-3088 (2015).</li><li>Katainen, R., 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=CTCF/cohesin-binding+sites+are+frequently+mutated+in+cancer.">CTCF/cohesin-binding sites are frequently mutated in cancer.</a> Nat Genet. 47, 818-821 (2015).</li><li>Murphy, M. W., 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=An+ancient+protein-DNA+interaction+underlying+metazoan+sex+determination.">An ancient protein-DNA interaction underlying metazoan sex determination.</a> Nat Struct Mol Biol. 22, 442-451 (2015).</li><li>Zere, T. R., 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=Genomic+Targets+and+Features+of+BarA-UvrY+(-SirA)+Signal+Transduction+Systems.">Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems.</a> PLoS One. 10, e0145035 (2015).</li><li>Rhee, H. S., Pugh, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-wide+structure+and+organization+of+eukaryotic+pre-initiation+complexes.">Genome-wide structure and organization of eukaryotic pre-initiation complexes.</a> Nature. 483, 295-301 (2012).</li><li>Rhee, H. S., Bataille, A. R., Zhang, L., Pugh, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Subnucleosomal+structures+and+nucleosome+asymmetry+across+a+genome.">Subnucleosomal structures and nucleosome asymmetry across a genome.</a> Cell. , 1377-1388 (2014).</li><li>Pugh, B. F., Venters, B. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genomic+Organization+of+Human+Transcription+Initiation+Complexes.">Genomic Organization of Human Transcription Initiation Complexes.</a> PLoS One. 11, e0149339 (2016).</li><li>Albert, I., Wachi, S., Jiang, C., Pugh, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GeneTrack--a+genomic+data+processing+and+visualization+framework.">GeneTrack--a genomic data processing and visualization framework.</a> Bioinformatics. 24, 1305-1306 (2008).</li><li>Guo, Y., Mahony, S., Gifford, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+resolution+genome+wide+binding+event+finding+and+motif+discovery+reveals+transcription+factor+spatial+binding+constraints.">High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.</a> PLoS computational biology. 8, e1002638 (2012).</li><li>Bardet, A. 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=Identification+of+transcription+factor+binding+sites+from+ChIP-seq+data+at+high+resolution.">Identification of transcription factor binding sites from ChIP-seq data at high resolution.</a> Bioinformatics. 29, 2705-2713 (2013).</li><li>Wang, L., 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=MACE:+model+based+analysis+of+ChIP-exo.">MACE: model based analysis of ChIP-exo.</a> Nucleic Acids Res. 42, e156 (2014).</li><li>Bentley, D. R., 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=Accurate+whole+human+genome+sequencing+using+reversible+terminator+chemistry.">Accurate whole human genome sequencing using reversible terminator chemistry.</a> Nature. 456, 53-59 (2008).</li><li>Rhee, H. S., Pugh, B. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChIP-exo+method+for+identifying+genomic+location+of+DNA-binding+proteins+with+near-single-nucleotide+accuracy.">ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy.</a> Curr Protoc Mol Biol. Chapter 21, Unit 21.24 (2012).</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 Res. 22, 1813-1831 (2012).</li><li>Serandour, A. A., Brown, G. D., Cohen, J. D., Carroll, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+an+Illumina-based+ChIP-exonuclease+method+provides+insight+into+FoxA1-DNA+binding+properties.">Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties.</a> Genome Biol. 14, R147 (2013).</li><li>He, Q., Johnston, J., Zeitlinger, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChIP-nexus+enables+improved+detection+of+in+vivo+transcription+factor+binding+footprints.">ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.</a> Nat Biotechnol. 33, 395-401 (2015).</li></ol>

We present a functional genomic protocol to determine the precise binding location for chromatin interacting proteins in an unbiased, genome-wide manner at near base pair resolution. The most critical step to achieve near base pair mapping resolution is the exonuclease treatment of the ChIP-enriched DNA while the immunoprecipitate remains on the magnetic resin. Ostensibly, protein complexes could potentially block in vivo footprinting of any given subunit (e.g., chromatin remodeling complexes or the nuc...

Chromatin immunoprecipitation (ChIP) is a powerful method to study mechanisms of gene regulation by selectively enriching for DNA fragments that interact with a given protein in living cells. Detection methods of ChIP-enriched DNA fragments have evolved as technology improves, from detection of a single locus (standard ChIP-qPCR) to hybridization on oligonucleotide microarrays (ChIP-chip) to high-throughput sequencing (ChIP-seq) 1. Although ChIP-seq has seen widespread application, chromatin heterogeneity and nonspecific DNA interactions have hampered data quality leading to false positives and imprecise mapping. To circumvent these limitations, Dr. Frank Pugh developed the ChIP-exo method 2. The salient feature of ChIP-exo is that it incorporates a 5&#39; to 3&#39; exonuclease, effectively footprinting transcription factor binding locations. As a result, the ChIP-exo methodology achieves higher resolution, greater dynamic range of detection, and lower background noise.
Although ChIP-exo is more technically challenging to master than ChIP-seq, it is being widely adopted as studies aim to gain unique ultra high-resolution insights using diverse biological systems 3-8. Indeed, ChIP-exo has been successfully applied to bacteria, yeast, mouse, rat, and human cell systems. As proof of principle, ChIP-exo was originally used to identify the precise binding motif for a handful of yeast transcription factors 2. The technique was also used in yeast to study the organization of the transcription pre-initiation complex, and to decipher subnucleosomal structure of various histones 9,10. More recently, we leveraged ChIP-exo to resolve adjacent TFIIB and Pol II binding events at human promoters, and showed that widespread divergent transcription arises from distinct initiation complexes 11.
The workflow presented here is optimized and streamlined for mammalian ChIP-exo (Figure 1). First, living primary or tissue culture cells are treated with formaldehyde to preserve in vivo protein-DNA interactions through a covalent crosslink. The cells are lysed and chromatin sheared to ~ 100 - 500 base pair size fragments. ChIP then selectively enriches for DNA fragments crosslinked to the protein of interest. At this point, ChIP-seq libraries are typically prepared, which inherently limits the detection resolution to the average fragment size of a few hundred base pairs. However, ChIP-exo overcomes this limitation by trimming the left and right 5&#39; DNA borders of the protein-DNA crosslink site with lambda exonuclease. Sequencing libraries are then constructed from exonuclease digested DNA as detailed below. The resulting nested 5&#39; borders represent an in vivo footprint of the protein-DNA interaction (Figure 1, step 14), and are detected by high throughput sequencing. Although the ChIP-exo methodology is more involved than ChIP-seq, transitions between most steps requires simple bead washing, which minimizes sample loss and experimental variability. Importantly, since ChIP-exo is a refined version of ChIP-seq, any sample that is successful with ChIP-seq should also be successful with ChIP-exo.
The in vivo footprinting of protein-DNA interactions with ChIP-exo results in a fundamentally distinct data structure from ChIP-seq. Although common ChIP-seq callers may be applied to ChIP-exo data, to obtain the most precise peak calls we recommend bioinformatics tools specifically designed with the unique structure of ChIP-exo data in mind. These include Genetrack, GEM, MACE, Peakzilla, and ExoProfiler 12-15.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr >
			<td >37% formaldehyde, methanol free, 10x10ml ampules</td>
			<td >ThermoFisher Scientific</td>
			<td >28908</td>
			<td >Section 3</td>
		</tr>
		<tr >
			<td >Complete Protease Inhibitor cocktail (CPI)</td>
			<td >Roche Life Science</td>
			<td >11873580001</td>
			<td >Sections 4, 8</td>
		</tr>
		<tr >
			<td >Bioruptor sonicator</td>
			<td >Diagenode</td>
			<td >UCD200</td>
			<td >Section 5</td>
		</tr>
		<tr >
			<td >15 ml polystyrene tubes</td>
			<td >BD Falcon</td>
			<td >352095</td>
			<td >Section 5</td>
		</tr>
		<tr >
			<td >MagSepharose Protein G Xtra beads</td>
			<td >GE Healthcare</td>
			<td >28-9670-66</td>
			<td >Section 6</td>
		</tr>
		<tr >
			<td >DynaMag-1.5ml Side Magnetic Rack</td>
			<td >Invitrogen</td>
			<td >12321D</td>
			<td >Sections 6-17, 22</td>
		</tr>
		<tr >
			<td >Mini-Tube Rotator</td>
			<td >Fisher Scientific</td>
			<td >05-450-127</td>
			<td >Sections 7, 22</td>
		</tr>
		<tr >
			<td >T4 DNA Polymerase</td>
			<td >New England BioLabs</td>
			<td >M0203</td>
			<td >Section 9</td>
		</tr>
		<tr >
			<td >DNA Polymerase I, Klenow</td>
			<td >New England BioLabs</td>
			<td >M0210</td>
			<td >Section 9</td>
		</tr>
		<tr >
			<td >10x NEBuffer 2 (10x Reaction Buffer 2)</td>
			<td >New England BioLabs</td>
			<td >B7002</td>
			<td >Sections 9-11, 13, 15, 20</td>
		</tr>
		<tr >
			<td >Thermomixer C</td>
			<td >Eppendorf</td>
			<td >5382</td>
			<td >Sections 9-16</td>
		</tr>
		<tr >
			<td >ATP</td>
			<td >Roche Life Science</td>
			<td >010419979001</td>
			<td >Sections 9, 11, 13</td>
		</tr>
		<tr >
			<td >dNTPs</td>
			<td >New England BioLabs</td>
			<td >N0447</td>
			<td >Sections 9, 12, 19, 23</td>
		</tr>
		<tr >
			<td >T4 Polynucleotide Kinase</td>
			<td >New England BioLabs</td>
			<td >M0201</td>
			<td >Sections 9, 13</td>
		</tr>
		<tr >
			<td >dATP</td>
			<td >New England BioLabs</td>
			<td >N0440</td>
			<td >Sections 10, 20</td>
		</tr>
		<tr >
			<td >Klenow 3&#39;-5&#39; Exo Minus</td>
			<td >New England BioLabs</td>
			<td >M0212</td>
			<td >Sections 10, 20</td>
		</tr>
		<tr >
			<td >T4 DNA ligase&#160;</td>
			<td >New England BioLabs</td>
			<td >M0202</td>
			<td >Sections 11, 21</td>
		</tr>
		<tr >
			<td >&#934;-29 DNA Polymerase</td>
			<td >New England BioLabs</td>
			<td >M0269</td>
			<td >Sections 12, 19</td>
		</tr>
		<tr >
			<td >10x &#934;-29 Buffer</td>
			<td >New England BioLabs</td>
			<td >B0269</td>
			<td >Sections 12, 19</td>
		</tr>
		<tr >
			<td >Lambda Exonuclease</td>
			<td >New England BioLabs</td>
			<td >M0262</td>
			<td >Section 14</td>
		</tr>
		<tr >
			<td >10x Lambda Buffer</td>
			<td >New England BioLabs</td>
			<td >B0262</td>
			<td >Section 14</td>
		</tr>
		<tr >
			<td >RecJf Exonuclease</td>
			<td >New England BioLabs</td>
			<td >M0264</td>
			<td >Section 15</td>
		</tr>
		<tr >
			<td >Proteinase K</td>
			<td >Roche Life Science</td>
			<td >03115828001</td>
			<td >Section 16</td>
		</tr>
		<tr >
			<td >Glycogen</td>
			<td >Roche Life Science</td>
			<td >010901393001</td>
			<td >Section 18</td>
		</tr>
		<tr >
			<td >10x T4 Ligase Buffer</td>
			<td >New England BioLabs</td>
			<td >B0202</td>
			<td >Section 21</td>
		</tr>
		<tr >
			<td >AMPure XP (clean up) beads&#160;</td>
			<td >Beckman Coulter</td>
			<td >A63881</td>
			<td >Section 22</td>
		</tr>
		<tr >
			<td >Q5 Hot Start DNA Polymerase&#160;</td>
			<td >New England BioLabs</td>
			<td >M0493</td>
			<td >Section 23</td>
		</tr>
		<tr >
			<td >5x Q5 Buffer (5x PCR Buffer)</td>
			<td >New England BioLabs</td>
			<td >B9027</td>
			<td >Section 23</td>
		</tr>
		<tr >
			<td >Qubit Fluorometer</td>
			<td >Invitrogen</td>
			<td >Q33216</td>
			<td >Section 25</td>
		</tr>
		<tr >
			<td >QIAquick Gel Extraction Kit</td>
			<td >Qiagen</td>
			<td >28704</td>
			<td >Section 25</td>
		</tr>
		<tr >
			<td >Optical Clear Qubit tubes&#160;</td>
			<td >Invitrogen</td>
			<td >Q32856</td>
			<td >Section 26</td>
		</tr>
		<tr >
			<td >Qubit dsDNA High Sensitivity Assay kit</td>
			<td >Invitrogen</td>
			<td >Q32851</td>
			<td >Section 26</td>
		</tr>
	</tbody>
</table>

the chip-exo method: identifying protein-dna interactions with near base pair precision

Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise. The key distinction of the ChIP-exo methodology is the incorporation of lambda exonuclease digestion in the library preparation workflow to effectively footprint the left and right 5&#39; DNA borders of the protein-DNA crosslink site. The ChIP-exo libraries are then subjected to high throughput sequencing. The resulting data can be leveraged to provide unique and ultra-high resolution insights into the functional organization of the genome. Here, we describe the ChIP-exo method that we have optimized and streamlined for mammalian systems and next-generation sequencing-by-synthesis platform.

The following figures illustrate representative results from the ChIP-exo protocol presented here. In contrast to traditional ChIP-seq methodologies with few enzymatic steps, ChIP-exo requires eleven sequentially dependent enzymatic reactions (Figure 1). Thus, care must be taken at each step to ensure that each reaction component is added to its respective reaction master mix. We recommend generating a formulaic spreadsheet based on the reaction Tables to automatically pe...

Watch this Scientific Journal Video about The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision at JoVE.com

The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision

Here, we present a protocol to achieve near base pair resolution of protein-DNA interactions. This is obtained by exonuclease treatment of DNA fragments selectively enriched by chromatin immunoprecipitation (ChIP-exo) followed by high throughput sequencing.

Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA ...

The overall goal of this functional genomic technology is to identify the precise genomic locations that a given protein occupies in living cells. This method can help answer key questions in the fields of gene regulation and epigenetics such as how the transcription machinery assembles and operates in the context of chromatin. The main advantage of this technique is it reveals the exact genomic location for protein DNA interactions at near-base pre-resolution with exceptionally low background.Generally, individuals new to this method will struggle because the protocol is complex and requires attention to detail throughout. To sonicate nuclear lysates, begin by placing resin adapters in 15 milliliter polystyrene tubes containing nuclear extracts. Sonicate the lysates in an ice cold water bath at medium power for 30 seconds on and 30 seconds off for a total of two 15-minute sessions.To check sonication results, transfer two 10 microliter samples from each tube into 1.5 milliliter tubes. Then reverse crosslinks by combining the first 10 microliter sample with 10 microliters of TE-RNase A and 0.2 microliters of proteinase K.Incubate the tube at 37 degrees Celsius for 30 minutes. Then add four microliters of 6X xylene DNA dye.To the second 10 microliter sample, preserve crosslinks by adding two microliters of 6X xylene DNA dye. Run both samples on a 1.5%agarose gel at 140 volts for approximately 30 to 45 minutes until the bromophenol dye in the latter is three-quarters of the way down the gel. If sonication was successful, transfer sonicated lysates to two milliliter tubes containing 150 microliters of 10%Triton X-100 and vortex to mix.Pellet the insoluble chromatin and debris by spinning the sonicated lysates at 20, 000 times g at four degrees Celsius for 10 minutes. Then transfer the supernatants to new two milliliter tubes. Store the samples at negative 80 degrees Celsius indefinitely.For each chromatin immunoprecipitation or ChIP reaction, combine 1.5 milliliters of sonicated extracts with antibody bead conjugates in 1.5 milliliter tubes. Incubate the tubes on a mini tube rotator at a speed of nine at four degrees Celsius overnight. Check after a few minutes to ensure samples are not leaking and are mixing properly.The following day, very briefly spin down the tubes to collect the liquid in the caps and place the tubes on a magnetic rack for one minute. Then aspirate the extract. Add 0.75 milliliters of RIPA buffer to each tube.Then remove the tubes from the magnetic rack and invert them several times to mix. After a brief spin, place the tubes back on the magnet and aspirate the supernatant. Following the last wash, add 0.75 milliliters of 10 millimolar Tris HCL to each tube.Remove the tubes from the magnetic rack and invert the samples several times to mix. After a brief spin, place the tubes back on the rack and aspirate the supernatant. After carrying out the polishing and detailing reactions according to the text protocol, fill out the ligation master mix calculations.Then make the ligation mix in a 1.5 milliliter tube on ice and pipette to mix the solution. With the sample tubes on the magnetic rack, add 48 microliters of P7 ligation master mix and two microliters of a different adapter index to each of the sample resins. Incubate the samples in a ThermoMixer at three times g in 25 degrees Celsius for two hours.After washing the samples and performing the Phy 29 nick repair and kinase reactions according to the text protocol, fill out the lambda exonuclease master mix calculations and make the lambda exonuclease mix in a 1.5 milliliter tube on ice. Add 50 microliters of lambda exonuclease mix to each sample resin while still on the magnetic rack. Then incubate the samples in a ThermoMixer at three times g in 37 degrees Celsius for 30 minutes.After aspirating the last wash as described in the text protocol, carry out RecJf nuclease reaction by filling out the RecJf master mix calculations and making the RecJf mix on ice. Add 50 microliters of the RecJf mix to each sample resin on the magnetic rack. Then incubate the samples in a ThermoMixer at three times g in 37 degrees Celsius for 30 minutes.After aspirating the last wash, prepare the ChIP elution buffer and proteinase K master mix and add 200 microliters of the solution to each sample resin. Incubate the samples in a ThermoMixer at three times g in 65 degrees Celsius overnight with a heated lid to prevent condensation. The following day, briefly spin the samples and place the tubes on the magnetic rack for one minute.Then transfer 200 microliters of supernatant to a new 1.5 milliliter tube containing 200 microliters of TE buffer. Following DNA extraction, P7 primary extension and ATL reactions, fill out the P5 adapter ligation table master mix calculations and make the ligation master mix on ice. Add 20 microliters of the ligation mix to each sample and pipette to mix.Then incubate the samples in a thermal cycler at 25 degrees Celsius for two hours. Carry out DNA purification and quantification according to the text protocol. As shown here, it is worth spending time to optimize sonication conditions to obtain high-quality chromatin extracts that yield DNA fragments between 100 to 500 base pairs.And electrophoretic mobility shift assay is used to verify that the sonicated extracts contain intact protein DNA crosslinks, evident as a super shift of DNA fragments. To assess background signal, a mock ChIP is routinely performed without antibody in the reaction. A high-quality ChIP exo-library will yield very little background in the mock sample compared to a ChIP-seq library preparation.Shown here is a bioanalyzer assessment of a ChIP-exo library. Analysis accurately ensures the library size distribution and detects contaminating adapter dimers that run at 125 base pairs. This panel illustrates the smooth distribution of strand-separated ChIP-exo tag five prime Ns for polymerase II, TFIIB and TBP at the human RPS12 gene in proliferating K562 cells.Shown in this figure are average ChIP-exo patterns relative to the transcriptional start sites of protein coding genes. The major peak locations for TBP, TFIIB and polymerase II in the composite plot reflect the genomic organization of human transcription initiation complexes. Once mastered, this technique can be done in four days if performed properly.After its development, this technique paved the way for researchers in the field of gene regulation to explore molecular details of subnuclear structure in assymetry in yeast. Following this procedure, other methods like RNase seek expression profiling can be performed to address questions such as whether a given factor influences the expression of a nearby gene. While attempting this procedure, it's important to remember to carefully fill out master mix tables for all enzymatic steps.Don't forget, working with carcinogens and other caustic agents can be extremely hazardous and precautions such as wearing personal protective equipment should always be taken while performing this procedure. After this watching video, you should have a good understanding of how to prepare a high-quality ChIP-exo library.

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Exploring Cognitive Functions in Babies, Children &amp; Adults with Near Infrared Spectroscopy

Exploring Cognitive Functions in Babies, Children & Adults with Near Infrared Spectroscopy

An explosion of functional Near Infrared Spectroscopy (fNIRS) studies investigating cortical activation in relation to higher cognitive processes, such as ...

Split-Ubiquitin Based Membrane Yeast Two-Hybrid (MYTH) System: A Powerful Tool For Identifying Protein-Protein Interactions

Split-Ubiquitin Based Membrane Yeast Two-Hybrid MYTH System: A Powerful Tool For Identifying Protein-Protein Interactions

The fundamental biological and clinical importance of integral membrane proteins prompted the development of a yeast-based system for the high-throughput ...

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Genetic information encoded by DNA is organized in a complex and highly regulated chromatin structure.  Each chromosome occupies a specific territory, ...

The MultiBac Protein Complex Production Platform at the EMBL

Proteomics  research revealed the impressive complexity of eukaryotic proteomes in  unprecedented detail. It is now a commonly accepted notion that ...

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

The paper describes the combination of optical tweezers and single molecule fluorescence detection for the study of protein-DNA interaction. The method ...

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may ...

Method for the Assessment of Effects of a Range of Wavelengths and Intensities of Red/near-infrared Light Therapy on Oxidative Stress In Vitro

Method for the Assessment of Effects of a Range of Wavelengths and Intensities of Red/near-infrared Light Therapy on Oxidative Stress In Vitro

Red/near-infrared light therapy (R/NIR-LT), delivered by laser or light emitting diode (LED), improves functional and morphological outcomes in a range of ...

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine ...

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health ...

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and ...