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Chromatin immunoprecipitation (ChIP) is a powerful technique that allows researchers to examine the interactions between epigenetic regulators and DNA in their natural context. With ChIP, researchers can identify specific genes and sequences where a protein of interest binds, across the entire genome, providing critical clues to their regulatory functions and mechanisms. By dissecting the temporal and spatial dynamics of protein-DNA interactions, ChIP provides insights into core biological processes and disease pathology.
ChIP is exceptionally versatile, with use in a broad scope of applications. From looking at sequence-specific protein binding to global regulatory processes, ChIP gives researchers the tools to integrate discoveries and paint a comprehensive picture of complex epigenetic regulatory systems.
ChIP has played a central role in elucidating gene regulation, transcriptional machinery, and chromatin structure. Here are some of the key proteins you can detect using ChIP.
Transcription factors. By examining where, and when, specific transcription factors bind across the genome, researchers have identified specific binding sites and sequences, pinpointed downstream gene activation, and revealed genome-wide regulatory programs of transcription factors.
Further investigation by ChIP and other methods has revealed these transcription factors to be master regulators behind disease pathology, where they orchestrate epigenetic dysregulation that results in cancers, autoimmune diseases, allergy, and many others. By identifying these master regulators and their downstream genetic programs, ChIP has provided novel targets for diagnostic and therapeutic strategies against a wide variety of diseases.
Transcriptional machinery. ChIP studies examining the binding of RNA polymerase II, and other components of transcription, reveal promoter and enhancer sequences and novel mechanisms of transcriptional regulation.
Chromatin Structure. ChIP studies were pivotal in the discovery and characterization of the histone code. By mapping the locations of specific histone modifications and comparing to known gene activation states, researchers have documented how acetylation or methylation on particular histone residues influence gene activation or silencing and higher order chromatin structure. These histone modification signatures can now be used to predict those aspects of epigenetic regulation at specific regions of the genome via ChIP.
As new histone modifications and chromatin regulatory elements are discovered, ChIP continues to be an essential tool for revealing the functions of these elements, and complexities of their interactions, in genomic regulation.
Combining ChIP analysis of multiple proteins is a powerful way to build a complete picture of genomic regulation. This approach enables researchers to study how different types of proteins, and protein complexes, interact spatially and temporally at specific sites along a particular gene, or across the entire genome, to regulate gene transcription (Barski et al., 2007).
ChIP expands the scope and precision of epigenetic research
ChIP facilitates the analysis of epigenetic mechanisms on a variety of scales, with unrivalled precision. These are some of the things you can achieve using ChIP.
Local epigenetic mechanism
Genome-wide epigenetic programming
Dynamic epigenetic processes
The ChIP procedure utilizes an antibody to immunoprecipitate a protein of interest, such as a transcription factor, along with its associated DNA. The associated DNA is then recovered and analyzed by PCR, microarray or sequencing to determine the genomic sequence and location where the protein was bound.
The procedure can be broken down into five parts (figure 6).
Figure 1: ChIP protocol workflow. Step-by-step approach to carrying out a ChIP experiment
In some cases, cross-linking of DNA and proteins may be required to stabilize their interactions, particularly for proteins that interact as part of large protein complexes and do not directly contact DNA. Crosslinking fixes these molecular interactions and freezes them at a particular point in time and is termed cross-linking ChIP (X-ChIP). In contrast, native ChIP (N-ChIP) which is performed without prior crosslinking.
Crosslinking is generally performed with formaldehyde, which reversibly crosslinks protein to DNA, RNA, and other proteins. Other chemicals like cisplatin can be used to selectively crosslink only between DNA and protein. Dual crosslinking with additional reagents may be required to study interactions between DNA and particularly large protein/RNA complexes. UV crosslinking is irreversible and therefore not compatible with ChIP.
2. Chromatin Fragmentation
Chromatin must be fragmented into small pieces for efficient immunoprecipitation and precise mapping of the target antigen to the genome. The size of the DNA fragments will ultimately determine the resolution of genomic mapping, so it is important to optimize the fragmentation protocol.
Steps 1 and 2 are incredibly important to optimize for each experiment to get the highest quality DNA possible for subsequent ChIP analysis.
The protein of interest and DNA fragment to which it is bound are then immunoprecipitated. The chromatin mixture is incubated with an antibody to the protein of interest, and either agarose or magnetic beads overnight at 4oC to form bead/antibody/protein/DNA complexes. The beads are then collected by either centrifugation, for Protein A, Protein G, or Protein A/G agarose beads, or by magnetic tube rack, for magnetic beads, to immunoprecipitate the antibody/protein/DNA complex. Non-specific binding is removed with subsequent washes.
4. DNA Recovery and Purification
The antibody/protein/DNA complex is eluted from the beads with SDS and heat. Crosslinking of protein and DNA must then be reversed with NaCl and heat for X-ChIP experiments. Any protein and RNA present are then degraded with proteinase K and RNase A, and the remaining DNA is purified with either phenolchloroform extraction or PCR purification kit.
5. Analyze the DNA
The purified DNA is then analyzed by qPCR, hybrid array (ChIP-on-ChIP) or next-generation sequencing (ChIP-seq) to identify and quantify the sequences that have been immunoprecipitated. These sequences are mapped to the genome to identify the genes and regions where the protein of interest was bound.
The aim of cross-linking is to fix the antigen of interest to its chromatin binding site. Histones themselves generally do not require cross-linking, as they are already tightly associated with the DNA. Other DNA binding proteins that with weaker affinities for DNA or histones may require cross-linking to hold them in place.
Chromatin fragmentation differences
While N-ChIP and X-ChIP both require chromatin fragmentation to make interactions accessible to antibodies, they require different fragmentation procedures utilizing micrococcal nuclease or sonication, respectively (Neill et al., 2003).
N-ChIP: For N-ChIP experiments, enzymatic digestion with micrococcal nuclease should sufficiently fragment your sample into single nucleosomes (monosomes containing ~175 base pairs of DNA).
• Purified monosomes are not suitable for analyzing interactions with certain chromatin binders, like transcription factors, which often bind inter-nucleosomal DNA. Sonication is recommended for these instances.
• Nucleosomes are dynamic and may rearrange during the enzymatic digestion. This may be a problem for mapping certain areas of the genome, and any changes should be monitored with suitable controls (see detection controls for quantitative PCR). X-ChIP should be performed as a control to assess any dynamic and unwanted changes in the absence of cross-linking.
• Enzymatic cleavage will not produce entirely random chromatin fragments. Micrococcal nuclease favors certain areas of genome sequence over others and will not digest DNA evenly or equally. Certain loci could be overrepresented, while others may be absent, potentially impacting the accuracy of the data.
• To get consistency in digestions, aliquot stock enzyme after purchase and run a new time course with a fresh aliquot every time you set up an experiment. Although enzyme quality may vary over time in storage, the risk of variation within chromatin preparations (degree of compaction, etc) is far higher; one chromatin sample should not be treated as being the same as all others before it.
X-ChIP: Formaldehyde cross-linking restricts access of enzymes such as micrococcal nuclease to their targets, making enzymatic digestion ineffective in X-ChIP experiments. Instead, sonication is used to generate random DNA fragments of 500–700 base pairs (2–3 nucleosomes).
• Avoid foaming, which decreases energy transfer within the solution and decreases sonication efficiency. Sonication may also be affected by cross-linking time, cell density, or cell type.
• While sonicated chromatin can be snap-frozen in liquid nitrogen and stored at -80°C for up to two months, avoid multiple cycles of freeze-thaw.
• Although sonication theoretically does not exhibit preferential cleavage of the genome, in practice this is rarely the case.
• DNA fragment sizes are typically larger, affecting the resolution of assay. Regardless, fragments up to 1.5 kb resolve well for most purposes in ChIP. Micrococcal nuclease digestion can improve resolution in combination with sonication and may be useful with gentle or incomplete cross-linked samples.
Regardless of which fragmentation method is chosen, it is important to always run a fragmentation time course to optimize fragment size when setting up an experiment.
Table 1: Advantages and disadvantages of N-ChIP vs X-ChIP.
Efficient precipitation of DNA and histone proteins
For non-histone proteins. Can be performed on all cell types, tissues, and organisms.
Specificity of the binding is more predictable
Enables DNA-protein, RNA-protein, and protein-protein cross-linking
High resolution (~175bp/mononucleosome)
Reduced chances of chromatin rearrangements
Only for histones
Over fixation can prevent effective sonication
Selective nuclease digestion may bias input chromatin
Formaldehyde can alter the binding properties of the antigen
High concentrations of nuclease may over-digest chromatin
Lower resolution compared to N-ChIP
Not all antibodies are appropriate for ChIP experiments, and many antibodies are not of ChIP-quality or validated for ChIP applications. Choosing the right ChIP-grade antibody is essential for the success of your ChIP experiment.
If not commercially available, or if you would like to try an antibody that is not yet ChIP-tested:
ChIP protocols and data analysis can be complex, so it is critical to include the right controls to ensure that the experiment worked as intended.
It is crucial to include an input sample control that has not been immunoprecipitated in all DNA recovery steps for comparison to pulldown sample results. It is ultimately this comparison that normalizes the data to provide interpretable results.
When immunoprecipitating for histone modifications, purified histone H3, and H1 can be used as positive controls for the quality of the histone preparation (histone H1 is commonly used for X-ChIP). Meanwhile, calf thymus histone preparation should be used as a positive control histone sample for checking antibody specificity in western blot.
Various antibody controls are important to ensure that immunoprecipitation was successful and to rule out the possibility of contamination. Here are some examples of key controls:
Also, chromatin remodeling may move or remove histones at a particular locus (eg an active promoter). To confirm the preservation of nucleosomes at particular genomic loci, use a control antibody against a non-modified histone such as histone H3. When analyzing histone modifications, normalize to histone content with an anti-H3 antibody.
Quantitative PCR controls
If analyzing data by qPCR, additional controls are necessary to ensure the quality of data analysis. Certain areas of the genome will purify better than others, and some nucleosomes may rearrange during enzymatic fragmentation. As a result, it is important to generate PCR primers to several regions in the starting material, as well as the purified/ChIP material, as controls for spurious results. Generate starting material by lysing the starting cells and take a sample for simple PCR of control regions in parallel with ChIP.
Also, during the qPCR stages, it is essential to perform positive and negative control qPCR for genomic loci where you know the protein of interest should or should not be bound. It is also necessary to perform a non-template control qPCR as a negative control to ensure there is no contamination in the PCR.
Figure 2: Example of sonication time-course experiment. U2OS cells were sonicated for 5, 10, 15 and 20 min. The cross-links were reversed and the purified DNA was resolved on a 1.5% agarose gel. The fragment size decreases during the time course. The optimal fragment size is observed at 15 min.
Antibody concentration. It is important to titer the antibody to optimize the signal to noise ratio. Start with 3–5 µg of antibody for every 25–35 mg of pure monosomes. For quantitative ChIP, you may need to match the amount of chromatin with the same amount of antibody. ChIP typically requires a large amount of primary antibody (1-10 µg per ug of beads). As with many techniques, it is essential to optimize the amount of antibody at the beginning before you run your experiment.
Wash buffers. Determine the correct composition for appropriate stringency of wash steps, typically between 250–500 mM NaCl or LiCl. Higher concentrations of salt and detergent will give cleaner results. However, balance must be achieved between low background and detrimental effects on the target. If the buffer is too stringent, it will destroy specific antibody interactions, resulting in low signal. If the buffer is not stringent enough, non-specific interactions will remain, resulting in high background. NP-40 can be used as a detergent, while RIPA is commonly used for X-ChIP.
Standard ChIP workflows require a large number of cells. Approximately 106 to 107cells as starting material, below which the assay is hindered by high background binding, poor enrichment efficiencies, and loss of enriched library complexity. However, these large sample sizes can be difficult to obtain, specifically when examining precious sample types like transgenic mouse tissues or clinical samples. To adjust for lower sample inputs, a number of strategies can be applied.
1. Improving enrichment efficiency and minimizing sample loss
Several adjustments to the ChIP workflow can increase enrichment efficiency and minimize sample loss for low input samples (Mao et al., 2013 and Dirks et al., 2016).
2. Readout and downstream data processing platforms
In addition to the assay itself, the choice and optimization of downstream processing (ie sequencing, array, or PCR) and bioinformatic analysis are also important.
Examining epigenetic mechanisms in specific tissues can reveal essential elements of tissue-specific genetic programming, development, and biological processes. ChIP can be a valuable tool for examining roles and mechanisms of tissue-specific transcription factors, gene activation and other aspects of epigenetic regulation. To perform ChIP from tissue samples requires specialized chromatin preparation protocols to ensure quality input material and reliable results.
The amount of tissue required will depend upon protein abundance, antibody affinity and the efficiency of cross-linking. The following protocol was optimized using 5–15 µg of chromatin for each ChIP assay, with 30 mg of liver tissue for each ChIP/antibody. Exact chromatin concentration should be determined for each tissue type before starting the X-ChIP assay.
Even with optimization, your results may not be perfect on the first attempt. Here you can find some common issues and solutions you can use to fix them.
High background in non-specific antibody control
Non-specific binding to beads
Add additional washes
Add a pre-clearing step by incubating sonicated chromatin with Protein A/G beads for 1 hour prior to immunoprecipitation
Beads give high background
Try different brands of beads and different blocking strategies to see which provide the lowest background in your non-specific control
Contaminated wash buffers
Cells not efficiently lysed
RIPA buffer should work well
Not enough starting material
ChIP typically requires a large input with at least 25 µg chromatin (3–4 million cells) per IP condition
Chromatin fragment size may be too small
Run on a gel to ensure correct size, repeat fragmentation optimization if necessary
Not enough antibody
3–5 µg is usually sufficient, but up to 10 µg may be required if no signal is observed
Monoclonal antibodies may not be suitable, particularly for X-ChIP as crosslinking may mask the epitope
Try a polyclonal antibody or ChIP grade/approved monoclonal
Wash buffer is too stringent, eliminating specific antibody binding
NaCl in buffer should not exceed 500 mM. Wash buffer should be optimized as described above
Wrong affinity beads
N-ChIP may not be suitable if you are not analyzing histones
If using X-Chip, cells may have been cross-linked for too long, reducing availability of epitopes, or not long enough, reducing pull-down of DNA from the IP
Make sure antibody species and immunoglobulin bind to chosen beads or use a protein/AG mix
X-ChIP may be required for analyzing proteins with weaker DNA affinity to keep proteins associated with DNA with crosslinking
Further optimize your cross-linking time course
Note: Low signal may be real, with no antibody enrichment at the region of interest.
Include positive control antibody and locus to confirm ChIP is working.
The antigen may be present, but not at the expected genomic loci.
Low resolution with high background across large regions
DNA fragment size may be too large
Fragment sizes should be less than 1 kb, but ideally 200–1000bp. The best resolution can be achieved with MNase digestion to single nucleosome level of 175 bp. Run on a gel and further optimize chromatin fragmentation steps if necessary.
PCR amplification problems
High signal in all samples after PCR including non-template control
qPCR solution may be contaminated
Prepare new solutions from stock
No DNA amplification in samples
Primers may not be working
Include input DNA control
What other treatments might affect my ChIP results?
Some antibodies are affected by relatively low concentrations of SDS. TSA, butyrate or colcemid addition do not generally affect ChIP.
Do not centrifuge sepharose beads at high rpm (do not exceed 6,000 rpm) as this will compact the beads and damage them.
Once pulled down DNA fragments have been immunoprecipitated and purified, they can be analyzed by several different methods.
Utilizes gene or target-specific primers to amplify known target loci among pulldown DNA
Employs microarrays to examine the presence of many loci of interest, specific domains, etc. across the genome. Pulldown and control samples are amplified and labeled with complementary fluorescent probes. Samples are combined and hybridized to a microarray of interest. The ratio of fluorescent signals indicates enriched regions where proteins of interest have bound.
Most commonly used method for genome-wide analysis with improved base-pair resolution and none of the limitations of ChIP-on-Chip. Pulldown DNA and control samples are amplified, followed by high throughput sequencing of the fragments, which are then aligned to the genome. Overlapping fragments form a peak, indicating where the protein of interest was bound to the genome.
Figure 3: ChIP seq overview. After ChIP is carried out, the precipitated DNA can be used for library preparation, sequencing and then these sequences are mapped to a reference genome to then undergo peak calling to determine binding sites of your protein of interest.
Data should always be normalized for the amount of starting material to eliminate errors introduced by uneven sample quantities. To normalize data, take the final amplicon value and divide it by the amplicon value of input material. For histone modifications, the immunoprecipitated material is usually normalized to the input amount and the amount of the relevant immunoprecipitated histone. For example, ChIP with an H3K4me3 antibody will be expressed relative to the input amount and the amount of H3 immunoprecipitated.
Measuring the amounts (and quality) of starting material is the key to interpreting your results effectively.
While ChIP-seq data analysis can be complex, it is arguably the most important part of the experiment. Robust data analysis is key to accurate and reliable results. A combination of online tools makes data interpretation accessible to bioinformatics specialists and wet lab biologists alike. There are many resources that demonstrate how to extract reliable results from ChIP-seq data, and how to interpret data sets for successful ChIP-seq analysis (Hurtado et al., 2010 and Yan et al., 2013).
This webinar covers the following ChIP-seq data analysis workflow:
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