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Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
Chapters
Summary January 14th, 2016
Chromatin immunoprecipitation is a powerful technique for the identification of DNA binding sites of Arabidopsis proteins in vivo. This procedure includes chromatin cross-linking and fragmentation, immunoprecipitation with selective antibodies against the protein of interest, and qPCR analysis of bound DNA. We describe a simple ChIP assay optimized for Arabidopsis plants.
Transcript
The overall goal of this procedure is to unveil interactions between proteins and DNA in the chromatin of arabidopsis cells. This method can help answer key questions in the plant biology field, such as which genes are regulated by a given transcription factor, or what system modifications are associated with a transcriptional status of genes. The main advantage of this technique is that through the cross-linking step, it is possible to fix and capture changes in chromatin organization occurring during plant development.
Though this method can provide a insight into protein interaction in arabidopsis thaliana, it also can be applied to different plant orders and adapted to other plant species. Demonstrating this procedure will be Dorota Komar and Alfonso Mouriz, two PhD students in our laboratory. After growing arabidopsis according to the text protocol, collect 1.5 grams of plant material in 50 milliliter tubes, and keep them on ice during cross-linking.
Then, use a laboratory burner-heated needle to make little holes in the lids of the tubes. Add 40 milliliters of 1x pbs and 1.08 milliliters of formaldehyde to the tubes. Screw the lids on the tubes, and place the tubes in a desiccator.
Vacuum infiltrate for 10 minutes, then carefully release the vacuum to prevent churning up the solution. After mixing the sample, repeat the vacuum and mixing steps. Upon infiltration, observe the plant material and confirm that it becomes slightly translucent and sinks to the bottom of the tube.
Add 2.5 milliliters of two molar glycine to a final concentration of 0.125 molar and apply the vacuum for five minutes. After releasing the vacuum, discard the solution by inverting the tubes and allowing it to drip through the holes in the lids. Use pbs to rinse the plantlets twice, and rinse with water once.
Then dry the plantlets on a paper towel before using liquid nitrogen to freeze. Per each immunoprecipitation, prepare 15 microliters of magnetic beads in a 1.5 milliliter microcentrifuge tube. Add one milliliter of chromatin immunoprecipitation, or chip dilution buffer, to the beads, mix by rotation, and place the 1.5 milliliter microcentrifuge tube in a magnetic rack.
After allowing the beads to attach to the magnet for about a minute, use a pipetman to remove the supernatant before repeating the wash. Re-suspend the beads in 200 microliters of chip dilution buffer. For immunoprecipitation add the required amount of the specific antibody to one of the two tubes prepared for each plant blind.
A key factor in successful chip experiment is the chosen antibody for the immunoprecipitation of the protein of interest. Antibodies raised against plant transcription factor can be useful for chip experiments, but the serum has to be thoroughly tested. For example, antibodies checked only in Western blot analysis are not necessarily valid for chip.
As a negative control, add the same amount of non-specific IGG to the second tube. Incubate the tubes at four degrees Celsius overnight on a rotating wheel to allow the antibody to attach to the beads. Using a mortar and pestle, thoroughly grind the frozen plant material in liquid nitrogen until the powder becomes homogeneous and light green.
Transfer the powder to a new 50 milliliter tube. Under a fume hood, add 30 milliliters of extraction buffer one, and mix well to soak the tissue powder. From this step on, keep the samples at four degrees Celsius at all times, and make sure that the tissue is completely thawed before moving forward.
Clear the slurry by passing it through a filtration tissue with a pore size of 22 to 25 micrometers into a new 50 milliliter tube. Then centrifuge at 1, 000 times g and four degrees Celsius for 20 minutes. Gently decant the supernatant from the pellet, which should be about two milliliters in volume.
With five milliliters of extraction buffer two, re-suspend the pellet. Then centrifuge at 1, 000 times g and four degrees Celsius for 10 minutes. After decanting the supernatant, re-suspend the pellet in 300 microliters of extraction buffer three.
In a separate tube, add 600 microliters of extraction buffer three and then carefully layer the re-suspended pellet on top of the clean buffer. Centrifuge the tube for one hour at 16, 000 times g at four degrees Celsius, followed by aspiration of the supernatant with a pipette. Next, use 300 microliters of sonication buffer to slowly re-suspend the nuclear pellet, avoiding bubble formation, which may affect sonication efficiency.
Carefully transfer the suspension to a clean, 1.5 milliliter tube. Sonicate the suspension to lyse the nuclei and randomly share the chromatin into 200 to 600 base pair fragments. Verify the DNA fragment sizes on an agarose gel, then spin the solution at 12, 000 times g and four degrees Celsius for 10 minutes.
Transfer the supernatant to a fresh 1.5 milliliter tube, and discard the pellet. Aliquot one-tenth of the supernatant into a new tube, and label it as input'before freezing at minus 20 degrees Celsius. Finally, make a ten-fold dilution of the chromatin in chip dilution buffer to achieve a final SDS concentration of 0.1 percent.
Samples can then be frozen and stored at minus 20 degrees Celsius for several weeks. After incubating the beads with antibodies overnight, use one milliliter of chip dilution buffer to wash the beads three times, then re-suspend the beads in one milliliter of the diluted chromatin, and incubate the tube overnight on a rotating wheel at four degrees Celsius. The following day, place the beads on the magnetic rack at four degrees Celsius, and after removing the solution, use one milliliter of low-salt washing buffer to wash the beads twice, then use high-salt washing buffer to wash the beads once.
After using one milliliter of lithium chloride washing buffer to wash the beads once, use one milliliter of TE buffer to wash the beads twice. Aspirate to thoroughly remove the TE wash buffer. Once the input samples are thawed, transfer five microliters of each into new 1.5 milliliter tubes, and moving forward, treat similarly to the chip samples.
Reverse the cross-linking by adding 200 microliters of five percent chelating ion exchange resin and incubate at 95 degrees Celsius for 10 minutes, shaking every two to three minutes. Spin down at 16, 000 times g for 30 seconds, and carefully transfer the supernatant into new microfuge tubes. Add two microliters of 10 milligrams per milliliter protonase K, and incubate at 37 degrees Celsius for 30 minutes to digest proteins and release DNA.
To stop the reaction, incubate at 95 degrees Celsius for 10 minutes, Quickly spin at 16, 000 times g for 30 seconds, and transfer the supernatant to a new tube. After cleaning the DNA according to the text protocol, dilute one to ten with water, and use five microliters per reaction to measure the abundance of binding sites by qPCR. Analyze the data according to the text protocol.
Aribidopsis leaves are covered in wax layers and trichomes favor the formation of air bubbles, both of which make it difficult for cross-linking reagents to penetrate the plant tissue. Shown here are cross-linked seedling samples that were vacuum cross-linked to increase fixation efficiency. This figure demonstrates that an increased number of sonication cycles progressively reduces the average size of the DNA in chip samples, reaching the optimum enrichment in the range of 200 to 600 base pairs after 20 to 30 cycles, as demonstrated here.
As seen in this figure, four regions important for the transcriptional regulation of the FT locus, a master gene of flowering, have been chosen for the analysis. Chip results demonstrate that the EBS protein combined one of the four regions tested, a regulatory sequence close to the transcriptional start site of FT.Finally, chip assays performed using an antibody directed against histone h3 acetylated in lysines nine and 14, which is correlated with transcriptionally active chromatin, revealed higher abundance of H3K9/14ac in mutant DBS versus wild type plants in all four genomic fragments of FT tested, consistent with the observed up-regulation of this master gene of flowering in this mutant. Once mastered, this technique can be done in two days if it is performed properly.
Following this procedure, together with other measures like gene expression analysis, can contribute to answering other questions, like:What is the biological role of the binding of the protein to DNA? Is it at transcriptional activation or repression? And Which histone modifications are associated?
After it's development, this technique paved the way for researchers in the field of plant epigenetics to explore chromatin states in our reductive cells. And this can be extended to other plant species. After watching this video, you should have a good understanding of how to analyse the binding of your aribidopsis protein of interest to DNA in vivo.
Don't forget that working with 2-methoxyethanol, formaldehyde or sonicator reagents, pathogens and stem mutations can be extremely hazardous, and precautions such as protective clothes, gloves or hearing protection should be always taken while using this procedure.
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