Have you any advice to optimize CUT&RUN for protein weakly bound to chromatin ?
We have done intensive valiation of our CUT&RUN protocol for proteins that are weakly bound to chromatin (cofactors), including Rpb1, SMARCC1, Brg1, RING1B, Bmi1, SUZ12, and EZH2, etc. Follow our protocol and choose a CUT&RUN validated antibody, you will get a good CUT&RUN result on cofactors.
About indirect DNA binders and the possibility of using fixation for solving that.
See above. Although we don't belive cell fixation is needed for cofactors, you may try if you really want to. However, CUT&RUN protocol might need to be optimized for the fixed cells as our protocol is only valiated for living cells.
Protecting PTMs by inhibiting PTM removal enzymes (such as HDACs and Phosphatases) during the CUTaTag/CutaRun procedure artifact
The question is incomplete. That said, CUT&RUN assay works for drug treated cells. Spike-in DNA can also be used to normalize the artifact that is induced by PTM removal inhibitors.
How convinced are you that the Antibody is directing Mnase and you are not just mapping hypersensitivity sites?
Based on the fact that CUT&RUN-NGS generates similar target protein binding pattern across genome as the ChIP-seq does, we believe Mnase is digesting the antibody binding loci but not random hypersensitivity sites.
How does normalization for CUT&RUN differ from ChIP spike-in normalization?
Normalization for CUT&RUN happens when the digestion is done. Yeast genomic DNA fragemnts are spiked in the CUT&RUN sample before DNA purification. In ChIP, both spike-in chromatin and spike-in antibody are added to the IP reacation. To compare them, ChIP spkie-in normalization occurs earlier in the experiment than CUT&RUN spike-in normalziation does, but the ChIP one is also more complicated than CUT&RUN one.
Do you have any advice for the spike-in ?
We suggest following our protocol #86652 for usage of spike-in DNA in qPCR and NGS. Please note that qPCR and NGS needs very different amount of spike-in DNA for detection. If both qPCR and NGS are required, please prepare two samples in parellel to satisfy different requirements of spike-in DNA amount.
Which method do you use for size selection during library preparation?
We don’t recommend size selection during library preparation, no matter for CUT&RUN or ChIP-seq. Based our own experience and many customers' feedback, size selection significantly decreases both diversity and yield of the library. If you really concerned with large DNA fragments (>1kb), decrease the extension time when amplifying the adaptor-ligated DNA sample during library prep. We see that 10-15s is enough for amplifying CUT&RUN library DNA, and no large DNA fragments (>1kb) have a chance to be amplified within such a short extension time.
What control would you do before sending for sequencing (not very well described in the protocol?
We recommend the input sample as negative control for NGS, although both Input sample and IgG sample are acceptable for publication purpose. Input sample saves more reagents than the IgG antibody control does and it has a higher diverstiy. Customers' feedbacks show that IgG may produce the high background issue (at some gene loci of interest).
Do you have any recommendation for library prep kit?
We use our SimpleChIP ChIP-seq DNA Library Prept Kit for Illumina (56795) and SimpleChIP ChIP-seq Multiplex Oligos for Illumina (29580, 47538)
For analyzing CUT&RUN results by qPCR, what are the primer requirements and what is flexible if ideal requirements can't be met?
Use shorter primers 60-80 bp instead of 100bp, but we have gotten it to work with primers that are 100bps
Is cut & Run analysed by qPCR as accurate as ChIP-qPCR ?
Yes. Our CUT&RUN-qPCR result is pretty compatible with the ChIP-qPCR result. However, to catch as much signal as possible, we suggest designing primer set with smaller amplicon size (ideally 60-80bp, ~100bp is also fine). The reason is that CUT&RUN DNA is smaller than ChIP DNA (size of TF/cofactor CUT&RUN DNA peaks around 80bp while size of histone CUT&RUN DNA peaks around 150bp).
What would be the most suitable control for a CUT&RUN? How can one perform a qPCR from CUT&RUN DNA (if possible) (asked 2 times)?
We provide a positive and negative control antibody in the kit, H3K4me3 #9751 and Rabbit IgG Isotype Control #66362, both of which can be purchased as stand-alones. The kit also provides both Human and Mouse positive Control primers, #7014, and #7015 which are also sold separately. The Sample Normalization Primers are only sold as part of the kit, and the amount of spike-in DNA that is provided in the bundle is only sufficient for NGS. Henikoff indicates that he felt the DNA from CUT&RUN would be too small for qPCR, but we have successfully performed qPCR on all three protein types (histones, TFs, cofactors). The qPCR is performed the exact same way as DNA from a ChIP experiment, with the only difference being that we recommend using primers that are 60-80 bps in length since CUT&RUN DNA is smaller than ChIP DNA. That being said we have successfully performed qPCR with CUT&RUN DNA using primers that are 100bps in length.
Alternatives to use a negative control for CUT&RUN, when your cell line has a tag that can be bound by RbIgG.
Use a negative gene locus as the control. In detail, design a primer set against the gene locus which is known not to be bound by the target protein.
What is the best way to choose an antibody? Especially if there are none which have previously been used for ChIP-seq/CUT&RUN? Is it important for antibody to work for IP? (3)
You can try a ChIP validated antibody, but we have found that ChIP validation is not a guarantee that it will work for CUT&RUN. Henikoff has indicated that IF might be a better indicator, but we have not validated this idea internally.
Have you done CUT&RUN on epitope-tagged endogenous targets?
We haven't. But we have heard positive resutls from customers (eg. flag).
When do you decide whether to use CUT&RUN/Tag? and how is your product different from other companies? (asked 4 times)
See Slide on CUT&RUN/Tag Comparison