Does CUT&RUN require adjustments for transcription factors or other chromatin proteins?

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Depending on your target, you may need to consider modifications to the CUTANA CUT&RUN DNA Purification protocol.

The current CUTANA CUT&RUN DNA Purification protocol uses a 1.4X SPRI bead ratio to capture mononucleosome-sized chromatin fragments (~140-180 bp). In EpiCypher’s experience, the majority of transcription factors, modifying enzymes, and other chromatin-associated proteins generate predominantly mononucleosome-sized fragments in CUT&RUN, and are successfully profiled using the current protocol.

However, some transcription factors and nuclear hormone receptors generate both mononucleosome- and subnucleosome-sized fragments (<120 bp). In these cases, a 1.8X volume of SPRI beads can be used to help enhance capture of smaller fragments. Additional SPRI beads are available via purchase of our CUTANA Quick Cleanup DNA Purification Kit (EpiCypher 14-0052). Perform Ethanol washes and elution as described in the CUT&RUN protocol.

If you routinely profile transcription factors in CUT&RUN, you may consider using our validated CTCF antibody (EpiCypher 13-2014) as a positive control, in addition to the H3K4me3 and H3K27me3 positive controls provided with the CUTANA CUT&RUN Kit.

If you are unsure what to expect for your target, reach out to EpiCypher Tech Support for guidance.