Preparation of optimized concanavalin A-conjugated Dynabeads® magnetic beads for CUT&Tag.

Epigenome research has employed various methods to identify the genomic location of proteins of interest, such as transcription factors and histone modifications. A recently established method called CUT&Tag uses a Protein-A Tn5 transposase fusion protein, which cuts the genome and inserts adapter sequences nearby the target protein. Throughout most of the CUT&Tag procedure, cells are held on concanavalin A (con A)-conjugated magnetic beads. Proper holding of cells would be decisive for the accessibility of Tn5 to the chromatin, and efficacy of the procedure of washing cells. However, BioMag®Plus ConA magnetic beads, used in the original CUT&Tag protocol, often exhibit poor suspendability and severe aggregation. Here, we compared the BioMag beads and Dynabeads® magnetic particles of which conjugation of con A was done by our hands, and examined the performance of these magnetic beads in CUT&Tag. Among tested, one of the Dynabeads, MyOne-T1, kept excessive suspendability in a buffer even after overnight incubation. Furthermore, the MyOne-T1 beads notably improved the sensitivity in CUT&Tag assay for H3K4me3. In conclusion, the arrangement and the selection of MyOne-T1 refine the suspendability of beads, which improves the association of chromatin with Tn5, which enhances the sensitivity in CUT&Tag assay.
Competing Interests: The authors report that there were material support and technical advice from VERITAS corporation for this study that could have influenced its outcome and that one of the authors, Y.T. is its employee. This does not alter our adherence to PLOS ONE policies on sharing data and materials." We believe our revised manuscript would suffice the reviewer’s concerns. It would be greatly appreciated if the editorial office and reviewers could consider this revision. All the authors have read the manuscript and have approved this submission. All study participants provided informed consent, and the study design was approved by an ethics review board.