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bioRxiv · 10.1101/2024.07.12.603224

NanoTag - an IgG-free method for mapping DNA-protein interactions

Dimitriu, M. A.·Arzate-Mejia, R. G.·Steg, L. C.·Germain, P.-L.·Mansuy, I. M.
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Abstract

Genome-wide profiling of DNA-protein interactions in cells can provide important information about mechanisms of gene regulation. Most current methods for genome-wide profiling of DNA-bound proteins, such as ChIP-seq and CUT&Tag, use conventional IgG antibodies to bind target protein(s), which limits their applicability to targets for which high affinity and high specificity antibodies are available. Here we describe NanoTag, a novel method derived from CUT&Tag that is IgG-free and uses a nanobody to profile DNA-protein interactions. NanoTag is based on an anti-GFP nanobody-Tn5 transposase fusion that allows mapping GFP-tagged proteins associated with chromatin in a fast and cost-effective manner. We demonstrate the utility of NanoTag by profiling the histone mark H3K4me3 via its binding partner TATA box-binding protein-associated factor 3 (TAF3) and the transcription factors Nanog and CTCF in mouse embryonic stem cells expressing GFP-tagged targets. For the targets examined, NanoTag data shows high correlation to CUT&Tag data and displays a similarly high signal-to-noise ratio. Overall, NanoTag provides a flexible, IgG-free and cost-effective method to generate high resolution DNA-binding profiles in cells or tissues.

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Dimitriu, M. A., Arzate-Mejia, R. G., Steg, L. C., Germain, P.-L., Mansuy, I. M.. 2024-07-12. NanoTag - an IgG-free method for mapping DNA-protein interactions. https://doi.org/10.1101/2024.07.12.603224

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