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bioRxiv · 10.1101/2022.03.08.483436

Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution

Stuart, T.·Hao, S.·Zhang, B.·Mekerishvili, L.·Landau, D.·Maniatis, S.·Satija, R.·Raimondi, I.
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Abstract

Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here, we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.

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Stuart, T., Hao, S., Zhang, B., Mekerishvili, L., Landau, D., Maniatis, S., Satija, R., Raimondi, I.. 2022-03-09. Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution. https://doi.org/10.1101/2022.03.08.483436

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