Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution

Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A. Landau, Silas Maniatis, Rahul Satija, Ivan Raimondi

Research output: Contribution to journalArticlepeer-review


Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility and other factors. Current methods for defining chromatin states cannot measure more than one aspect in a single experiment at single-cell resolution. Here we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), an assay capable of measuring the genome-wide presence of up to three histone modifications and protein–DNA binding sites at single-cell resolution. NTT-seq uses 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-cell and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in human immune cells. We also extend NTT-seq to enable simultaneous profiling of cell surface protein expression and multimodal chromatin states to study cells of the immune system.

Original languageEnglish (US)
Pages (from-to)806-812
Number of pages7
JournalNature Biotechnology
Issue number6
StatePublished - Jun 2023

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Bioengineering
  • Molecular Medicine
  • Biotechnology
  • Biomedical Engineering


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