RT Journal Article
SR Electronic
T1 Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.03.08.483436
DO 10.1101/2022.03.08.483436
A1 Tim Stuart
A1 Stephanie Hao
A1 Bingjie Zhang
A1 Levan Mekerishvili
A1 Dan A Landau
A1 Silas Maniatis
A1 Rahul Satija
A1 Ivan Raimondi
YR 2022
UL http://biorxiv.org/content/early/2022/03/09/2022.03.08.483436.abstract
AB 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.Competing Interest StatementIn the past 3 years, R.S. has worked as a consultant for Bristol-Myers Squibb, Regeneron and Kallyope and served as an SAB member for ImmunAI, Resolve Biosciences, Nanostring, and the NYC Pandemic Response Lab. I.R. and S.M. have filed a patent application based on this work (US Provisional Application No. 63/276,533). The remaining authors declare no competing interests.