High-throughput single-cell epigenomic profiling by targeted insertion of promoters (Tip-seq)

Daniel A. Bartlett, Vishnu Dileep, Tetsuya Handa, Yasuyuki Ohkawa, Hiroshi Kimura, Steven Henikoff, David M. Gilbert

Research output: Contribution to journalArticlepeer-review

Abstract

Chromatin profiling in single cells has been extremely challenging and almost exclusively limited to histone proteins. In cases where single-cell methods have shown promise, many require highly specialized equipment or cell type–specific protocols and are relatively low throughput. Here, we combine the advantages of tagmentation, linear amplification, and combinatorial indexing to produce a high-throughput single-cell DNA binding site mapping method that is simple, inexpensive, and capable of multiplexing several independent samples per experiment. Targeted insertion of promoters sequencing (TIP-seq) uses Tn5 fused to proteinA to insert a T7 RNA polymerase promoter adjacent to a chromatin protein of interest. Linear amplification of flanking DNA with T7 polymerase before sequencing library preparation provides ∼10-fold higher unique reads per single cell compared with other methods. We applied TIP-seq to map histone modifications, RNA polymerase II (RNAPII), and transcription factor CTCF binding sites in single human and mouse cells.

Original languageEnglish
Article numbere202103078
JournalJournal of Cell Biology
Volume220
Issue number12
DOIs
Publication statusPublished - Dec 6 2021

All Science Journal Classification (ASJC) codes

  • Cell Biology

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