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

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 (TIP-seq) uses Tn5 fused to protein A to insert a T7 RNA polymerase promoter adjacent to a chromatin protein of interest. Linear amplification of flanking DNA with T7 polymerase prior to sequencing library preparation provides ~10-fold higher unique reads per single cell compared to other methods. We apply TIP-seq to map histone modifications, RNA Polymerase II (RNAPII) and transcription factor CTCF binding sites in single human and mouse cells. Overall design: Targeted insertion of promoters (TIP-seq) uses a custom-designed proteinA-Tn5 transposase fusion protein (pA-Tn5), that carries with it a transposon containing a T7 promoter, that is recruited to antibody-bound chromatin sites where the Tn5 transposome simultaneously cuts and inserts (tagmentation) the T7 promoter into adjacent genomic DNA to permit linear amplification. In-vitro transcription (IVT) by T7 RNA polymerase creates thousands of RNA copies of the insertion sites, and after reverse transcription, second-strand synthesis, and cDNA fragmentation, TIP-seq amplicons are prepared for sequencing via limited-cycle number PCR indexing.