Journal
JOURNAL OF CELL BIOLOGY
Volume 220, Issue 12, Pages -Publisher
ROCKEFELLER UNIV PRESS
DOI: 10.1083/jcb.202103078
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Funding
- National Institutes of Health [R21 HG010403]
- Japan Science and Technology Agency Core Research for Evolutional Science and Technology [JPMJCR16G1]
- Japan Society for the Promotion of Science [JP18H05527]
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The study introduces a high-throughput single-cell DNA binding site mapping method, TIP-seq, that is simple, cost-effective, and capable of multiplexing multiple samples per experiment.
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 similar to 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.
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