TY - JOUR
T1 - High-throughput single-cell epigenomic profiling by targeted insertion of promoters (Tip-seq)
AU - Bartlett, Daniel A.
AU - Dileep, Vishnu
AU - Handa, Tetsuya
AU - Ohkawa, Yasuyuki
AU - Kimura, Hiroshi
AU - Henikoff, Steven
AU - Gilbert, David M.
N1 - Funding Information:
This work was funded by National Institutes of Health grant R21 HG010403 (D.M. Gilbert), Japan Science and Technology Agency Core Research for Evolutional Science and Technology grant JPMJCR16G1 (Y. Ohkawa and H. Kimura), and Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research grant JP18H05527 (Y. Ohkawa and H. Kimura). The authors declare no competing financial interests.
Publisher Copyright:
© 2021 Bartlett et al.
PY - 2021/12/6
Y1 - 2021/12/6
N2 - 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.
AB - 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.
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U2 - 10.1083/jcb.202103078
DO - 10.1083/jcb.202103078
M3 - Article
C2 - 34783858
AN - SCOPUS:85120715452
VL - 220
JO - Journal of Cell Biology
JF - Journal of Cell Biology
SN - 0021-9525
IS - 12
M1 - e202103078
ER -