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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6 December 2021
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November 16 2021
High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq)
Daniel A. Bartlett
,
Daniel A. Bartlett
1
Department of Biological Science, Florida State University, Tallahassee, FL
5
San Diego Biomedical Research Institute, La Jolla, CA
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Vishnu Dileep,
Vishnu Dileep
1
Department of Biological Science, Florida State University, Tallahassee, FL
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Tetsuya Handa
,
Tetsuya Handa
2
Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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Yasuyuki Ohkawa
,
Yasuyuki Ohkawa
3
Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Hiroshi Kimura
,
Hiroshi Kimura
2
Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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Steven Henikoff
,
Steven Henikoff
4
Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
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David M. Gilbert
1
Department of Biological Science, Florida State University, Tallahassee, FL
5
San Diego Biomedical Research Institute, La Jolla, CA
Correspondence to David M. Gilbert: gilbert@sdbri.org
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Daniel A. Bartlett
1
Department of Biological Science, Florida State University, Tallahassee, FL
5
San Diego Biomedical Research Institute, La Jolla, CA
Vishnu Dileep
1
Department of Biological Science, Florida State University, Tallahassee, FL
Tetsuya Handa
2
Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
Yasuyuki Ohkawa
3
Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
Hiroshi Kimura
2
Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
Steven Henikoff
4
Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
Correspondence to David M. Gilbert: gilbert@sdbri.org
Daniel A. Bartlett: dbart1807@gmail.com
A preprint of this paper was posted to bioRxiv on March 19, 2021.
Received:
March 13 2021
Revision Received:
September 15 2021
Accepted:
October 27 2021
Online Issn: 1540-8140
Print Issn: 0021-9525
Funding
Funder(s):
National Institutes of Health
- Award Id(s): R21 HG010403
Funder(s):
Japan Science and Technology Agency
- Award Id(s): JPMJCR16G1
Funder(s):
Japan Society for the Promotion of Science
- Award Id(s): JP18H05527
© 2021 Bartlett et al.
2021
This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).
J Cell Biol (2021) 220 (12): e202103078.
Article history
Received:
March 13 2021
Revision Received:
September 15 2021
Accepted:
October 27 2021
Citation
Daniel A. Bartlett, Vishnu Dileep, Tetsuya Handa, Yasuyuki Ohkawa, Hiroshi Kimura, Steven Henikoff, David M. Gilbert; High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). J Cell Biol 6 December 2021; 220 (12): e202103078. doi: https://doi.org/10.1083/jcb.202103078
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