Abstract
Chromatin plays a crucial role in gene regulation, and chromatin immunoprecipitation followed by sequencing (ChIP–seq) has been the standard technique for examining protein–DNA interactions across the whole genome. However, it is difficult to obtain epigenomic information from limited numbers of cells by ChIP–seq because of sample loss during chromatin preparation and inefficient immunoprecipitation. In this study, we established an immunoprecipitation-free epigenomic profiling method named chromatin integration labelling (ChIL), which enables the amplification of genomic sequences closely associated with the target molecules before cell lysis. Using ChIL followed by sequencing (ChIL–seq), we reliably detected the distributions of histone modifications and DNA-binding factors in 100–1,000 cells. In addition, ChIL–seq successfully detected genomic regions associated with histone marks at the single-cell level. Thus, ChIL–seq offers an alternative method to ChIP–seq for epigenomic profiling using small numbers of cells, in particular, those attached to culture plates and after immunofluorescence.
| Original language | English |
|---|---|
| Pages (from-to) | 287-296 |
| Number of pages | 10 |
| Journal | Nature Cell Biology |
| Volume | 21 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - Feb 1 2019 |
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All Science Journal Classification (ASJC) codes
- Cell Biology
Cite this
A chromatin integration labelling method enables epigenomic profiling with lower input. / Harada, Akihito; Maehara, Kazumitsu; Handa, Tetsuya; Arimura, Yasuhiro; Nogami, Jumpei; Hayashi-Takanaka, Yoko; Shirahige, Katsuhiko; Kurumizaka, Hitoshi; Kimura, Hiroshi; Ohkawa, Yasuyuki.
In: Nature Cell Biology, Vol. 21, No. 2, 01.02.2019, p. 287-296.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A chromatin integration labelling method enables epigenomic profiling with lower input
AU - Harada, Akihito
AU - Maehara, Kazumitsu
AU - Handa, Tetsuya
AU - Arimura, Yasuhiro
AU - Nogami, Jumpei
AU - Hayashi-Takanaka, Yoko
AU - Shirahige, Katsuhiko
AU - Kurumizaka, Hitoshi
AU - Kimura, Hiroshi
AU - Ohkawa, Yasuyuki
PY - 2019/2/1
Y1 - 2019/2/1
N2 - Chromatin plays a crucial role in gene regulation, and chromatin immunoprecipitation followed by sequencing (ChIP–seq) has been the standard technique for examining protein–DNA interactions across the whole genome. However, it is difficult to obtain epigenomic information from limited numbers of cells by ChIP–seq because of sample loss during chromatin preparation and inefficient immunoprecipitation. In this study, we established an immunoprecipitation-free epigenomic profiling method named chromatin integration labelling (ChIL), which enables the amplification of genomic sequences closely associated with the target molecules before cell lysis. Using ChIL followed by sequencing (ChIL–seq), we reliably detected the distributions of histone modifications and DNA-binding factors in 100–1,000 cells. In addition, ChIL–seq successfully detected genomic regions associated with histone marks at the single-cell level. Thus, ChIL–seq offers an alternative method to ChIP–seq for epigenomic profiling using small numbers of cells, in particular, those attached to culture plates and after immunofluorescence.
AB - Chromatin plays a crucial role in gene regulation, and chromatin immunoprecipitation followed by sequencing (ChIP–seq) has been the standard technique for examining protein–DNA interactions across the whole genome. However, it is difficult to obtain epigenomic information from limited numbers of cells by ChIP–seq because of sample loss during chromatin preparation and inefficient immunoprecipitation. In this study, we established an immunoprecipitation-free epigenomic profiling method named chromatin integration labelling (ChIL), which enables the amplification of genomic sequences closely associated with the target molecules before cell lysis. Using ChIL followed by sequencing (ChIL–seq), we reliably detected the distributions of histone modifications and DNA-binding factors in 100–1,000 cells. In addition, ChIL–seq successfully detected genomic regions associated with histone marks at the single-cell level. Thus, ChIL–seq offers an alternative method to ChIP–seq for epigenomic profiling using small numbers of cells, in particular, those attached to culture plates and after immunofluorescence.
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U2 - 10.1038/s41556-018-0248-3
DO - 10.1038/s41556-018-0248-3
M3 - Article
C2 - 30532068
AN - SCOPUS:85058147329
VL - 21
SP - 287
EP - 296
JO - Nature Cell Biology
JF - Nature Cell Biology
SN - 1465-7392
IS - 2
ER -