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Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input

Abstract

Cell identity is determined by the selective activation or silencing of specific genes via transcription factor binding and epigenetic modifications on the genome. Chromatin immunoprecipitation (ChIP) has been the standard technique for mapping the sites of transcription factor binding and histone modification. Recently, alternative methods to ChIP have been developed for addressing the increasing demands for low-input epigenomic profiling. Chromatin integration labeling (ChIL) followed by sequencing (ChIL-seq) has been demonstrated to be particularly useful for epigenomic profiling of low-input samples or even single cells because the technique amplifies the target genomic sequence before cell lysis. After labeling the target protein or modification in situ with an oligonucleotide-conjugated antibody (ChIL probe), the nearby genome sequence is amplified by Tn5 transposase-mediated transposition followed by T7 RNA polymerase-mediated transcription. ChIL-seq enables the detection of the antibody target localization under a fluorescence microscope and at the genomic level. Here we describe the detailed protocol of ChIL-seq with assessment methods for the key steps, including ChIL probe reaction, transposition, in situ transcription and sequencing library preparation. The protocol usually takes 3 d to prepare the sequencing library, including overnight incubations for the ChIL probe reaction and in situ transcription. The ChIL probe can be separately prepared and stored for several months, and its preparation and evaluation protocols are also documented in detail. An optional analysis for multiple targets (multitarget ChIL-seq) is also described. We anticipate that the protocol presented here will make the ChIL technique more widely accessible for analyzing precious samples and facilitate further applications.

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Fig. 1: ChIL-seq strategy.
Fig. 2: ChIL probe design and validation.
Fig. 3: Results of ChIL-seq.
Fig. 4: Results of mtChIL-seq.

Data availability

ChIL-seq and mtChIL-seq data in this study have been deposited in the Gene Expression Omnibus (GEO) under the accession code GSE140659. Source data are provided with this paper.

Code availability

All performance metrics of low-input epigenomic profiling methods in Table 2 are the re-evaluation of our original ChIL-seq data analysis (except for the adapted information from previous reports, specified in the table legend). The main workhorse is the tableTPFP function in RScripts/myROC.R in https://github.com/kazumits/DataAnalysisForChILT. The use case of calculating ROC at TSS is according to the example described at https://github.com/kazumits/DataAnalysisForChILT/blob/master/ChILT_optimalResolution.md. The evaluation of genome-wide prediction performance (for example, precision, recall) against gold-standard ChIP-seq peaks is shown at https://github.com/kazumits/DataAnalysisForChILT/blob/master/ChILT_sensitivity-specificity.md. Source data are provided with this paper.

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Acknowledgements

We are grateful to the staff of Ohkawa Lab. The computation was carried out using the computer resource offered under the category of Intensively Promoted Projects by Research Institute for Information Technology, Kyushu University. This work was in part supported by MEXT/JSPS KAKENHI (JP17K17719 to T.H.; JP18K19432, JP19H03211, JP19H05425 and JP20H05368 to A.H.; JP18H04904, JP19H04970, JP19H03158 and JP20H05393 to K.M.; JP18H05534 to H.Ku.; JP18H04802, JP18H05527, JP19H05244, JP17H03608, JP20H00456, JP20H04846 and JP20K21398 to Y.O.; and JP18H05527 and JP17H01417 to H.Ki), JST CREST (JPMJCR16G1 to Y.O., H.Ku. and H.Ki.), JST PRESTO JPMJPR19K7 to A.H, AMED JP20ek0109489h0001 to Y.O. and AMED BINDS (JP19am0101076 to H.Ku. and JP19am0101105 to H.Ki.).

Author information

Authors and Affiliations

Authors

Contributions

T.H., A.H., Y.O. and H. Ki. designed the experiments. T.H. and A.H. performed the ChIL experiments with deep-sequencing analyses. K.M. performed the bioinformatics and statistical analyses. S.S. and H.Ku. produced the in-house Tn5 transposase. M.N. and N.G. contributed to the assay for in situ transcription. T.H., A.H., K.M., Y.O. and H.Ki. wrote the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Yasuyuki Ohkawa or Hiroshi Kimura.

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Competing interests

The authors declare no competing financial interests except T.H., A.H., H. Ku., Y.O. and H.Ki, who are involved in a pending patent related to ChIL.

Additional information

Peer review information Nature Protocols thanks Chang Lu, Sinem K. Saka and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Key reference using this protocol:

Harada, A. et al. Nat. Cell Biol. 21, 287−296 (2019): https://doi.org/10.1038/s41556-018-0248-3

Supplementary information

Supplementary Information

Supplementary Tables 1–5 and Figs. 1–9.

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Source data

Source Data Fig. 2

Unprocessed gels.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 4

Statistical source data.

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Handa, T., Harada, A., Maehara, K. et al. Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input. Nat Protoc 15, 3334–3360 (2020). https://doi.org/10.1038/s41596-020-0375-8

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