Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

Ku, Wai Lim; Nakamura, Kôsuke; Gao, Weiying; Cui, Kairong; Hu, Gangqing; Tang, Qingsong; Ni, Bing; Zhao, Keji

doi:10.1038/s41592-019-0361-7

Cited by 152 publications

(111 citation statements)

References 30 publications

(25 reference statements)

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“…Importantly, the mock controls, in which no chromatin was present, did not show any recovery for either the To evaluate the results of the optimized microfluidic ChIP procedure, we compared our results to conventional ChIP-qPCRs using the equivalent of 500,000 or 10,000 mESCs from a bulk mESC sonicated sample as input. In line with the fact that that lower input quantities affect the efficiency of ChIPs (Kidder et al 2011;Ku et al 2019), we observed a 5-fold reduction in recovery in conventional bench ChIP-qPCRs performed using 10,000 mESCs as compared to the ChIP-qPCRs performed using 500,000 mESCs ( Fig. 2f, left part labeled 1-3).…”

Section: Microfluidic Chip Is Sensitive and Robustsupporting

confidence: 76%

“…Low-input cell numbers affect sensitivity of ChIPs (Kidder et al 2011;Ku et al 2019), which is clear in the current study from the H3K4me3 average profiles ( Fig S8).…”

Section: Discussionmentioning

confidence: 59%

“…The drop in peak calls for the small quantities was mainly caused by a concentration-dependent decrease of H3K4me3 signals (Fig. 4c & S8b), which is known for low input ChIP-Seq (Kidder et al 2011;Ku et al 2019). Notably, even though we started with only 15,000 mESCs in the MNase-based protocol, the H3K4me3 PnP-ChIP-Seq profiles showed higher signal-to-noise ratios compared to the H3K4me3 PnP-ChIP-Seq profiles generated using chromatin that was sonicated in bulk ( Fig.…”

Section: Pnp-chip-seq Is Compatible With Low Abundant Populations Of mentioning

confidence: 82%

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A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation

Dirks

Thomas

Jones

et al. 2020

Preprint

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Epigenetic profiling by ChIP-Seq has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks and for screening for biomarkers. However, the ChIP-Seq protocol for low-input samples is laborious, time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput.Although prototypic microfluidic ChIP-Seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelisation. To enable standardized, automated ChIP-Seq profiling of low-input samples, we constructed PDMS-based plates containing microfluidic Integrated Fluidic Circuits capable of performing 24 sensitive ChIP reactions within 30 minutes hands-on time. These disposable plates can conveniently be loaded into a widely available controller for pneumatics and thermocycling, making the ChIP-Seq procedure Plug and Play (PnP). We demonstrate high-quality ChIP-seq on hundreds to few thousands of cells for multiple widely-profiled post-translational histone modifications, together allowing genome-wide identification of regulatory elements. As proof of principle, we managed to generate high-quality epigenetic profiles of rare totipotent subpopulations of mESCs using our platform. In light of the ready-to-go ChIP plates and the automated workflow, we named our procedure PnP-ChIP-Seq.PnP-ChIP-Seq allows non-expert labs worldwide to conveniently run robust, standardized ChIP-Seq, while its high-throughput, consistency and sensitivity paves the way towards large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.

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Section: Microfluidic Chip Is Sensitive and Robustsupporting

confidence: 76%

“…Low-input cell numbers affect sensitivity of ChIPs (Kidder et al 2011;Ku et al 2019), which is clear in the current study from the H3K4me3 average profiles ( Fig S8).…”

Section: Discussionmentioning

confidence: 59%

Section: Pnp-chip-seq Is Compatible With Low Abundant Populations Of mentioning

confidence: 82%

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A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation

Dirks

Thomas

Jones

et al. 2020

Preprint

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“…3C), single cell cleavage under targets and tagmentation (scCUT&Tag) (Kaya-Okur et al, 2019) ( Fig. 3D), and single cell chromatin immunocleavage followed by sequencing (scChIC-seq) (Ku et al, 2019) (Fig. 3E).…”

Section: Box 1 Metrics Of Single Cell Technologiesmentioning

confidence: 99%

Mapping chromatin modifications at the single cell level

Ludwig

Bintu

2019

Development

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Understanding chromatin regulation holds enormous promise for controlling gene regulation, predicting cellular identity, and developing diagnostics and cellular therapies. However, the dynamic nature of chromatin, together with cell-to-cell heterogeneity in its structure, limits our ability to extract its governing principles. Single cell mapping of chromatin modifications, in conjunction with expression measurements, could help overcome these limitations. Here, we review recent advances in single cell-based measurements of chromatin modifications, including optimization to reduce DNA loss, improved DNA sequencing, barcoding, and antibody engineering. We also highlight several applications of these techniques that have provided insights into cell-type classification, mapping modification co-occurrence and heterogeneity, and monitoring chromatin dynamics.

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“…The recent development of single-cell methods to study the epigenome enables the appreciation of the heterogeneity of chromatin features within a population, which cannot be assessed using bulk ATAC-seq or ChIP-seq method. Such methods include scChIP-seq (Grosselin et al, 2019;Rotem et al, 2015), scChIL-seq (Harada et al, 2019), scChIC-seq (Ku et al, 2019) and scCUT&Tag (Kaya-Okur et al, 2019) which identify genomic regions enriched for repressive or active histone marks (H3K27me3, H3K4me3, ...) and scATACseq (Chen et al, 2018;Cusanovich et al, 2015;Lareau et al, 2019) which assesses regions of open chromatin. There are existing tools publicly available to analyze scATAC-seq such as chromVar (Schep et al, 2017), Cicero (Pliner et al, 2018) or Scasat (Baker et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

ChromSCape : a Shiny/R application for interactive analysis of single-cell chromatin profiles

Prompsy

Kirchmeier

Vallot

2019

Preprint

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Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

Cited by 152 publications

References 30 publications

A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation

A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation

Mapping chromatin modifications at the single cell level

ChromSCape : a Shiny/R application for interactive analysis of single-cell chromatin profiles

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