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Literature DB >> 30923384

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

Wai Lim Ku¹, Kosuke Nakamura^1,2, Weiwu Gao^1,3, Kairong Cui¹, Gangqing Hu¹, Qingsong Tang¹, Bing Ni⁴, Keji Zhao⁵.

Abstract

Our method for analyzing histone modifications, scChIC-seq (single-cell chromatin immunocleavage sequencing), involves targeting of the micrococcal nuclease (MNase) to a histone mark of choice by tethering to a specific antibody. Cleaved target sites are then selectively PCR amplified. We show that scChIC-seq reliably detects H3K4me3 and H3K27me3 target sites in single human white blood cells. The resulting data are used for clustering of blood cell types.

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Year: 2019 PMID： 30923384 PMCID： PMC7187538 DOI： 10.1038/s41592-019-0361-7

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

20 in total

1. High-resolution profiling of histone methylations in the human genome.

Authors: Artem Barski; Suresh Cuddapah; Kairong Cui; Tae-Young Roh; Dustin E Schones; Zhibin Wang; Gang Wei; Iouri Chepelev; Keji Zhao
Journal: Cell Date: 2007-05-18 Impact factor: 41.582

2. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states.

Authors: Ronnie Blecher-Gonen; Zohar Barnett-Itzhaki; Diego Jaitin; Daniela Amann-Zalcenstein; David Lara-Astiaso; Ido Amit
Journal: Nat Protoc Date: 2013-02-21 Impact factor: 13.491

3. Nucleosome Occupancy and Methylome Sequencing (NOMe-seq).

Authors: Fides D Lay; Theresa K Kelly; Peter A Jones
Journal: Methods Mol Biol Date: 2018

4. Single-cell chromatin accessibility reveals principles of regulatory variation.

Authors: Jason D Buenrostro; Beijing Wu; Ulrike M Litzenburger; Dave Ruff; Michael L Gonzales; Michael P Snyder; Howard Y Chang; William J Greenleaf
Journal: Nature Date: 2015-06-17 Impact factor: 49.962

5. Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells.

Authors: Sebastian Pott
Journal: Elife Date: 2017-06-27 Impact factor: 8.140

6. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites.

Authors: Peter J Skene; Steven Henikoff
Journal: Elife Date: 2017-01-16 Impact factor: 8.140

7. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

Authors: Alicia N Schep; Beijing Wu; Jason D Buenrostro; William J Greenleaf
Journal: Nat Methods Date: 2017-08-21 Impact factor: 28.547

8. A microfluidic device for epigenomic profiling using 100 cells.

Authors: Zhenning Cao; Changya Chen; Bing He; Kai Tan; Chang Lu
Journal: Nat Methods Date: 2015-07-27 Impact factor: 28.547

9. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples.

Authors: Wenfei Jin; Qingsong Tang; Mimi Wan; Kairong Cui; Yi Zhang; Gang Ren; Bing Ni; Jeffrey Sklar; Teresa M Przytycka; Richard Childs; David Levens; Keji Zhao
Journal: Nature Date: 2015-12-03 Impact factor: 49.962

10. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.

Authors: Assaf Rotem; Oren Ram; Noam Shoresh; Ralph A Sperling; Alon Goren; David A Weitz; Bradley E Bernstein
Journal: Nat Biotechnol Date: 2015-10-12 Impact factor: 54.908

54 in total

Review 1. Towards a comprehensive catalogue of validated and target-linked human enhancers.

Authors: Molly Gasperini; Jacob M Tome; Jay Shendure
Journal: Nat Rev Genet Date: 2020-01-27 Impact factor: 53.242

Review 2. Mapping chromatin modifications at the single cell level.

Authors: Connor H Ludwig; Lacramioara Bintu
Journal: Development Date: 2019-06-27 Impact factor: 6.868

3. Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions.

Authors: Haiqing Xiong; Yingjie Luo; Qianhao Wang; Xianhong Yu; Aibin He
Journal: Nat Methods Date: 2021-05-06 Impact factor: 28.547

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

1. High-resolution profiling of histone methylations in the human genome.

2. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states.

3. Nucleosome Occupancy and Methylome Sequencing (NOMe-seq).

4. Single-cell chromatin accessibility reveals principles of regulatory variation.

5. Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells.

6. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites.

7. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

8. A microfluidic device for epigenomic profiling using 100 cells.

9. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples.

10. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.

Review 1. Towards a comprehensive catalogue of validated and target-linked human enhancers.

Review 2. Mapping chromatin modifications at the single cell level.

3. Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions.

Review 4. The epigenetic basis of cellular heterogeneity.

5. Multiplexed and Ultralow-Input ChIP-seq Enabled by Tagmentation-Based Indexing and Facile Microfluidics.

Review 6. Asymmetric inheritance of epigenetic states in asymmetrically dividing stem cells.

7. Profiling chromatin states using single-cell itChIP-seq.

Review 8. Improved mouse models and advanced genetic and genomic technologies for the study of neutrophils.

Review 9. The evolving metabolic landscape of chromatin biology and epigenetics.

10. Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells.