Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing Article Swipe
Wai Lim Ku
,
Lixia Pan
,
Yaqiang Cao
,
Weiwu Gao
,
Keji Zhao
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/gr.260893.120
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/gr.260893.120
Recently, multiple single-cell assays were developed for detecting histone marks at the single-cell level. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these problems, we introduce indexing single-cell immunocleavage sequencing (iscChIC-seq), a multiplex indexing method based on TdT terminal transferase and T4 DNA ligase-mediated barcoding strategy and single-cell ChIC-seq, which is capable of readily analyzing histone modifications across tens of thousands of single cells in one experiment. Application of iscChIC-seq to profiling H3K4me3 and H3K27me3 in human white blood cells (WBCs) enabled successful detection of more than 10,000 single cells for each histone modification with 11 K and 45 K nonredundant reads per cell, respectively. Cluster analysis of these data allowed identification of monocytes, T cells, B cells, and NK cells from WBCs. The cell types annotated from H3K4me3 single-cell data are specifically correlated with the cell types annotated from H3K27me3 single-cell data. Our data indicate that iscChIC-seq is a reliable technique for profiling histone modifications in a large number of single cells, which may find broad applications in studying cellular heterogeneity and differentiation status in complex developmental and disease systems.
Related Topics
Concepts
H3K4me3
Biology
Histone
Single-cell analysis
Computational biology
Chromatin
Cell
Genetics
DNA
Gene
Gene expression
Promoter
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1101/gr.260893.120
- https://genome.cshlp.org/content/31/10/1831.full.pdf
- OA Status
- hybrid
- Cited By
- 27
- References
- 34
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3152804038
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3152804038Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/gr.260893.120Digital Object Identifier
- Title
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Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencingWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2021Year of publication
- Publication date
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2021-04-14Full publication date if available
- Authors
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Wai Lim Ku, Lixia Pan, Yaqiang Cao, Weiwu Gao, Keji ZhaoList of authors in order
- Landing page
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https://doi.org/10.1101/gr.260893.120Publisher landing page
- PDF URL
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https://genome.cshlp.org/content/31/10/1831.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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hybridOpen access status per OpenAlex
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https://genome.cshlp.org/content/31/10/1831.full.pdfDirect OA link when available
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H3K4me3, Biology, Histone, Single-cell analysis, Computational biology, Chromatin, Cell, Genetics, DNA, Gene, Gene expression, PromoterTop concepts (fields/topics) attached by OpenAlex
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27Total citation count in OpenAlex
- Citations by year (recent)
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2025: 3, 2024: 5, 2023: 5, 2022: 8, 2021: 6Per-year citation counts (last 5 years)
- References (count)
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34Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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