Table 4 Current methods available for single-cell Histone Modification sequencing
From: Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity
Technique | Technical features | Designed by |
|---|---|---|
scChIP-seq | scChIP-seq is used to study the localization and analysis of protein-chromatin interactions on specific chromatin in a single cell; it features single-cell resolution, chromatin localization, and multi-omics correlation; higher signal-to-noise ratios; technological complexity | [108] |
scCUT&Tag | scCUT&Tag is a single-cell chromatin analysis technique for studying chromatin characteristics and transcription factor-chromatin interactions in individual cells; with single-cell resolution, rapid acquisition of chromatin information, and low amplification bias; experimental complexity; data noise; | [105] |
CoBATCH | CoBATCH is a sequencing technology based on combined barcoding and targeted chromatin release for single-cell analysis of protein-DNA interactions | [106] |
scChIC–seq | scChIC-seq is a method for studying chromatin 3D interactions in individual cells; direct measurement of DNA interactions; combines chromatin immunoprecipitation and chromatin conformation capture techniques to obtain high resolution; technical complexity; data complexity | [107] |
itChIP-seq | itChIP-seq is a technique used to study intracellular chromatin characterization; specific antibodies selectively immunoprecipitate target chromatin modifications; preservation of intracellular chromatin organization and spatial information; error and noise depending on the specificity of the antibody and the abundance of chromatin modifications; technical complexity | [109] |
ACT-seq | ACT-seq is a high-throughput sequencing technology for analyzing chromatin openness and accessibility; features chromatin accessibility analysis, high-resolution and high-throughput sequencing; feasibility is limited by tissue source and cell type; experimental complexity | [110] |
scChIL-seq | scChIL is a method that amplifies genomic sequences closely related to target molecules prior to cell lysis Immunoprecipitation-free epigenomic analysis method | [111] |
uliCUT&RUN | uliCUT&RUN is a technology for the study of chromatin and genome-related features; featuring low-input samples, high resolution, and direct sequencing; applied to chromatin modification analysis, transcription factor binding site identification, and cell type identification and phenotyping | [112] |
sciTIP-seq | sciTIP-seq is a labeling-based, linear amplification and combinatorial indexing method for mapping histone modifications of individual cells to transcription factor CTCF binding sites | [113] |
AutoCUT&Tag | AutoCUT&Tag is a technology for high-throughput, automated chromatin accessibility sequencing; high-throughput, automated, high-resolution; high throughput | [114] |
iscChIC-seq | scChIC-seq is a technique for the analysis of chromatin interactions in individual cells; other information (chromatin modifications, transcript determinations) can be obtained simultaneously; there are limitations in signal-to-noise ratios; technological complexity; applications in gene regulation studies, three-dimensional genome structure, and developmental studies | [115] |