MobiChIP：基于液滴的单细胞 ChIP-seq 兼容文库构建方法。

IF 3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular omics Pub Date : 2024-11-08 DOI:10.1039/d4mo00111g

Xianhong Yu, Guantao Zheng, Liting Xu, Weiyi Guo, Guodong Chen, Yiling Zhu, Tingting Li, Mingming Rao, Linyan Wang, Rong Cong, Hao Pei

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引用次数: 0

摘要

为了说明表观遗传异质性，单细胞 ChIP-seq （scChIP-seq）的多功能工具在方便性和准确性方面都是必不可少的。我们开发了 MobiChIP，这是一种基于当前单细胞应用测序平台的兼容 ChIP-seq 文库构建方法。MobiChIP 能从不同物种的标记细胞核中有效捕获片段，并允许不同组织或物种的样本混合。这种策略可提供稳健的核小体扩增和灵活的测序，无需定制引物。MobiChIP揭示了外周血单核细胞（PBMCs）中具有活性（H3K27ac）和抑制性（H3K27me3）组蛋白修饰的染色质调控图谱，并准确鉴定了Hox基因簇的表观遗传抑制，优于ATAC-seq。同时，我们还将 scChIP-seq 与 scRNA-seq 结合起来，进一步说明了细胞的遗传和表观遗传异质性。

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MobiChIP: a compatible library construction method of single-cell ChIP-seq based droplets.

To illustrate epigenetic heterogeneity, versatile tools of single-cell ChIP-seq (scChIP-seq) are essential for both convenience and accuracy. We developed MobiChIP, a compatible ChIP-seq library construction method based on current sequencing platforms for single-cell applications. MobiChIP efficiently captures fragments from tagmented nuclei across various species and allows sample mixing from different tissues or species. This strategy offers robust nucleosome amplification and flexible sequencing without customized primers. MobiChIP reveals regulatory landscapes of chromatin with active (H3K27ac) and repressive (H3K27me3) histone modification in peripheral blood mononuclear cells (PBMCs) and accurately identifies epigenetic repression of the Hox gene cluster, outperforming ATAC-seq. Meanwhile, we also integrated scChIP-seq with scRNA-seq to further illustrate cellular genetic and epigenetic heterogeneity.

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来源期刊

Molecular omics Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

5.40

自引率

3.40%

发文量

期刊介绍： Molecular Omics publishes high-quality research from across the -omics sciences. Topics include, but are not limited to: -omics studies to gain mechanistic insight into biological processes – for example, determining the mode of action of a drug or the basis of a particular phenotype, such as drought tolerance -omics studies for clinical applications with validation, such as finding biomarkers for diagnostics or potential new drug targets -omics studies looking at the sub-cellular make-up of cells – for example, the subcellular localisation of certain proteins or post-translational modifications or new imaging techniques -studies presenting new methods and tools to support omics studies, including new spectroscopic/chromatographic techniques, chip-based/array technologies and new classification/data analysis techniques. New methods should be proven and demonstrate an advance in the field. Molecular Omics only accepts articles of high importance and interest that provide significant new insight into important chemical or biological problems. This could be fundamental research that significantly increases understanding or research that demonstrates clear functional benefits. Papers reporting new results that could be routinely predicted, do not show a significant improvement over known research, or are of interest only to the specialist in the area are not suitable for publication in Molecular Omics.