CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

Wang, Qianhao; Xiong, Haiqing; Ai, Shanshan; Yu, Xianhong; Liu, Yaxi; Zhang, Jiejie; He, Aibin

doi:10.1016/j.molcel.2019.07.015

Cited by 162 publications

(111 citation statements)

References 71 publications

(64 reference statements)

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“…However, due to the large differences in H3K27ac signal, we suspect that measured changes in candidate enhancer activity could be due to a combination of both enhancer remodeling and shift in cell type composition. Thus, future studies profiling snATAC-seq and H3K27ac in parallel from the same cardiac sample or novel approaches to profile histone modifications in single nuclei 54,55 will provide greater insight into the extent of changes in chromatin accessibility and enhancer activity in individual cardiac cell types from diseased hearts.…”

Section: Discussionmentioning

confidence: 99%

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

Hocker

Poirion

Zhu

et al. 2020

Preprint

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BackgroundCis-regulatory elements such as enhancers and promoters are crucial for directing gene expression in the human heart. Dysregulation of these elements can result in many cardiovascular diseases that are major leading causes of morbidity and mortality worldwide. In addition, genetic variants associated with cardiovascular disease risk are enriched within cis-regulatory elements. However, the location and activity of these cis-regulatory elements in individual cardiac cell types remains to be fully defined.MethodsWe performed single nucleus ATAC-seq and single nucleus RNA-seq to define a comprehensive catalogue of candidate cis-regulatory elements (cCREs) and gene expression patterns for the distinct cell types comprising each chamber of four non-failing human hearts. We used this catalogue to computationally deconvolute dynamic enhancers in failing hearts and to assign cardiovascular disease risk variants to cCREs in individual cardiac cell types. Finally, we applied reporter assays, genome editing and electrophysiogical measurements in in vitro differentiated human cardiomyocytes to validate the molecular mechanisms of cardiovascular disease risk variants.ResultsWe defined >287,000 candidate cis-regulatory elements (cCREs) in human hearts at single-cell resolution, which notably revealed gene regulatory programs controlling specific cell types in a cardiac region/structure-dependent manner and during heart failure. We further report enrichment of cardiovascular disease risk variants in cCREs of distinct cardiac cell types, including a strong enrichment of atrial fibrillation variants in cardiomyocyte cCREs, and reveal 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Two such risk variants residing within a cardiomyocyte-specific cCRE at the KCNH2/HERG locus resulted in reduced enhancer activity compared to the non-risk allele. Finally, we found that deletion of the cCRE containing these variants decreased KCNH2 expression and prolonged action potential repolarization in an enhancer dosage-dependent manner.ConclusionsThis comprehensive atlas of human cardiac cCREs provides the foundation for not only illuminating cell type-specific gene regulatory programs controlling human hearts during health and disease, but also interpreting genetic risk loci for a wide spectrum of cardiovascular diseases.

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Section: Discussionmentioning

confidence: 99%

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

Hocker

Poirion

Zhu

et al. 2020

Preprint

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“…Lastly, we have collected and generated proteinfusion reporters (GFP or mNeonGreen) for over 260 TFs (86 new endogenous protein fusion reporters in this work), strains expressing which can be directly used in ChIP-seq experiments to identify potential targets. With the single-cell ChIP-seq techniques developed recently(Ai et al, 2019;Wang et al, 2019) and the single-cell expression patterns resolved here, building a cell-resolution molecular circuit of in vivo lineage differentiation is imaginable.…”

mentioning

confidence: 99%

Single-Cell Protein Atlas of Transcription Factors Reveals the Combinatorial Code for Spatiotemporal Patterning theC. elegansEmbryo

Zhao

Xiao

et al. 2020

Preprint

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SUMMARYA high-resolution protein atlas is essential for understanding the molecular basis of biological processes. Using protein-fusion reporters and imaging-based single-cell analyses, we present a protein expression atlas of C. elegans embryogenesis encompassing 266 transcription factors (TFs) in nearly all (90%) lineage-resolved cells. Single-cell analysis reveals a combinatorial code and cascade that elucidate the regulatory hierarchy between a large number of lineage-, tissue-, and time-specific TFs in spatiotemporal fate patterning. Guided by expression, we identify essential functions of CEH-43/DLX, a lineage-specific TF, and ELT-1/GATA3, a well-known skin fate specifier, in neuronal specification; and M03D4.4 as a pan-muscle TF in converging muscle differentiation in the body wall and pharynx. Finally, systems-level analysis of TF regulatory state uncovers lineage- and time-specific kinetics of fate progression and widespread detours of the trajectories of cell differentiation. Collectively, our work reveals a single-cell molecular atlas and general principles underlying the spatiotemporal patterning of a metazoan embryo.

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“…Combinatorial barcoding and targeted chromatin release (CoBatch) can not only profile the epigenetic landscape of samples with relatively low cellular input, but also be applied to the scale of thousands of single cells in the native or fixed state with a high signal-to-noise ratio [38]. This approach applies an enzyme called PAT, which is the fusion of the N-terminal of Tn5 transposase with protein A.…”

Section: Single-cell Chip-seqmentioning

confidence: 99%

“…Using the single-cell data generated from coBatch, researchers successfully achieved highthroughput identification of cell types such as endothelial cells and mesenchymal cells, revealing the heterogeneity of the endothelial cell population in depth. However, the shortcoming of this method is that it cannot be directly applied to samples with input as low as a dozen cells, such as preimplantation embryos [38].…”

Section: Single-cell Chip-seqmentioning

confidence: 99%

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

Zhang

2020

Mol Biomed

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Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.

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CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

Abstract: Highlights d Development of an immunoprecipitation-free single-cell ChIP-seq technology d CoBATCH acquires 12,000 usable reads per cell with extremely low background d CoBATCH reveals multi-layer epigenetic heterogeneity during cell lineage diversification

Cited by 162 publications

References 71 publications

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

Single-Cell Protein Atlas of Transcription Factors Reveals the Combinatorial Code for Spatiotemporal Patterning theC. elegansEmbryo

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

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