scholarly journals DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Wanwen Zeng ◽  
Xi Chen ◽  
Zhana Duren ◽  
Yong Wang ◽  
Rui Jiang ◽  
...  
Keyword(s):  
Single Cell ◽  
Target Genes ◽  
Single Cells ◽  
Regulatory System ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cellular Level ◽  
Joint Analysis ◽  
Cell Assays ◽  
Cell Expression

Abstract Characterizing and interpreting heterogeneous mixtures at the cellular level is a critical problem in genomics. Single-cell assays offer an opportunity to resolve cellular level heterogeneity, e.g., scRNA-seq enables single-cell expression profiling, and scATAC-seq identifies active regulatory elements. Furthermore, while scHi-C can measure the chromatin contacts (i.e., loops) between active regulatory elements to target genes in single cells, bulk HiChIP can measure such contacts in a higher resolution. In this work, we introduce DC3 (De-Convolution and Coupled-Clustering) as a method for the joint analysis of various bulk and single-cell data such as HiChIP, RNA-seq and ATAC-seq from the same heterogeneous cell population. DC3 can simultaneously identify distinct subpopulations, assign single cells to the subpopulations (i.e., clustering) and de-convolve the bulk data into subpopulation-specific data. The subpopulation-specific profiles of gene expression, chromatin accessibility and enhancer-promoter contact obtained by DC3 provide a comprehensive characterization of the gene regulatory system in each subpopulation.

scholarly journals Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Elliott Swanson ◽  
Cara Lord ◽  
Julian Reading ◽  
Alexander T Heubeck ◽  
Palak C Genge ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Single Cell ◽  
Human Peripheral Blood ◽  
Single Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Test Case ◽  
Cell Assays ◽  
Paired Measurement

Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, cellular responses to signals, and human disease. Recent advances have allowed paired capture of protein abundance and transcriptomic state, but a lack of epigenetic information in these assays has left a missing link to gene regulation. Using the heterogeneous mixture of cells in human peripheral blood as a test case, we developed a novel scATAC-seq workflow that increases signal-to-noise and allows paired measurement of cell surface markers and chromatin accessibility: integrated cellular indexing of chromatin landscape and epitopes, called ICICLE-seq. We extended this approach using a droplet-based multiomics platform to develop a trimodal assay that simultaneously measures transcriptomics (scRNA-seq), epitopes, and chromatin accessibility (scATAC-seq) from thousands of single cells, which we term TEA-seq. Together, these multimodal single-cell assays provide a novel toolkit to identify type-specific gene regulation and expression grounded in phenotypically defined cell types.

scholarly journals TEA-seq: a trimodal assay for integrated single cell measurement of transcription, epitopes, and chromatin accessibility

2020 ◽  
Author(s):  
Elliott Swanson ◽  
Cara Lord ◽  
Julian Reading ◽  
Alexander T. Heubeck ◽  
Adam K. Savage ◽  
...  
Keyword(s):  
Cell Surface ◽  
Single Cell ◽  
Human Peripheral Blood ◽  
Signal To Noise Ratio ◽  
Single Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Test Case ◽  
Cell Assays

AbstractSingle-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, cellular responses to extracellular signals, and human disease states. scATAC-seq has been particularly challenging due to the large size of the human genome and processing artefacts resulting from DNA damage that are an inherent source of background signal. Downstream analysis and integration of scATAC-seq with other single-cell assays is complicated by the lack of clear phenotypic information linking chromatin state and cell type. Using the heterogeneous mixture of cells in human peripheral blood as a test case, we developed a novel scATAC-seq workflow that increases the signal-to-noise ratio and allows simultaneous measurement of cell surface markers: Integrated Cellular Indexing of Chromatin Landscape and Epitopes (ICICLE-seq). We extended this approach using a droplet-based multiomics platform to develop a trimodal assay to simultaneously measure Transcriptomic state (scRNA-seq), cell surface Epitopes, and chromatin Accessibility (scATAC-seq) from thousands of single cells, which we term TEA-seq. Together, these multimodal single-cell assays provide a novel toolkit to identify type-specific gene regulation and expression grounded in phenotypically defined cell types.

scholarly journals NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene expression in single cells

2021 ◽  
Author(s):  
Amy F Chen ◽  
Benjamin Parks ◽  
Arwa Kathiria ◽  
Benjamin Ober-Reynolds ◽  
Jorg Goronzy ◽  
...  
Keyword(s):  
T Cells ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Nuclear Protein ◽  
Single Cells ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
T Cell Subsets ◽  
Protein Abundance ◽  
Joint Measurement

Oligonucleotide-conjugated antibodies have allowed for joint measurement of surface protein abundance and the transcriptome in single cells using high-throughput sequencing. Extending these measurements to gene regulatory proteins in the nucleus would provide a powerful means to link changes in abundance of trans-acting TFs to changes in activity of cis-acting elements and expression of target genes. Here, we introduce Nuclear protein Epitope, chromatin Accessibility, and Transcriptome sequencing (NEAT-seq), a technique to simultaneously measure nuclear protein abundance, chromatin accessibility, and the transcriptome in single cells. We apply this technique to profile CD4 memory T cells using a panel of master transcription factors (TFs) that drive distinct helper T cell subsets and regulatory T cells (Tregs) and identify examples of TFs with regulatory activity gated by three distinct mechanisms: transcription, translation, and regulation of chromatin binding. Furthermore, we identify regulatory elements and target genes associated with each TF, which we use to link a non-coding GWAS SNP within a GATA motif to both strong allele-specific chromatin accessibility in cells expressing high levels of GATA3 protein, and a putative target gene.

scholarly journals Single-cell regulatory landscape and disease vulnerability map of adult Macaque cortex

2020 ◽  
Author(s):  
Ying Lei ◽  
Mengnan Cheng ◽  
Zihao Li ◽  
Zhenkun Zhuang ◽  
Liang Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Neurological Diseases ◽  
Single Cells ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Nucleotide Polymorphisms ◽  
Cell Type

Non-human primates (NHP) provide a unique opportunity to study human neurological diseases, yet detailed characterization of the cell types and transcriptional regulatory features in the NHP brain is lacking. We applied a combinatorial indexing assay, sci-ATAC-seq, as well as single-nuclei RNA-seq, to profile chromatin accessibility in 43,793 single cells and transcriptomics in 11,477 cells, respectively, from prefrontal cortex, primary motor cortex and the primary visual cortex of adult cynomolgus monkey Macaca fascularis. Integrative analysis of these two datasets, resolved regulatory elements and transcription factors that specify cell type distinctions, and discovered area-specific diversity in chromatin accessibility and gene expression within excitatory neurons. We also constructed the dynamic landscape of chromatin accessibility and gene expression of oligodendrocyte maturation to characterize adult remyelination. Furthermore, we identified cell type-specific enrichment of differentially spliced gene isoforms and disease-associated single nucleotide polymorphisms. Our datasets permit integrative exploration of complex regulatory dynamics in macaque brain tissue at single-cell resolution.

scholarly journals A combinatorial indexing strategy for epigenomic profiling of plant single cells

2021 ◽  
Author(s):  
Xiaoyu Tu ◽  
Alexandre P Marand ◽  
Robert J. Schmitz ◽  
Silin Zhong
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Arabidopsis Root ◽  
Indexing Method ◽  
Specialized Equipment ◽  
Cell Type Specific ◽  
Accessible Chromatin ◽  
Insight Into

Understanding how cis-regulatory elements facilitate gene expression is a key question in biology. Recent advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs. However, the high equipment and reagent costs of commercial systems limit their applications for many laboratories. In this study, we profiled the Arabidopsis root single-cell epigenome using a combinatorial index and dual PCR barcode strategy without the need of any specialized equipment. We generated chromatin accessibility profiles for 13,576 Arabidopsis thaliana root nuclei with an average of 12,784 unique Tn5 integrations per cell and 85% of the Tn5 insertions localizing to discrete accessible chromatin regions. Comparison with data generated from a commercial microfluidic platform revealed that our method is capable of unbiased identification of cell type-specific chromatin accessibility with improved throughput, quality, and efficiency. We anticipate that by removing cost, instrument, and other technical obstacles, this combinatorial indexing method will be a valuable tool for routine investigation of single-cell epigenomes and usher new insight into plant growth, development and their interactions with the environment.

scholarly journals Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

2018 ◽  
Author(s):  
Longqi Liu ◽  
Chuanyu Liu ◽  
Andrés Quintero ◽  
Liang Wu ◽  
Yue Yuan ◽  
...  
Keyword(s):  
Single Cell ◽  
Target Genes ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cell Populations ◽  
Single Cell Level ◽  
Complex Cell ◽  
Cell Level ◽  
Distinct Cell ◽  
Cell Variation

AbstractIntegrative analysis of multi-omics layers at single cell level is critical for accurate dissection of cell-to-cell variation within certain cell populations. Here we report scCAT-seq, a technique for simultaneously assaying chromatin accessibility and the transcriptome within the same single cell. We show that the combined single cell signatures enable accurate construction of regulatory relationships between cis-regulatory elements and the target genes at single-cell resolution, providing a new dimension of features that helps direct discovery of regulatory patterns specific to distinct cell identities. Moreover, we generated the first single cell integrated maps of chromatin accessibility and transcriptome in human pre-implantation embryos and demonstrated the robustness of scCAT-seq in the precise dissection of master transcription factors in cells of distinct states during embryo development. The ability to obtain these two layers of omics data will help provide more accurate definitions of “single cell state” and enable the deconvolution of regulatory heterogeneity from complex cell populations.

scholarly journals Epigenetic Landscapes of Single-Cell Chromatin Accessibility and Transcriptomic Immune Profiles of T Cells in COVID-19 Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Shun Li ◽  
Bin Wu ◽  
Yun Ling ◽  
Mingquan Guo ◽  
Boyin Qin ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Signaling Pathway ◽  
Single Cells ◽  
Critical Role ◽  
Regulatory Elements ◽  
Mapk Signaling ◽  
Chromatin Accessibility ◽  
Integrated Analysis ◽  
Activation Markers

T cells play a critical role in coronavirus diseases. How they do so in COVID-19 may be revealed by analyzing the epigenetic chromatin accessibility of cis- and trans-regulatory elements and creating transcriptomic immune profiles. We performed single-cell assay for transposase-accessible chromatin (scATAC) and single-cell RNA (scRNA) sequencing (seq) on the peripheral blood mononuclear cells (PBMCs) of severely ill/critical patients (SCPs) infected with COVID-19, moderate patients (MPs), and healthy volunteer controls (HCs). About 76,570 and 107,862 single cells were used, respectively, for analyzing the characteristics of chromatin accessibility and transcriptomic immune profiles by the application of scATAC-seq (nine cases) and scRNA-seq (15 cases). The scATAC-seq detected 28,535 different peaks in the three groups; among these peaks, 41.6 and 10.7% were located in the promoter and enhancer regions, respectively. Compared to HCs, among the peak-located genes in the total T cells and its subsets, CD4+ T and CD8+ T cells, from SCPs and MPs were enriched with inflammatory pathways, such as mitogen-activated protein kinase (MAPK) signaling pathway and tumor necrosis factor (TNF) signaling pathway. The motifs of TBX21 were less accessible in the CD4+ T cells of SCPs compared with those in MPs. Furthermore, the scRNA-seq showed that the proportion of T cells, especially the CD4+ T cells, was decreased in SCPs and MPs compared with those in HCs. Transcriptomic results revealed that histone-related genes, and inflammatory genes, such as NFKBIA, S100A9, and PIK3R1, were highly expressed in the total T cells, CD4+ T and CD8+ T cells, both in the cases of SCPs and MPs. In the CD4+ T cells, decreased T helper-1 (Th1) cells were observed in SCPs and MPs. In the CD8+T cells, activation markers, such as CD69 and HLA class II genes (HLA-DRA, HLA-DRB1, and HLA-DRB5), were significantly upregulated in SCPs. An integrated analysis of the data from scATAC-seq and scRNA-seq showed some consistency between the approaches. Cumulatively, we have generated a landscape of chromatin epigenetic status and transcriptomic immune profiles of T cells in patients with COVID-19. This has provided a deeper dissection of the characteristics of the T cells involved at a higher resolution than from previously obtained data merely by the scRNA-seq analysis. Our data led us to suggest that the T-cell inflammatory states accompanied with defective functions in the CD4+ T cells of SCPs may be the key factors for determining the pathogenesis of and recovery from COVID-19.

scholarly journals Profiling of transcribed cis-regulatory elements in single cells

2021 ◽  
Author(s):  
Jonathan Moody ◽  
Tsukasa Kouno ◽  
Akari Suzuki ◽  
Youtaro Shibayama ◽  
Chikashi Terao ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cell Analysis ◽  
Cell Type ◽  
Simultaneous Quantification ◽  
Promoter Usage

Profiling of cis-regulatory elements (CREs, mostly promoters and enhancers) in single cells allows the interrogation of the cell-type and -state specific contexts of gene regulation and genetic predisposition to diseases. Here we demonstrate single-cell RNA-5′end-sequencing (sc-end5-seq) methods can detect transcribed CREs (tCREs), enabling simultaneous quantification of gene expression and enhancer activities in a single assay with no extra cost. We show enhancer RNAs can be effectively detected using sc-end5-seq methods with either random or oligo(dT) priming. To analyze tCREs in single cells, we developed SCAFE (Single Cell Analysis of Five-prime Ends) to identify genuine tCREs and analyze their activities (https://github.com/chung-lab/scafe). As compared to accessible CRE (aCRE, based on chromatin accessibility), tCREs are more accurate in predicting CRE interactions by co-activity, more sensitive in detecting shifts in alternative promoter usage and more enriched in diseases heritability. Our results highlight additional dimensions within sc-end5-seq data which can be used for interrogating gene regulation and disease heritability.

scholarly journals Decoding gene regulation in the fly brain

2021 ◽  
Author(s):  
Jasper Janssens ◽  
Sara Aibar ◽  
Ibrahim Ihsan Taskiran ◽  
Joy N. Ismail ◽  
Katina I. Spanier ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Motif Discovery ◽  
Target Genes ◽  
Single Cells ◽  
Neuronal Cell ◽  
Cell Types ◽  
Regulatory Elements ◽  
Specific Cell ◽  
Drosophila Brain

The Drosophila brain is a work horse in neuroscience. Single-cell transcriptome analysis, 3D morphological classification, and detailed EM mapping of the connectome have revealed an immense diversity of neuronal and glial cell types that underlie the wide array of functional and behavioral traits in the fruit fly. The identities of these cell types are controlled by still unknown gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. To characterize the GRN for each cell type in the Drosophila brain, we profiled chromatin accessibility of 240,919 single cells spanning nine developmental timepoints, and integrated this data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which around 70,000 are linked to specific developmental trajectories, involving neurogenesis, reprogramming and maturation. For 40 cell types, their uniquely accessible regions could be associated with their expressed transcription factors and downstream target genes, through a combination of motif discovery, network inference techniques, and deep learning. We illustrate how these enhancer-GRNs can be used to reveal enhancer architectures leading to a better understanding of neuronal regulatory diversity. Finally, our atlas of regulatory elements can be used to design genetic driver lines for specific cell types at specific timepoints, facilitating the characterization of brain cell types and the manipulation of brain function.

scholarly journals Chromatin accessibility dynamics of myogenesis at single cell resolution

2017 ◽  
Author(s):  
Hannah A. Pliner ◽  
Jonathan Packer ◽  
José L. McFaline-Figueroa ◽  
Darren A. Cusanovich ◽  
Riza Daza ◽  
...  
Keyword(s):  
Single Cell ◽  
Chromatin Remodeling ◽  
Target Genes ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
New Approach ◽  
Genome Wide ◽  
A Genome ◽  
Histone Modifying Enzymes ◽  
Dna Regulatory Elements

AbstractOver a million DNA regulatory elements have been cataloged in the human genome, but linking these elements to the genes that they regulate remains challenging. We introduce Cicero, a statistical method that connects regulatory elements to target genes using single cell chromatin accessibility data. We apply Cicero to investigate how thousands of dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of co-accessible regulatory elements linked by Cicero meet criteria of “chromatin hubs”, in that they are physically proximal, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of gene expression. Pseudotemporal analysis revealed a subset of elements bound by MYOD in myoblasts that exhibit early opening, potentially serving as the initial sites of recruitment of chromatin remodeling and histone-modifying enzymes. The methodological framework described here constitutes a powerful new approach for elucidating the architecture, grammar and mechanisms of cis-regulation on a genome-wide basis.

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