scholarly journals Chromatin-accessibility estimation of single-cell on ATAC data

2019 ◽  
Author(s):  
Zhijian Li ◽  
Christoph Kuppe ◽  
Susanne Ziegler ◽  
Mingbo Cheng ◽  
Nazanin Kabgani ◽  
...  
Keyword(s):  
Single Cell ◽  
Chromatin Accessibility ◽  
Computational Method ◽  
Open Chromatin ◽  
Myofibroblast Differentiation ◽  
Chromatin Conformation ◽  
Major Drawback ◽  
Kidney Fibrosis ◽  
Regulatory Changes

AbstractA major drawback of single cell ATAC (scATAC) are the so-called dropout events, i.e. open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. We propose scOpen, a computational method for quantifying the open chromatin status of regulatory regions from scATAC-seq experiments. We demonstrate that scOpen improves all down-stream analysis steps of scATAC-seq data as clustering, visualisation and chromatin conformation. Moreover, we show the power of scOpen and single cell-based transcription factor footprinting analysis (scHINT) to dissect regulatory changes in the development of fibrosis in the kidney. This identified a novel role of Runx1 promoting fibroblast to myofibroblast differentiation driving kidney fibrosis.

scholarly journals Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhijian Li ◽  
Christoph Kuppe ◽  
Susanne Ziegler ◽  
Mingbo Cheng ◽  
Nazanin Kabgani ◽  
...  
Keyword(s):  
Single Cell ◽  
Target Genes ◽  
Chromatin Accessibility ◽  
Computational Method ◽  
Open Chromatin ◽  
Major Drawback ◽  
Kidney Fibrosis ◽  
Regulatory Changes ◽  
Downstream Analysis ◽  
Regulatory Dna

AbstractA major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we propose scOpen, a computational method based on regularized non-negative matrix factorization for imputing and quantifying the open chromatin status of regulatory regions from sparse scATAC-seq experiments. We show that scOpen improves crucial downstream analysis steps of scATAC-seq data as clustering, visualization, cis-regulatory DNA interactions, and delineation of regulatory features. We demonstrate the power of scOpen to dissect regulatory changes in the development of fibrosis in the kidney. This identifies a role of Runx1 and target genes by promoting fibroblast to myofibroblast differentiation driving kidney fibrosis.

scholarly journals The cis-regulatory dynamics of embryonic development at single cell resolution

2017 ◽  
Author(s):  
Darren A. Cusanovich ◽  
James P. Reddington ◽  
David A. Garfield ◽  
Riza Daza ◽  
Raquel Marco-Ferreres ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Germ Layer ◽  
Regulatory Changes ◽  
Single Cell Profiling ◽  
Transgenic Embryos ◽  
Cell Trajectories

ABSTRACTSingle cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. During mid embryogenesis, tissue granularity emerges such that cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. We identify over 30,000 distal elements with tissue-specific accessibility. Using transgenic embryos, we tested the germ layer specificity of a subset of predicted enhancers, achieving near-perfect accuracy. Overall, these data demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in open chromatin during development, and to uncover the cis-regulatory programs of germ layers and cell types.

scholarly journals The frequency spectrum of chromatin accessibility in Yorubans points toward a significant role of random genetic drift in shaping the chromatin landscape

2016 ◽  
Author(s):  
Mariah Weavil-Abueg ◽  
Joshua G. Schraiber
Keyword(s):  
Human Genome ◽  
Genetic Drift ◽  
Nucleotide Diversity ◽  
Mammalian Species ◽  
Low Frequency ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Evolutionary Mechanisms ◽  
Random Mutation

AbstractThe function of non-coding variation in the human genome is hotly debated. While much of the genome appears to be involved in some kind of molecular activity, a relatively small portion of the genome appears to be conserved across mammalian species. To try to understand part of this seeming paradox, we examined chromatin accessibility as a model molecular phenotype. We modeled chromatin state as either open or closed as looked at the frequency of open chromatin across 70 Yoruban cell lines. We saw that most regions of chromatin accessibility occurred in only a small number of individuals, although there are a number of regions that are accessible across the entire panel. To delve further into understanding the evolutionary mechanisms, we examined nucleotide diversity in and around accessible regions. We found that in the open chromatin access, low frequency regions had decreased nucleotide diversity, however, they were situated within regions of elevated nucleotide diversity. These results point toward a role of random mutation and genetic drift shaping the distribution of accessible regions in the human genome.

scholarly journals Terminal selectors organize postmitotic chromatin accessibility for acquisition of serotonergic identity

2021 ◽  
Author(s):  
Xinrui L Zhang ◽  
William C Spencer ◽  
Nobuko Tabuchi ◽  
Evan S Deneris
Keyword(s):  
Single Cell ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Regulatory Sequences ◽  
Early Maturation ◽  
Accessible Chromatin

Assembly of transcriptomes encoding unique neuronal identities requires selective accessibility of regulatory inputs to cis-regulatory sequences in nucleosome-embedded chromatin. Yet the mechanisms involved in shaping postmitotic neuronal chromatin are poorly understood. Here we used ATAC-seq, ChIPmentation, and single-cell analyses to show that unique distal enhancers and super-enhancers define the Pet1 neuron lineage that generates serotonin (5-HT) neurons. Heterogeneous single cell chromatin landscapes are established early in postmitotic Pet1 neurons and reveal the regulatory programs driving Pet1 neuron subtype identities. Terminal selectors, Pet1 and Lmx1b, control chromatin accessibility in Pet1 neurons to select enhancers for 5-HT neurotransmission and synaptogenesis. In addition, these factors are required to maintain chromatin accessibility during early maturation suggesting that postmitotic open chromatin is unstable and requires continuous terminal selector input. Together our findings reveal a previously unrecognized function of terminal selectors in organizing postmitotic accessible chromatin for the development of specialized neuronal identities.

P16.09 Regulation of chromatin accessibility in the hypoxic tumor microenvironment of glioblastoma

2021 ◽  
Vol 23 (Supplement_2) ◽  
pp. ii57-ii57
Author(s):  
M Dzwigonska ◽  
J Mieczkowski ◽  
P Pilanc ◽  
S Cyranowski ◽  
A Kominek ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Single Cell ◽  
Cancer Cells ◽  
Single Cells ◽  
Therapy Resistance ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Dependent Manner ◽  
Protein Markers ◽  
Hypoxic Tumor

Abstract BACKGROUND Chromatin structure is often dysregulated in cancers, including glioblastoma (GBM), the most aggressive type of primary brain tumor. GBM has the poorest prognosis with no efficient cure to date due to diffusive growth into the brain, resistance to treatments and the immunosuppressive tumor microenvironment (TME). The growth and invasiveness of GBM is supported by the heterogeneous TME including local microglia and bone-marrow-derived macrophages (collectively known as glioma-associated microglia and macrophages, GAMs). In addition, tumor hypoxia is a key factor in the progression of GBM, as it can globally and rapidly alter gene expression, induce cancer cell invasiveness, stemness and lead to therapy resistance. Hypoxia can influence the pro-tumorigenic function of GAMs by inducing the expression of cytokines and cell surface receptors. However, little is known on the hypoxia-imposed chromatin changes of GAMs and GBM cells, which can in turn impact the interaction between these cell populations. Here we analyze these changes using a single-cell method, which preserves in situ hypoxia within the TME of GBM. MATERIAL AND METHODS Single-cell Pi-ATAC-seq (Protein-indexed Assay of Transposase Accessible Chromatin with sequencing) method in a GL261 murine glioma model was used to simultaneously assess genome-wide chromatin accessibility and expression of intracellular protein markers in single cells, enabling accurate selection of hypoxic and non-hypoxic tumor cells and GAMs. Pi-ATAC-seq is used on paraformaldehyde-perfused tumors and therefore allows capturing unaltered hypoxia-dependent cellular states, that often become distorted during dissociation and preparation of fresh material in most common single-cell methods. RESULTS We optimized Pi-ATAC method in a GL261 GBM mouse model, with specific sorting of GAMs using CD11b+ immunosorting followed by separation of microglia and macrophages, based on intensity of CD45 staining. HIF-1α induction and binding of pimonidazole were used to mark hypoxic populations. Currently, we are investigating the chromatin accessibility profiles of cancer cells and GAMs within the hypoxic tumor microenvironment of GBM. Exploring open chromatin profiles in GAMs and glioma-microglia co-cultures will allow to unravel the mechanisms of chromatin accessibility modulation in the oxygen-dependent manner. CONCLUSION In summary, we optimized the Pi-ATAC method in a mouse GBM model to characterize the chromatin openness changes in GAMs and cancer cells in response to hypoxic stress. Further validation of these results will provide the potential to identify novel markers for GAMs/glioma interactions in hypoxic GBMs and develop novel therapeutic targets.

scholarly journals EPCO-32. AN EPIGENETIC SINGLE-CELL ATLAS OF IDH-MUTANT GLIOMA REVEALS THE ROLE OF ATRX IN SHAPING TUMOR COMPOSITION

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii76-ii76
Author(s):  
Husam Babikir ◽  
Lin Wang ◽  
Karin Shamardani ◽  
Sweta Sudhir ◽  
Gary Kohanbash ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Rna Sequencing ◽  
Myeloid Cell ◽  
Cell Types ◽  
Open Chromatin ◽  
Helix Loop Helix ◽  
Local Immunosuppression ◽  
Single Cell Rna Sequencing

Abstract Recent single-cell RNA-sequencing studies have identified a hierarchy of cell types that is common to all isocitrate dehydrogenase (IDH) -mutant gliomas. This finding is somewhat paradoxical since the genetic differences between IDH-mutant astrocytomas and IDH-mutant oligodendrogliomas are prognostic, predictive of therapeutic response, and correlated with differences in immune infiltrates. To integrate these disparate findings, we constructed a single-cell atlas of 28 human IDH-mutant primary untreated grade-II/III gliomas. All specimens were profiled by single-cell assay for transposase-accessible chromatin, with additional cohorts profiled via single-cell RNA-sequencing and single-cell spatial proteomics. We determined the cell-type specific differences between IDH-mutant gliomas in transcription-factor utilization, associated targeting and cis-regulatory grammars. To elucidate the role of the chromatin remodeler ATRX (inactivated in over 86% of IDH-mutant astrocytomas) in shaping observed differences in open chromatin, we knocked out ATRX in an immunocompetent model of IDH-mutant glioma and subjected murine tumors to single-cell profiling. We found: 1. ATRX-deficient, IDH-mutant human and murine gliomas both upregulate an astrocytic regulatory program driven by Nuclear Factor I genes and downregulate an oligodendrocytic program driven by basic helix-loop-helix transcription factors. 2. Both human and mouse ATRX-deficient, IDH-mutant gliomas up-regulate genes that promote myeloid-cell chemotaxis and both have significantly higher percentages of myeloid-derived immune-suppressive cells than controls; 3. A transcription-factor program is conserved between human and murine ATRX-deficient tumors that shapes glial identity and promotes local immunosuppression. These studies elucidate how IDH-mutant gliomas from different subtypes can have distinct cellular morphologies and tumor micronenvironments despite a common lineage hierarchy.

scholarly journals Single-Cell RNA Sequencing and Assay for Transposase-Accessible Chromatin Using Sequencing Reveals Cellular and Molecular Dynamics of Aortic Aging in Mice

2021 ◽  
Author(s):  
Wenhui Xie ◽  
Yilang Ke ◽  
Qinyi You ◽  
Jing Li ◽  
Lu Chen ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Vascular Aging ◽  
Chromatin States ◽  
Single Cell Rna Sequencing ◽  
The Impact ◽  
Accessible Chromatin

Objective: The impact of vascular aging on cardiovascular diseases has been extensively studied; however, little is known regarding the cellular and molecular mechanisms underlying age-related vascular aging in aortic cellular subpopulations. Approach and Results: Transcriptomes and transposase-accessible chromatin profiles from the aortas of 4-, 26-, and 86-week-old C57/BL6J mice were analyzed using single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing. By integrating the heterogeneous transcriptome and chromatin accessibility data, we identified cell-specific TF (transcription factor) regulatory networks and open chromatin states. We also determined that aortic aging affects cell interactions, inflammation, cell type composition, dysregulation of transcriptional control, and chromatin accessibility. Endothelial cells 1 have higher gene set activity related to cellular senescence and aging than do endothelial cells 2. Moreover, construction of senescence trajectories shows that endothelial cell 1 and fibroblast senescence is associated with distinct TF open chromatin states and an mRNA expression model. Conclusions: Our data provide a system-wide model for transcriptional and epigenetic regulation during aortic aging at single-cell resolution.

scholarly journals scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

2017 ◽  
Author(s):  
Stephen J. Clark ◽  
Ricard Argelaguet ◽  
Chantriolnt-Andreas Kapourani ◽  
Thomas M. Stubbs ◽  
Heather J. Lee ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Cell ◽  
Single Cells ◽  
Embryonic Stem ◽  
Transcriptome Profiling ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Dynamic Coupling ◽  
Single Cell Sequencing ◽  
Molecular Layers

AbstractParallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a novel single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.

scholarly journals Combinatorial action of transcription factors in open chromatin contributes to early cellular heterogeneity and organizer mesendoderm specification

2020 ◽  
Author(s):  
Ann Rose Bright ◽  
Siebe van Genesen ◽  
Qingqing Li ◽  
Simon J. van Heeringen ◽  
Alexia Grasso ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Single Cell ◽  
Marginal Zone ◽  
Chromatin Accessibility ◽  
Cellular Heterogeneity ◽  
Open Chromatin ◽  
Cell Clusters ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

ABSTRACTDuring gastrulation, mesoderm is induced in pluripotent cells, concomitant with dorsal-ventral patterning and establishing of the dorsal axis. How transcription factors operate within the constraints of chromatin accessibility to mediate these processes is not well-understood. We applied chromatin accessibility and single cell transcriptome analyses to explore the emergence of heterogeneity and underlying gene-regulatory mechanisms during early gastrulation in Xenopus. ATAC-sequencing of pluripotent animal cap cells revealed a state of open chromatin of transcriptionally inactive lineage-restricted genes, whereas chromatin accessibility in dorsal marginal zone cells more closely reflected the transcriptional activity of genes. We characterized single cell trajectories in animal cap and dorsal marginal zone in early gastrula embryos, and inferred the activity of transcription factors in single cell clusters by integrating chromatin accessibility and single cell RNA-sequencing. We tested the activity of organizer-expressed transcription factors in mesoderm-competent animal cap cells and found combinatorial effects of these factors on organizer gene expression. In particular the combination of Foxb1 and Eomes induced a gene expression profile that mimicked those observed in head and trunk organizer single cell clusters. In addition, genes induced by Eomes, Otx2 or the Irx3-Otx2 combination, were enriched for promoters with maternally regulated H3K4me3 modifications, whereas promoters selectively induced by Lhx8 were marked more frequently by zygotically controlled H3K4me3. Our results show that combinatorial activity of zygotically expressed transcription factors acts on maternally-regulated accessible chromatin to induce organizer gene expression.

scholarly journals Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data

2020 ◽  
Author(s):  
Chunman Zuo ◽  
Luonan Chen
Keyword(s):  
Single Cell ◽  
Learning Strategies ◽  
Gaussian Mixture ◽  
Heterogeneous Data ◽  
Chromatin Accessibility ◽  
Cellular Heterogeneity ◽  
Open Chromatin ◽  
Analysis Model ◽  
Joint Learning ◽  
Transcriptional Regulatory Mechanisms

Abstract Simultaneous profiling transcriptomic and chromatin accessibility information in the same individual cells offers an unprecedented resolution to understand cell states. However, computationally effective methods for the integration of these inherent sparse and heterogeneous data are lacking. Here, we present a single-cell multimodal variational autoencoder model, which combines three types of joint-learning strategies with a probabilistic Gaussian Mixture Model to learn the joint latent features that accurately represent these multilayer profiles. Studies on both simulated datasets and real datasets demonstrate that it has more preferable capability (i) dissecting cellular heterogeneity in the joint-learning space, (ii) denoising and imputing data and (iii) constructing the association between multilayer omics data, which can be used for understanding transcriptional regulatory mechanisms.

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