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.

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 Comprehensive analysis of single cell ATAC-seq data with SnapATAC

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rongxin Fang ◽  
Sebastian Preissl ◽  
Yang Li ◽  
Xiaomeng Hou ◽  
Jacinta Lucero ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Cellular Heterogeneity ◽  
Specific Gene ◽  
Open Chromatin ◽  
Cell Type ◽  
Process Data ◽  
Cell Type Specific

AbstractIdentification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.

scholarly journals Quantitative Single-Cell Transcript Assessment of Biomarkers Supports Cellular Heterogeneity in the Bovine IVD

2019 ◽  
Vol 6 (2) ◽  
pp. 42 ◽  
Author(s):  
Kangning Li ◽  
Devin Kapper ◽  
Sumona Mondal ◽  
Thomas Lufkin ◽  
Petra Kraus
Keyword(s):  
In Situ Hybridization ◽  
Single Cell ◽  
Gaussian Mixture ◽  
Cellular Heterogeneity ◽  
Rna In Situ Hybridization ◽  
Ivd Degeneration

Severe and chronic low back pain is often associated with intervertebral disc (IVD) degeneration. While imposing a considerable socio-economic burden worldwide, IVD degeneration is also severely impacting on the quality of life of affected individuals. Cell-based regenerative medicine approaches have moved into clinical trials, yet IVD cell identities in the mature disc remain to be fully elucidated and tissue heterogeneity exists, requiring a better characterization of IVD cells. The bovine coccygeal IVD is an accepted research model to study IVD mechano-biology and disc homeostasis. Recently, we identified novel IVD biomarkers in the outer annulus fibrosus (AF) and nucleus pulposus (NP) of the mature bovine coccygeal IVD through RNA in situ hybridization (AP-RISH) and z-proportion test. Here we follow up on Lam1, Thy1, Gli1, Gli3, Noto, Ptprc, Scx, Sox2 and Zscan10 with fluorescent RNA in situ hybridization (FL-RISH) and confocal microscopy. This permits sub-cellular transcript localization and the addition of quantitative single-cell derived values of mRNA expression levels to our previous analysis. Lastly, we used a Gaussian mixture modeling approach for the exploratory analysis of IVD cells. This work complements our earlier cell population proportion-based study, confirms the previously proposed biomarkers and indicates even further heterogeneity of cells in the outer AF and NP of a mature IVD.

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 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 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 SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq

2019 ◽  
Author(s):  
Rongxin Fang ◽  
Sebastian Preissl ◽  
Yang Li ◽  
Xiaomeng Hou ◽  
Jacinta Lucero ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Expression Patterns ◽  
Sampling Technique ◽  
Regulatory Elements ◽  
Cellular Heterogeneity ◽  
Low Rank ◽  
Specific Gene ◽  
Open Chromatin ◽  
Process Data

AbstractIdentification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by heterogeneity of the samples. Single cell analysis of transposase-accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volumes of data could pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC can efficiently dissect cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, a sampling technique that generates the low rank embedding for large-scale dataset, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC was applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis revealed ∼370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate transcriptional regulators in each of the cell types.

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 Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

2017 ◽  
Author(s):  
Bogdan Budnik ◽  
Ezra Levy ◽  
Guillaume Harmange ◽  
Nikolai Slavov
Keyword(s):  
Mass Spectrometry ◽  
Single Cell ◽  
Mammalian Cells ◽  
Human Cancer ◽  
Es Cells ◽  
Single Cells ◽  
Embryonic Stem ◽  
Cellular Heterogeneity ◽  
Protein Levels ◽  
Transcriptional Regulatory Mechanisms

Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and validated its ability to identify distinct human cancer cell types based on their proteomes. We used SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem (ES) cells. The single-cell proteomes enabled us to deconstruct cell populations and infer protein abundance relationships. Comparison between single-cell proteomes and transcriptomes indicated coordinated mRNA and protein covariation. Yet many genes exhibited functionally concerted and distinct regulatory patterns at the mRNA and the protein levels, suggesting that post-transcriptional regulatory mechanisms contribute to proteome remodeling during lineage specification, especially for developmental genes. SCoPE-MS is broadly applicable to measuring proteome configurations of single cells and linking them to functional phenotypes, such as cell type and differentiation potentials.

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