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 Chromatin potential identified by shared single cell profiling of RNA and chromatin

2020 ◽  
Author(s):  
Sai Ma ◽  
Bing Zhang ◽  
Lindsay LaFave ◽  
Zachary Chiang ◽  
Yan Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Fate ◽  
Mouse Skin ◽  
Chromatin Accessibility ◽  
Lineage Commitment ◽  
Single Cell Profiling ◽  
Lineage Priming ◽  
And Function ◽  
Computational Strategy

SummaryCell differentiation and function are regulated across multiple layers of gene regulation, including the modulation of gene expression by changes in chromatin accessibility. However, differentiation is an asynchronous process precluding a temporal understanding of the regulatory events leading to cell fate commitment. Here, we developed SHARE-seq, a highly scalable approach for measurement of chromatin accessibility and gene expression within the same single cell. Using 34,774 joint profiles from mouse skin, we develop a computational strategy to identify cis-regulatory interactions and define Domains of Regulatory Chromatin (DORCs), which significantly overlap with super-enhancers. We show that during lineage commitment, chromatin accessibility at DORCs precedes gene expression, suggesting changes in chromatin accessibility may prime cells for lineage commitment. We therefore develop a computational strategy (chromatin potential) to quantify chromatin lineage-priming and predict cell fate outcomes. Together, SHARE-seq provides an extensible platform to study regulatory circuitry across diverse cells within tissues.

scholarly journals Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

2019 ◽  
Author(s):  
Ricard Argelaguet ◽  
Hisham Mohammed ◽  
Stephen J Clark ◽  
L Carine Stapel ◽  
Christel Krueger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Cell ◽  
Cell Fate ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
List Type ◽  
Germ Layer ◽  
Epigenetic Landscape ◽  
Germ Layers ◽  
Cell Fate Decisions

AbstractFormation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers.HighlightsFirst map of mouse gastrulation using comprehensive single cell triple-omic analysis.Exit from pluripotency is associated with a global repressive epigenetic landscape, driven by a sharp gain of DNA methylation and a gradual decrease of chromatin accessibility.DNA methylation and chromatin accessibility changes in enhancers, but not in promoters, are associated with germ layer formation.Mesoderm and endoderm enhancers become open and demethylated upon lineage commitment.Ectoderm enhancers are primed in the early epiblast and protected from the global repressive dynamics, supporting a default model of ectoderm commitment in vivo.

scholarly journals Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Anneke Dixie Kakebeen ◽  
Alexander Daniel Chitsazan ◽  
Madison Corinne Williams ◽  
Lauren M Saunders ◽  
Andrea Elizabeth Wills
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Neural Progenitor Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Tail Regeneration ◽  
Cell Fate Decisions ◽  
Transcriptional Regulatory ◽  
Regulatory Dynamics

Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.

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 epigenomic atlas of the developing human brain and organoids

2019 ◽  
Author(s):  
Ryan S. Ziffra ◽  
Chang N. Kim ◽  
Amy Wilfert ◽  
Tychele N. Turner ◽  
Maximilian Haeussler ◽  
...  
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Cell Fate ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Chromatin State ◽  
Cell Type ◽  
Fate Specification ◽  
Cell Type Specific

AbstractDynamic changes in chromatin accessibility coincide with important aspects of neuronal differentiation, such as fate specification and arealization and confer cell type-specific associations to neurodevelopmental disorders. However, studies of the epigenomic landscape of the developing human brain have yet to be performed at single-cell resolution. Here, we profiled chromatin accessibility of >75,000 cells from eight distinct areas of developing human forebrain using single cell ATAC-seq (scATACseq). We identified thousands of loci that undergo extensive cell type-specific changes in accessibility during corticogenesis. Chromatin state profiling also reveals novel distinctions between neural progenitor cells from different cortical areas not seen in transcriptomic profiles and suggests a role for retinoic acid signaling in cortical arealization. Comparison of the cell type-specific chromatin landscape of cerebral organoids to primary developing cortex found that organoids establish broad cell type-specific enhancer accessibility patterns similar to the developing cortex, but lack many putative regulatory elements identified in homologous primary cell types. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

scholarly journals Droplet-based combinatorial indexing for massive scale single-cell epigenomics

2019 ◽  
Author(s):  
Caleb A. Lareau ◽  
Fabiana M. Duarte ◽  
Jennifer G. Chew ◽  
Vinay K. Kartha ◽  
Zach D. Burkett ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Droplet Microfluidics ◽  
Massive Scale ◽  
Single Cell Profiling ◽  
Bone Marrow Derived Cells ◽  
Accessible Chromatin

AbstractWhile recent technical advancements have facilitated the mapping of epigenomes at single-cell resolution, the throughput and quality of these methods have limited the widespread adoption of these technologies. Here, we describe a droplet microfluidics platform for single-cell assay for transposase accessible chromatin (scATAC-seq) for high-throughput single-cell profiling of chromatin accessibility. We use this approach for the unbiased discovery of cell types and regulatory elements within the mouse brain. Further, we extend the throughput of this approach by pairing combinatorial indexing with droplet microfluidics, enabling single-cell studies at a massive scale. With this approach, we measure chromatin accessibility across resting and stimulated human bone marrow derived cells to reveal changes in the cis- and trans- regulatory landscape across cell types and upon stimulation conditions at single-cell resolution. Altogether, we describe a total of 502,207 single-cell profiles, demonstrating the scalability and flexibility of this droplet-based platform.

scholarly journals Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors

2021 ◽  
Author(s):  
Sylvia Hilliard ◽  
Giovane Tortelote ◽  
Hongbing Liu ◽  
Chao-Hui Chen ◽  
Samir S El-Dahr
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Cell Fate ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Bulk Analysis ◽  
Disease States ◽  
Differentiated Cells ◽  
Nephron Progenitors

Background: Cis-regulatory elements (CREs), such as enhancers and promoters, and their cognate transcription factors play a central role in cell fate specification. Bulk analysis of CREs has provided insights into gene regulation in nephron progenitor cells (NPCs). However, the cellular resolution required to unravel the dynamic changes in regulatory elements associated with cell fate choices remains to be defined. Methods: We integrated single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) in embryonic E16.5 (self-renewing) and postnatal P2 (primed) mouse Six2GFP NPCs. This analysis revealed NPC diversity and identified candidate CREs. To validate these findings and gain additional insights into more differentiated cell types, we performed a multiome analysis of E16.5 and P2 kidneys. Results: CRE accessibility recovered the diverse states of NPCs and precursors of differentiated cells. Single-cell types such as podocytes, proximal and distal precursors are marked by differentially accessible CREs. Domains of regulatory chromatin as defined by rich CRE-gene associations identified NPC fate-determining transcription factors (TF). Likewise, key TF expression correlates well with its regulon activity. Young NPCs exhibited enrichment in accessible motifs for bHLH, homeobox, and Forkhead TFs, while older NPCs were enriched in AP-1, HNF1, and HNF4 motif activity. A subset of Forkhead factors exhibiting high chromatin activity in podocyte precursors. Conclusion: Defining the regulatory landscape of nephrogenesis at single-cell resolution informs the basic mechanisms of nephrogenesis and provides a foundation for future studies in disease states characterized by abnormal nephrogenesis.

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 Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rohit Singh ◽  
Brian L. Hie ◽  
Ashwin Narayan ◽  
Bonnie Berger
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Metric Learning ◽  
Disease Status ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Multiple Modalities ◽  
Technological Advances ◽  
Single Cell Profiling ◽  
Or Gene

AbstractA complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease status, or gene expression. Technological advances in single-cell profiling have enabled researchers to assay multiple modalities simultaneously. We present Schema, which uses a principled metric learning strategy that identifies informative features in a modality to synthesize disparate modalities into a single coherent interpretation. We use Schema to infer cell types by integrating gene expression and chromatin accessibility data; demonstrate informative data visualizations that synthesize multiple modalities; perform differential gene expression analysis in the context of spatial variability; and estimate evolutionary pressure on peptide sequences.

scholarly journals Single-cell epigenomics reveals mechanisms of human cortical development

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 205-213
Author(s):  
Ryan S. Ziffra ◽  
Chang N. Kim ◽  
Jayden M. Ross ◽  
Amy Wilfert ◽  
Tychele N. Turner ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Cortical Development ◽  
Chromatin Accessibility ◽  
Chromatin State ◽  
Open Chromatin ◽  
Cell Fate Specification ◽  
Cell Type ◽  
Fate Specification ◽  
Cell Type Specific

AbstractDuring mammalian development, differences in chromatin state coincide with cellular differentiation and reflect changes in the gene regulatory landscape1. In the developing brain, cell fate specification and topographic identity are important for defining cell identity2 and confer selective vulnerabilities to neurodevelopmental disorders3. Here, to identify cell-type-specific chromatin accessibility patterns in the developing human brain, we used a single-cell assay for transposase accessibility by sequencing (scATAC-seq) in primary tissue samples from the human forebrain. We applied unbiased analyses to identify genomic loci that undergo extensive cell-type- and brain-region-specific changes in accessibility during neurogenesis, and an integrative analysis to predict cell-type-specific candidate regulatory elements. We found that cerebral organoids recapitulate most putative cell-type-specific enhancer accessibility patterns but lack many cell-type-specific open chromatin regions that are found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed unexpected diversity among neural progenitor cells in the cerebral cortex and implicated retinoic acid signalling in the specification of neuronal lineage identity in the prefrontal cortex. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

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