Similar Datasets
Project description:Single-cell technologies allow measuring chromatin accessibility and gene expression in each cell, but jointly utilizing both layers to map bona fide gene regulatory networks and enhancers remains challenging. Here, we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering). To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~ 85% of enhancers in which chromatin accessibility and enhancer activity are coupled. Next, we infer enhancer-to-gene relationships in the virtual space, finding that genes are mostly regulated by multiple, often redundant, enhancers. Exploiting cell type-specific enhancers, we deconvolute cell type-specific effects of bulk-derived chromatin accessibility QTLs. Finally, we discover that Prospero drives neuronal differentiation through the binding of a GGG motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue.
| S-EPMC7237818 | biostudies-literature
Project description:Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~85% of enhancers for which chromatin accessibility and enhancer activity patterns agree; while the remaining ~15% are ubiquitously accessible regions bound by the pioneer transcription factor Grainyhead, for which accessibility and activity do not correlate. Next, we infer linear and non-linear enhancer-to-target gene relationships in the virtual space, and find that genes are mostly regulated by multiple -and in some cases, redundant - enhancers. In addition, using cell-type specific enhancers learned from the scATAC-seq data, we deconvolute the cell-type specific effects of chromatin accessibility QTLs from a panel of 50 bulk ATAC-seq profiles from Drosophila inbred lines. Finally, we identify Prospero as a key transcription factor driving neuronal photoreceptor differentiation through the binding of a GGG recognition motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue, which can be explored via SCope (http://scope.aertslab.org/#/Bravo_et_al_EyeAntennalDisc) and the UCSC Genome browser (http://genome.ucsc.edu/s/cbravo/Bravo_et_al_EyeAntennalDisc).
2020-04-08 | GSE141589 | GEO
Project description:Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~85% of enhancers for which chromatin accessibility and enhancer activity patterns agree; while the remaining ~15% are ubiquitously accessible regions bound by the pioneer transcription factor Grainyhead, for which accessibility and activity do not correlate. Next, we infer linear and non-linear enhancer-to-target gene relationships in the virtual space, and find that genes are mostly regulated by multiple -and in some cases, redundant - enhancers. In addition, using cell-type specific enhancers learned from the scATAC-seq data, we deconvolute the cell-type specific effects of chromatin accessibility QTLs from a panel of 50 bulk ATAC-seq profiles from Drosophila inbred lines. Finally, we identify Prospero as a key transcription factor driving neuronal photoreceptor differentiation through the binding of a GGG recognition motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue, which can be explored via SCope (http://scope.aertslab.org/#/Bravo_et_al_EyeAntennalDisc) and the UCSC Genome browser (http://genome.ucsc.edu/s/cbravo/Bravo_et_al_EyeAntennalDisc).
2020-04-08 | GSE141586 | GEO
Project description:Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~85% of enhancers for which chromatin accessibility and enhancer activity patterns agree; while the remaining ~15% are ubiquitously accessible regions bound by the pioneer transcription factor Grainyhead, for which accessibility and activity do not correlate. Next, we infer linear and non-linear enhancer-to-target gene relationships in the virtual space, and find that genes are mostly regulated by multiple -and in some cases, redundant - enhancers. In addition, using cell-type specific enhancers learned from the scATAC-seq data, we deconvolute the cell-type specific effects of chromatin accessibility QTLs from a panel of 50 bulk ATAC-seq profiles from Drosophila inbred lines. Finally, we identify Prospero as a key transcription factor driving neuronal photoreceptor differentiation through the binding of a GGG recognition motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue, which can be explored via SCope (http://scope.aertslab.org/#/Bravo_et_al_EyeAntennalDisc) and the UCSC Genome browser (http://genome.ucsc.edu/s/cbravo/Bravo_et_al_EyeAntennalDisc).
2020-04-08 | GSE141580 | GEO
Project description:Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~85% of enhancers for which chromatin accessibility and enhancer activity patterns agree; while the remaining ~15% are ubiquitously accessible regions bound by the pioneer transcription factor Grainyhead, for which accessibility and activity do not correlate. Next, we infer linear and non-linear enhancer-to-target gene relationships in the virtual space, and find that genes are mostly regulated by multiple -and in some cases, redundant - enhancers. In addition, using cell-type specific enhancers learned from the scATAC-seq data, we deconvolute the cell-type specific effects of chromatin accessibility QTLs from a panel of 50 bulk ATAC-seq profiles from Drosophila inbred lines. Finally, we identify Prospero as a key transcription factor driving neuronal photoreceptor differentiation through the binding of a GGG recognition motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue, which can be explored via SCope (http://scope.aertslab.org/#/Bravo_et_al_EyeAntennalDisc) and the UCSC Genome browser (http://genome.ucsc.edu/s/cbravo/Bravo_et_al_EyeAntennalDisc).
2020-04-08 | GSE141573 | GEO
Project description:Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. To validate spatially predicted enhancers, we use a large collection of enhancer-reporter lines and identify ~85% of enhancers for which chromatin accessibility and enhancer activity patterns agree; while the remaining ~15% are ubiquitously accessible regions bound by the pioneer transcription factor Grainyhead, for which accessibility and activity do not correlate. Next, we infer linear and non-linear enhancer-to-target gene relationships in the virtual space, and find that genes are mostly regulated by multiple -and in some cases, redundant - enhancers. In addition, using cell-type specific enhancers learned from the scATAC-seq data, we deconvolute the cell-type specific effects of chromatin accessibility QTLs from a panel of 50 bulk ATAC-seq profiles from Drosophila inbred lines. Finally, we identify Prospero as a key transcription factor driving neuronal photoreceptor differentiation through the binding of a GGG recognition motif. In summary, we provide a comprehensive spatial characterization of gene regulation in a 2D tissue, which can be explored via SCope (http://scope.aertslab.org/#/Bravo_et_al_EyeAntennalDisc) and the UCSC Genome browser (http://genome.ucsc.edu/s/cbravo/Bravo_et_al_EyeAntennalDisc).
2020-04-08 | GSE141584 | GEO
Project description:Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics
| PRJNA594012 | ENA
Project description:Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [10X_scRNAseq]
| PRJNA594014 | ENA
Project description:Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [ATACseq]
| PRJNA593991 | ENA
Project description:Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [10X_scATACseq]
| PRJNA594015 | ENA