Spatially mapped single-cell chromatin accessibility

AbstractHigh-throughput single-cell epigenomic assays can resolve the heterogeneity of cell types and states in complex tissues, however, spatial orientation within the network of interconnected cells is lost. Here, we present a novel method for highly scalable, spatially resolved, single-cell profiling of chromatin states. We use high-density multiregional sampling to perform single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin (sciMAP-ATAC) to produce single-cell data of an equivalent quality to non-spatially resolved single-cell ATAC-seq, where each cell is localized to a three-dimensional position within the tissue. A typical experiment comprises between 96 and 384 spatially mapped tissue positions, each producing 10s to over 100 individual single-cell ATAC-seq profiles, and a typical resolution of 214 cubic microns; with the ability to tune the resolution and cell throughput to suit each target application. We apply sciMAP-ATAC to the adult mouse primary somatosensory cortex, where we profile cortical lamination and demonstrate the ability to analyze data from a single tissue position or compare a single cell type in adjacent positions. We also profile the human primary visual cortex, where we produce spatial trajectories through the cortex. Finally, we characterize the spatially progressive nature of cerebral ischemic infarct in the mouse brain using a model of transient middle cerebral artery occlusion. We leverage the spatial information to identify novel and known transcription factor activities that vary by proximity to the ischemic infarction core with cell type specificity.

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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

Nature Methods ◽

10.1038/s41592-021-01264-7 ◽

2021 ◽

Author(s):

Tommaso Biancalani ◽

Gabriele Scalia ◽

Lorenzo Buffoni ◽

Raghav Avasthi ◽

Ziqing Lu ◽

...

Keyword(s):

Single Cell ◽

Spatial Data ◽

Spatial Information ◽

Chromatin Accessibility ◽

Spatially Resolved ◽

A Genome ◽

Single Nucleus ◽

Histological Images ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractCharting an organs’ biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas.

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

10.1101/2020.06.17.156943 ◽

2020 ◽

Cited By ~ 6

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.

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Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

Nature Biotechnology ◽

10.1038/s41587-021-01065-5 ◽

2021 ◽

Author(s):

Evgenij Fiskin ◽

Caleb A. Lareau ◽

Leif S. Ludwig ◽

Gökcen Eraslan ◽

Feimei Liu ◽

...

Keyword(s):

Single Cell ◽

Chromatin Accessibility ◽

Single Cell Profiling

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Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

10.1101/2019.12.11.873398 ◽

2019 ◽

Cited By ~ 8

Author(s):

Chongyuan Luo ◽

Hanqing Liu ◽

Fangming Xie ◽

Ethan J. Armand ◽

Kimberly Siletti ◽

...

Keyword(s):

Single Cell ◽

Disease Risk ◽

Single Cells ◽

Cortical Cell ◽

Cell Types ◽

Chromatin Accessibility ◽

Integrative Approach ◽

Risk Variants ◽

Human Frontal Cortex ◽

Single Nucleus

ABSTRACTSingle-cell technologies enable measure of unique cellular signatures, but are typically limited to a single modality. Computational approaches allow integration of diverse single-cell datasets, but their efficacy is difficult to validate in the absence of authentic multi-omic measurements. To comprehensively assess the molecular phenotypes of single cells in tissues, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmC2T-seq) and applied it to post-mortem human frontal cortex tissue. We developed a computational framework to validate fine-grained cell types using multi-modal information and assessed the effectiveness of computational integration methods. Correlation analysis in individual cells revealed distinct relations between methylation and gene expression. Our integrative approach enabled joint analyses of the methylome, transcriptome, chromatin accessibility and conformation for 63 human cortical cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling prediction of cell types with causal roles in disease.

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Faculty Opinions recommendation of Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725479886.793507185 ◽

2015 ◽

Author(s):

Andrew D Sharrocks

Keyword(s):

Single Cell ◽

Chromatin Accessibility ◽

Single Cell Profiling

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SNARE-seq2 v2

10.17504/protocols.io.bzcvp2w6 ◽

2021 ◽

Author(s):

Nongluk Plongthongkum ◽

Dinh H Diep ◽

Song Chen ◽

Blue Lake ◽

Kun Zhang

Keyword(s):

Gene Expression ◽

High Throughput ◽

Chromatin Accessibility ◽

Single Experiment ◽

Data Set ◽

Whole Cells ◽

High Throughput Method ◽

Single Nucleus ◽

Accessible Chromatin ◽

Entire Procedure

To study the heterogeneity of complex tissues by joint profiling of gene expression and its regulation, we require an accurate and high-throughput method. Here we described improved high-throughput combinatorial indexing-based single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-Seq2) co-assay. This protocol involves fixing and permeabilizing the nucleus followed by tagmentation, chromatin barcode ligation, reverse transcription, pooling and splitting for the next rounds of cell barcode ligation into cDNA and accessible chromatin (AC) on the same nucleus. The captured cDNA and AC are co-amplified before splitting and enrichment into single-nucleus RNA and single-nucleus AC sequencing libraries. The protocol can also be applied to both nuclei and whole cells to capture mRNA in the cytoplasm. This improvement allows us to generate hundreds of thousands of data set of each assay and can be scaled up to half a million cells from a single experiment. The entire procedure can be complete in 3.5 d for generating joint single-nucleus RNA and single-nucleus ATAC sequencing libraries.

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Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Science ◽

10.1126/science.aab1601 ◽

2015 ◽

Vol 348 (6237) ◽

pp. 910-914 ◽

Cited By ~ 500

Author(s):

D. A. Cusanovich ◽

R. Daza ◽

A. Adey ◽

H. A. Pliner ◽

L. Christiansen ◽

...

Keyword(s):

Single Cell ◽

Chromatin Accessibility ◽

Single Cell Profiling

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Linking transcriptome and chromatin accessibility in nanoliter droplets for single-cell sequencing

10.1101/692608 ◽

2019 ◽

Cited By ~ 1

Author(s):

Song Chen ◽

Blue B Lake ◽

Kun Zhang

Keyword(s):

Mrna Expression ◽

Single Cell ◽

Adult Mouse ◽

Single Cells ◽

Cell Types ◽

Chromatin Accessibility ◽

Single Cell Sequencing ◽

Single Nucleus

Linked profiling of transcriptome and chromatin accessibility from single cells can provide unprecedented insights into cellular status. Here we developed a droplet-based Single-Nucleus chromatin Accessibility and mRNA Expression sequencing (SNARE-seq) assay, that we used to profile neonatal and adult mouse cerebral cortices. To demonstrate the strength of single-cell dual-omics profiling, we reconstructed transcriptome and epigenetic landscapes of cell types, uncovered lineage-specific accessible sites, and connected dynamics of promoter accessibility with transcription during neurogenesis.

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SNARE-seq2 v2

10.17504/protocols.io.bzdrp256 ◽

2021 ◽

Author(s):

Nongluk Plongthongkum ◽

Dinh H Diep ◽

Song Chen ◽

Blue Lake ◽

Kun Zhang

Keyword(s):

Gene Expression ◽

High Throughput ◽

Chromatin Accessibility ◽

Single Experiment ◽

Data Set ◽

Whole Cells ◽

High Throughput Method ◽

Single Nucleus ◽

Accessible Chromatin ◽

Entire Procedure

To study the heterogeneity of complex tissues by joint profiling of gene expression and its regulation, we require an accurate and high-throughput method. Here we described improved high-throughput combinatorial indexing-based single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-Seq2) co-assay. This protocol involves fixing and permeabilizing the nucleus followed by tagmentation, chromatin barcode ligation, reverse transcription, pooling and splitting for the next rounds of cell barcode ligation into cDNA and accessible chromatin (AC) on the same nucleus. The captured cDNA and AC are co-amplified before splitting and enrichment into single-nucleus RNA and single-nucleus AC sequencing libraries. The protocol can also be applied to both nuclei and whole cells to capture mRNA in the cytoplasm. This improvement allows us to generate hundreds of thousands of data set of each assay and can be scaled up to half a million cells from a single experiment. The entire procedure can be complete in 3.5 d for generating joint single-nucleus RNA and single-nucleus ATAC sequencing libraries.

Download Full-text