Single-cell epigenomics reveals mechanisms of human cortical development : (Ziffra_2021)

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Single-cell epigenomics reveals mechanisms of human cortical development

Abstract

• Wanted to better understand cell fate specification and topography

• Used scATAC-seq on primary tissue samples from human forebrain

• Found genomic loci that undergo a lot of cell-type and brain-region-specific changes in chromatin accessibility during neurogenesis

  • Also did an analysis to predict cell-type-speicific candidate regulatory elements

• Compared chromatin accessibility across brain regions

  • Found a lot of diversity amoung neural progenitor cells in the cerebral cortex

  • Retinoic acid singalling causes the specification of neuronal lineage identity in the prefrontal cortex

Intro

• The chromatin states defines the functional architecture of the genome because it allows access to gene regulatory elements(enhancers)

• Cascades of transcription factors remodel and refine the differential patterns of chromatin

• They think identifying cell-type-specific patterns of enhancer activity will lead to a better understanding of cell fate specification

• They point out that few studies have profiled chromatin state during brain development

  • scATAC-seq has recently enabled this. They've been using it in the developing mouse brain

  • They need to extend this to human primary tissue to better understand human-specific neurodevelopmental enhancers

Chromatin states of the developing brain

Identifying cell-type-specific enhancers

Disease risk in the regulatory landscape

Dynamic chromatin states in neurogenesis

Area-specific chromatin states

Retinoic acid in cortical arealization

Benchmarking cerebral organoids

Discussion

Methods

Cell types

• radial glia (RGs)

  • dividing (dRGs)

  • ventricular (vRGs)

  • outer (oRGs)

  • truncated (tRGs)

• intermediate progenitor cells (IPCs)

• deep layer (cortical layers V–VI)

• excitatory neurons (dlENs)

• upper layer (cortical layers II–IV)

• excitatory neurons (ulENs)

• MGE- and CGE-derived cortical interneurons (IN-MGEs and IN-CGEs, respectively)

• insular neurons

• progenitors from the MGE

• microglia

• oligodendrocyte progenitor cells (OPCs)

• endothelial cells

• mural cells

Calculating gene activity scores

• Created a proxy for gene expression

• ATACseq fragments in the gene body plus promoter (2 kb upstream from transcription start sites) of all protein-coding genes were summed for each cell to generate gene activity scores

Fig. 1 Single-cell chromatin state atlas of the developing human brain.

Fig. 2 Dynamic changes in chromatin accessibility during human cortical neurogenesis.

• Why 3n in scATAC-seq and 2n in scRNA-seq?

• Right, UMAP projection of co-embedded scATAC-seq and scRNA-seq cells coloured by Leiden clusters

Fig. 3 Areal differences in chromatin state of progenitor cells foreshadow the emergence of area-specific types of excitatory neurons.

Fig. 4 Cell type-specific differences in chromatin accessibility between cerebral organoids and the developing human brain.

Extended Data Fig. 1 Batch correction and quality control metrics for primary scATAC-seq data.

Extended Data Fig. 2 Batch Correction of primary scATAC-seq samples.

Extended Data Fig. 3 Gene activity scores correlate with cell type-specific expression of marker genes.

Extended Data Fig. 4 Annotation of primary scATAC-seq peaks.

Extended Data Fig. 5 scATAC-seq peaks overlap with previously annotated bulk ATAC-seq peaks and validated forebrain enhancers.

Extended Data Fig. 6 Enrichment and depletion of disease associated variants in scATACseq peaks.

Extended Data Fig. 7 Dynamic patterns of gene expression, chromatin accessibility, and transcription factor motif enrichment across pseudotime.

Extended Data Fig. 8 Chromatin state profiling reveals divergence of PFC and V1 excitatory lineages.

Extended Data Fig. 9 Modelling the PFC–V1 split in the developing cortex.

Extended Data Fig. 10 Comparison of organoid and primary peaks reveal significant differences in chromatin landscapes.