The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

Torre-Ubieta, Luis de la; Stein, Jason L.; Won, Hyejung; Opland, Carli K.; Liang, Dan; Lu, Daning; Geschwind, Daniel H.

doi:10.1016/j.cell.2017.12.014

Cited by 306 publications

(366 citation statements)

References 89 publications

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“…We then used chromVAR to analyze the putative progression of transcription factor activities, as measured by the accessibility of the associated DNA motif genome-wide 31 . We found that multiple waves of transcription factor motif opening occur during organoid differentiation, including known patterns that have been observed in single-cell transcriptomic studies of murine corticogenesis, and bulk ATAC-seq in fetal human samples 32,33 . The earliest waves can be explained by a Points are unique reads aligned to the genome.…”

Section: Mainmentioning

confidence: 62%

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Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

Mulqueen

DeRosa

Thornton

et al. 2019

Preprint

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Development is a complex process that requires the precise modulation of regulatory gene networks controlled through dynamic changes in the epigenome. Single-cell -omic technologies provide an avenue for understanding the mechanisms of these processes by capturing the progression of epigenetic cell states during the course of cellular differentiation using in vitro or in vivo models 1 . However, current single-cell epigenomic methods are limited in the information garnered per individual cell, which in turn limits their ability to measure chromatin dynamics and state shifts. Single-cell combinatorial indexing (sci-) has been applied as a strategy for identifying single-cell -omic originating libraries and removes the necessity of single-cell, single-compartment chemistry 2 . Here, we report an improved sci-assay for transposase accessible chromatin by sequencing (ATAC-seq), which utilizes the small molecule inhibitor Pitstop 2™ (scip-ATAC-seq) 3 . We demonstrate that these improvements, which theoretically could be applied to any in situ transposition method for single-cell library preparation, significantly increase the ability of transposase to enter the nucleus and generate highly complex singlecell libraries, without altering biological signal. We applied sci-ATAC-seq and scip-ATAC-seq to characterize the chromatin dynamics of developing forebrain-like organoids, an in vitro model of human corticogenesis 4 . Using these data, we characterized novel putative regulatory elements, compared the epigenome of the organoid model to human cortex data, generated a high-resolution pseudotemporal map of chromatin accessibility through differentiation, and measured epigenomic changes coinciding with a neurogenic fate decision point. Finally, we combined transcription factor motif accessibility with gene activity (GA) scores to directly observe the dynamics of complex regulatory programs that regulate neurogenesis through developmental pseudotime. Overall, scip-ATAC-seq increases information content per cell and bolsters the potential for future single-cell studies into complex developmental processes. F.J.S. and R.R. are employees of Illumina Inc. Data and software availabilityA wrapper for the entire analysis (scitools) as well as custom scripts used will be made available on github.com/adeylab/organoid. All sequence read data for CIRM lines will be made available on dbGAP, with processed data available on GEO. Extended Data Fig 1. | Fluorescent microscopy analysis of transposome complex. a, Representative fluorescent images of DAPI stained fixed nuclei with Cy3 complexed transposomes without Pitstop 2 treatment. Scale bar is 10 μm. b, Representative fluorescent images of DAPI stained fixed nuclei with Cy3 complexed transposomes and treated with 70 μM Pitstop 2. Scale bar is 10 μm. c, 3D reconstruction of DAPI and ATAC-see signal showing blend projection function of Imaris Software. Nuclear blebbing as well as bursting of a 150 μM Pitstop 2 treated nuclei and diffusion of DAPI+ DNA into the environment is visualized in ...

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Section: Mainmentioning

confidence: 62%

“…3b). Transient increases in transcription factors associated with radial-glial proliferation, e.g., POU3F3 (aka BRN1), EOMES and NFIX, precede the waves of transcription factors such as MEF2C, NEUROD6, NEUROG2, and BACH2, which are linked to neuronal migration and maturation 32,33 .…”

Section: Mainmentioning

confidence: 99%

Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

Mulqueen

DeRosa

Thornton

et al. 2019

Preprint

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“…Extending previous work identifying EGFR expressing cells as astro-glial precursors of the late SVZ in rodents (Burrows et al, 1997;Lillien and Raphael, 2000;Sun et al, 2005) and monkey (Rash BG et al, PNAS 2019, in press) From the first generation of neurons from pluripotent sources in vitro (Kim et al, 2002;Okabe et al, 1996) to the many recent studies of the transcriptomic and epigenetic landscapes of the developing cerebral cortex (de la Torre-Ubieta et al, 2018;Nowakowski et al, 2017;Zhu et al, 2018), it is becoming clear that NSC differentiation requires precise temporal and spatial regulation of cellular identities. Here, after demonstrating the most efficient generation of excitatory neurons occurred at a specific early passage, we explored the origins of this neurogenic state focusing on the regional patterning mechanisms, known in vivo to intrinsically coordinate the overall cortical structure prior to the inputs induced by the thalamic afferents (Armentano et al, 2007;Bishop et al, 2000;Cholfin and Rubenstein, 2007;Miyashita-Lin et al, 1999;Nakagawa et al, 1999;Shimogori and Grove, 2005).…”

Section: Discussionmentioning

confidence: 82%

Variation of human neural stem cells generating organizer statesin vitrobefore committing to cortical excitatory or inhibitory neuronal fates

Micali

Kim

Diaz-Bustamante

et al. 2019

Preprint

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SUMMARYBetter understanding the progression of neural stem cells (NSCs) in the developing cerebral cortex is important for modeling neurogenesis and defining the pathogenesis of neuropsychiatric disorders. Here we used RNA-sequencing, cell imaging and lineage tracing of mouse and human in vitro NSCs to model the generation of cortical neuronal fates. We show that conserved signaling mechanisms regulate the acute transition from proliferative NSCs to committed glutamatergic excitatory neurons. As human telencephalic NSCs developed from pluripotency in vitro, they first transitioned through organizer states that spatially pattern the cortex before generating glutamatergic precursor fates. NSCs derived from multiple human pluripotent lines varied in these early patterning states leading differentially to dorsal or ventral telencephalic fates. This work furthers systematic analysis of the earliest patterning events that generate the major neuronal trajectories of the human telencephalon.

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“…2D-E). We further annotated SNPs using ChromHMMbased genomic features in brain such as promoters and enhancers (7). We found a higher percentage of cell-type-specific ASoC SNPs (30% vs. 16% of the shared SNPs) in enhancers (Fig.…”

Section: Main Textmentioning

confidence: 96%

“…For neuropsychiatric disorders, despite recent progress on transcriptomic and epigenomic studies of human postmortem brains (e.g., PsychENCODE) (1-4), most disease causal variants/genes remain unknown. Because open/accessible chromatin often overlaps with regulatory DNA sequence (5,6), co-localization of disease risk variants within open chromatin regions (OCRs) of human postmortem brains or iPSC-derived neurons can help prioritize putative functional noncoding risk variants for neuropsychiatric disorders (7)(8)(9)(10). However, not all the variants within OCRs are functional, and as a result, the enrichment of GWAS signals in OCRs is often modest (8).…”

Section: Main Textmentioning

confidence: 99%

Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants

Zhang

Qiao

et al. 2019

Preprint

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Functional interpretation of noncoding disease variants, which likely regulate gene expression, has been challenging. Chromatin accessibility strongly influences gene expression during neurodevelopment; however, to what extent genetic variants can alter chromatin accessibility in the context of brain disorders/traits is unknown. Using human induced pluripotent stem cell (iPSC)-derived neurons as a neurodevelopmental model, we identified abundant open-chromatin regions absent in adult brain samples and thousands of genetic variants exhibiting allele-specific open-chromatin (ASoC). ASoC variants are overrepresented in brain enhancers, transcription-factor-binding sites, and quantitative-trait-loci associated with gene expression, histone modification, and DNA methylation. Notably, compared to open chromatin regions and other commonly used functional annotations, neuronal ASoC variants showed much stronger enrichments of risk variants for various brain disorders/traits. Our study provides the first snapshot of the neuronal ASoC landscape and a powerful framework for prioritizing functional disease variants.One Sentence SummaryAllele-specific open chromatin informs functional disease variants

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The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

Cited by 306 publications

References 89 publications

Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

Variation of human neural stem cells generating organizer statesin vitrobefore committing to cortical excitatory or inhibitory neuronal fates

Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants

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