Cited by 493Single-cell and spatial transcriptomicsGenomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

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Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

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Trevino, Alexandro E., Müller, Fabian, Andersen, Jimena, Sundaram, Laksshman, Kathiria, Arwa, Shcherbina, Anna, Farh, Kyle, Chang, Howard Y., Pașca, Anca M., Kundaje, Anshul, Pașca, Sergiu P., Greenleaf, William J.·2021·Cell

DOI 10.1016/j.cell.2021.07.039

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Abstract

Genetic perturbations of cortical development can lead to neurodevelopmental disease, including autism spectrum disorder (ASD). To identify genomic regions crucial to corticogenesis, we mapped the activity of gene-regulatory elements generating a single-cell atlas of gene expression and chromatin accessibility both independently and jointly. This revealed waves of gene regulation by key transcription factors (TFs) across a nearly continuous differentiation trajectory, distinguished the expression programs of glial lineages, and identified lineage-determining TFs that exhibited strong correlation between linked gene-regulatory elements and expression levels. These highly connected genes adopted an active chromatin state in early differentiating cells, consistent with lineage commitment. Base-pair-resolution neural network models identified strong cell-type-specific enrichment of noncoding mutations predicted to be disruptive in a cohort of ASD individuals and identified frequently disrupted TF binding sites. This approach illustrates how cell-type-specific mapping can provide insights into the programs governing human development and disease.

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Additional file 1 of scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics
Li, Q. (2023) · Figshare · doi:10.6084/m9.figshare.23573716
Additional file 7 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617490
Additional file 4 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617478
Additional file 1 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2023) · Figshare · doi:10.6084/m9.figshare.24439339
Additional file 8 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636634
Additional file 10 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632048
Additional file 14 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636652
Additional file 2 of Current genomic deep learning models display decreased performance in cell type-specific accessible regions
Kathail, P., Shuai, R. W., Chung, R., Ye, C. J., Loeb, G. B., & Ioannidis, N. M. (2024) · Figshare · doi:10.6084/m9.figshare.26461884
Additional file 1 of CMOT: Cross-Modality Optimal Transport for multimodal inference
Alatkar, S. A., & Wang, D. (2024) · Figshare · doi:10.6084/m9.figshare.26603554
Additional file 5 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617481
Additional file 3 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632027
Additional file 15 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617514
Additional file 1 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617469
Additional file 5 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636625
Additional file 14 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617511
Additional file 9 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632045
Additional file 4 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632030
Additional file 7 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632039
Additional file 1 of Current genomic deep learning models display decreased performance in cell type-specific accessible regions
Kathail, P., Shuai, R. W., Chung, R., Ye, C. J., Loeb, G. B., & Ioannidis, N. M. (2024) · Figshare · doi:10.6084/m9.figshare.26461775
Additional file 2 of Predicting the impact of sequence motifs on gene regulation using single-cell data
Hepkema, J., Lee, N. K., Stewart, B. J., Ruangroengkulrith, S., Charoensawan, V., Clatworthy, M. R., & Hemberg, M. (2023) · Figshare · doi:10.6084/m9.figshare.23962000
Additional file 10 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636640
Additional file 3 of CMOT: Cross-Modality Optimal Transport for multimodal inference
Alatkar, S. A., & Wang, D. (2024) · Figshare · doi:10.6084/m9.figshare.26603560
Additional file 6 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636628
Additional file 2 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617472
Additional file 2 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Wang, J., Cheng, X., Liang, Q., Owen, L. A., Lu, J., Zheng, Y., Wang, M., Chen, S., DeAngelis, M. M., Li, Y., et al. (2024) · Figshare · doi:10.6084/m9.figshare.24647311
Additional file 11 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636643
Additional file 12 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636646
Additional file 5 of scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics
Li, Q. (2023) · Figshare · doi:10.6084/m9.figshare.23573737
Additional file 4 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636622
Additional file 3 of Current genomic deep learning models display decreased performance in cell type-specific accessible regions
Kathail, P., Shuai, R. W., Chung, R., Ye, C. J., Loeb, G. B., & Ioannidis, N. M. (2024) · Figshare · doi:10.6084/m9.figshare.26756767
Additional file 7 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636631
Additional file 1 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Wang, J., Cheng, X., Liang, Q., Owen, L. A., Lu, J., Zheng, Y., Wang, M., Chen, S., DeAngelis, M. M., Li, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24647213
Additional file 13 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636649
Additional file 16 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617517
Additional file 3 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617475
Additional file 9 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636637
Additional file 3 of Predicting the impact of sequence motifs on gene regulation using single-cell data
Hepkema, J., Lee, N. K., Stewart, B. J., Ruangroengkulrith, S., Charoensawan, V., Clatworthy, M. R., & Hemberg, M. (2023) · Figshare · doi:10.6084/m9.figshare.23962003
Additional file 4 of CMOT: Cross-Modality Optimal Transport for multimodal inference
Alatkar, S. A., & Wang, D. (2024) · Figshare · doi:10.6084/m9.figshare.26603563
Additional file 1 of Predicting the impact of sequence motifs on gene regulation using single-cell data
Hepkema, J., Lee, N. K., Stewart, B. J., Ruangroengkulrith, S., Charoensawan, V., Clatworthy, M. R., & Hemberg, M. (2023) · Figshare · doi:10.6084/m9.figshare.23961997
Additional file 6 of Human cortical spheroids with a high diversity of innately developing brain cell types
Kleijn, K. M. A. D., Zuure, W. A., Straasheijm, K. R., Martens, M. B., Avramut, M. C., Koning, R. I., & Martens, G. J. M. (2023) · Figshare · doi:10.6084/m9.figshare.22617484
Additional file 2 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.24439484
Additional file 6 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632036
Additional file 5 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632033
Additional file 3 of Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation
Wang, J., Cheng, X., Liang, Q., Owen, L. A., Lu, J., Zheng, Y., Wang, M., Chen, S., DeAngelis, M. M., Li, Y., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26645521
Additional file 1 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636613
Additional file 8 of Unveiling adcyap1 as a protective factor linking pain and nerve regeneration through single-cell RNA sequencing of rat dorsal root ganglion neurons
Chen, Q., Zhang, X.-Y., Wang, Y.-P., Fu, Y.-J., Cao, F., Xu, Y.-N., Kong, J.-G., Tian, N.-X., Xu, Y., & Wang, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26632042
Additional file 15 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636655
Additional file 2 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636616
Additional file 2 of CMOT: Cross-Modality Optimal Transport for multimodal inference
Alatkar, S. A., & Wang, D. (2024) · Figshare · doi:10.6084/m9.figshare.26603557
Additional file 3 of Integrative single-cell RNA-seq analysis of vascularized cerebral organoids
Sato, Y., Asahi, T., & Kataoka, K. (2024) · Figshare · doi:10.6084/m9.figshare.26636619
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Authors: Trevino, A. E., Müller, F., Andersen, J., Sundaram, L., Kathiria, A., Shcherbina, A., Farh, K., Chang, H. Y., Pașca, A. M., Kundaje, A., Pașca, S. P., & Greenleaf, W. J.
Affiliations: Stanford University (US)
Saarland University (DE)
Stanford Medicine (US)
Illumina (United States) (US)
Howard Hughes Medical Institute (US)
Chan Zuckerberg Biohub San Francisco (US)
Corresponding author: Pașca, Sergiu P.
Greenleaf, William J.
ORCID: Trevino, Alexandro E.
Müller, Fabian
Andersen, Jimena
Sundaram, Laksshman
Shcherbina, Anna
Farh, Kyle
Chang, Howard Y.
Pașca, Anca M.
Kundaje, Anshul
Pașca, Sergiu P.
Greenleaf, William J.
Venue: Cell
Publisher: Elsevier BV
Published: 2021-09
Volume: 184
Issue: 19
Pages: 5053-5069.e23
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2021.07.039
OpenAlex: W3194509722
Cited by: 478
References: 78
Citations by year: 2026: 76 · 2025: 99 · 2024: 110 · 2023: 99 · 2022: 75 · 2021: 17
FWCI: 24.80
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 380 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Cell (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, other-oa)
PubMed (publishedVersion)
Funders: Leland Stanford Junior University
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
Keywords: cortical development, chromatin accessibility, gene regulatory elements, single-cell atlas, transcription factors, lineage commitment, autism spectrum disorder, non-coding mutations, transcription factor binding sites, neural network model, neurodevelopmental disorders
MeSH terms: Deep Learning, Astrocytes, Cell Differentiation, Cerebral Cortex, Chromatin, Glutamates, Humans, Mutation, Neurons, Regulatory Sequences, Nucleic Acid, Cluster Analysis, Fuzzy Logic, Gene Expression Regulation, Developmental, Cell Lineage, Epigenesis, Genetic, Single-Cell Analysis

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Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

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