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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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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