TBR1 regulates autism risk genes in the developing neocortex
Open accessAbstract
Exome sequencing studies have identified multiple genes harboring de novo loss-of-function (LoF) variants in individuals with autism spectrum disorders (ASD), including TBR1, a master regulator of cortical development. We performed ChIP-seq for TBR1 during mouse cortical neurogenesis and show that TBR1-bound regions are enriched adjacent to ASD genes. ASD genes were also enriched among genes that are differentially expressed in Tbr1 knockouts, which together with the ChIP-seq data, suggests direct transcriptional regulation. Of the nine ASD genes examined, seven were misexpressed in the cortices of Tbr1 knockout mice, including six with increased expression in the deep cortical layers. ASD genes with adjacent cortical TBR1 ChIP-seq peaks also showed unusually low levels of LoF mutations in a reference human population and among Icelanders. We then leveraged TBR1 binding to identify an appealing subset of candidate ASD genes. Our findings highlight a TBR1-regulated network of ASD genes in the developing neocortex that are relatively intolerant to LoF mutations, indicating that these genes may play critical roles in normal cortical development.
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ChIP-Seq of TBR1 in developing neocortex found that it binds next to high-confidence ASD genes more frequently than other brain-expressed transcription factors.
“Chromatin Immunoprecipitation Sequencing (ChIP-Seq) of TBR1 in the developing neocortex found that this protein binds next to high-confidence ASD genes more frequently than other transcription factors that are expressed in the brain (Notwell et al., 2016).”
From Getting to the cores of autism (2019) · cites this paper as Notwell et al., 2016
Transcriptomic analysis of developing brain in transgenic mouse models of SETD5, FOXP1, and TBR1 suggests that mutations in these genes lead to dysregulation of ASD genes in trans.
“Similarly transcriptomic analysis of developing brain in transgenic mouse models of SETD5 (Pizzo et al., 2018), FOXP1 (Araujo et al., 2015), TBR1 (Notwell et al., 2016) suggests that mutations in these genes leads to the dysregulation of ASD genes in trans.”
From Getting to the cores of autism (2019) · cites this paper as Notwell et al., 2016
Few public ChIP-seq profiles exist for neural-specific transcription factors, and most of those have been performed in the developing mouse neocortex.
“However, very few public chromatin immunoprecipitation sequencing (ChIP-seq) profiles exist, and most of those have been performed in the developing mouse neocortex (Bayam et al., 2015, Notwell et al., 2016, Sun et al., 2015).”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Notwell et al., 2016
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- Authors
- Notwell, J. H., Heavner, W. E., Darbandi, S. F., Katzman, S., McKenna, W. L., Ortiz-Londono, C. F., Tastad, D., Eckler, M. J., Rubenstein, J. L. R., McConnell, S. K., Chen, B., & Bejerano, G.
- Affiliations
- Stanford University (US)
- University of California, San Francisco (US)
- University of California, Santa Cruz (US)
- Stanford Medicine (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2016-06-20
- Volume
- 26
- Issue
- 8
- Pages
- 1013-1022
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC4971772
- OpenAlex
- W2462978951
- Cited by
- 74
- References
- 62
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 4 · 2023: 6 · 2022: 10 · 2021: 9 · 2020: 11 · 2019: 10 · 2018: 5 · 2017: 11
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Science Foundation (DGE-1147470)
- Bio-X Stanford
- National Institute of Neurological Disorders and Stroke (R01 NS34661)
- National Institute of Mental Health (R37 MH049428)
- National Institutes of Health (R01 MH51864)
- Stanford Bio-X Interdisciplinary Initiatives Seed
- NIH (R01 MH094589, U01 MH105949)
- Packard
- Microsoft Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- Tbr1, autism spectrum disorder, neocortex development, cortical neurogenesis, transcriptional regulation, deep cortical layers, Icelanders
- MeSH terms
- Autism Spectrum Disorder, Animals, Disease Models, Animal, DNA-Binding Proteins, Gene Expression Regulation, Humans, Mutation, Neurons, Risk Factors, Neocortex, T-Box Domain Proteins, Mice, Neurogenesis, Gene Knockout Techniques, Exome
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