Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families
Open accessAbstract
Reciprocal copy-number variation (CNV) of a 593 kb region of 16p11.2 is a common genetic cause of autism spectrum disorder (ASD), yet it is not completely penetrant and can manifest in a wide array of phenotypes. To explore its molecular consequences, we performed RNA sequencing of cerebral cortex from mouse models with CNV of the syntenic 7qF3 region and lymphoblast lines from 34 members of 7 multiplex ASD-affected families harboring the 16p11.2 CNV. Expression of all genes in the CNV region correlated well with their DNA copy number, with no evidence of dosage compensation. We observed effects on gene expression outside the CNV region, including apparent positional effects in cis and in trans at genomic segments with evidence of physical interaction in Hi-C chromosome conformation data. One of the most significant positional effects was telomeric to the 16p11.2 CNV and includes the previously described "distal" 16p11.2 microdeletion. Overall, 16p11.2 CNV was associated with altered expression of genes and networks that converge on multiple hypotheses of ASD pathogenesis, including synaptic function (e.g., NRXN1, NRXN3), chromatin modification (e.g., CHD8, EHMT1, MECP2), transcriptional regulation (e.g., TCF4, SATB2), and intellectual disability (e.g., FMR1, CEP290). However, there were differences between tissues and species, with the strongest effects being consistently within the CNV region itself. Our analyses suggest that through a combination of indirect regulatory effects and direct effects on nuclear architecture, alteration of 16p11.2 genes disrupts expression networks that involve other genes and pathways known to contribute to ASD, suggesting an overlap in mechanisms of pathogenesis.
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GO analysis indicates that the largest portion of downregulated genes are classified as transcription factors (17.7%), consistent with prior RNA-seq data.
“GO analysis indicates that the largest portion of downregulated genes are classified as “Transcription Factors” (17.7%), consistent with prior RNA-seq data [76].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [76]
RNA-sequencing identifies 2,344 and 1,504 significant differentially expressed genes in the cortex of 16p11.2+/− and 16p11.2dp/+ mice (Mills), respectively, as well as 908 and 1,290 nominally significant DEGs in lymphoblastoid cell lines from human 16p11.2 deletion or duplication carriers, respectively.
“RNA-sequencing identifies 2,344 and 1,504 significant differentially expressed genes (DEGs) in the cortex of 16p11.2+/− and 16p11.2dp/+ mice (Mills), respectively, as well as 908 and 1,290 nominally significant DEGs in lymphoblastoid cell lines (LCLs) from human 16p11.2 deletion or duplication carriers, respectively [76].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [76]
Combined transcriptomic analyses of 16p11.2 CNV mice and human RNAseq datasets found overrepresentation of histone methylation pathways.
“Combined transcriptomic analyses of 16p11.2 CNV mice and human RNAseq datasets have identified overrepresentation of pathways related to histone methylation [76]”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [76]
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Han, J. Y., Cho, Y. G., Jo, D. S., & Park, J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms25010253 · Cited by 5 · see citing works
Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal modelPreprint
Ward, T. R., Zhang, X., Leung, L. C., Zhou, B., Muench, K. L., Roth, J. G., Khechaduri, A., Plastini, M. J., Charlton, C. A., Pattni, R., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.09.940965 · Cited by 4 · see citing works
Ward, T. R., Qu, P.-P., Leung, L. C., Zhou, B., Muench, K. L., Khechaduri, A., Plastini, M. J., Charlton, C. A., Pattni, R., Ho, S. S., et al. (2025) · European Journal of Human Genetics · doi:10.1038/s41431-025-01856-3 · Cited by 5 · see citing works
Nomura, Y., Nomura, J., Kamiguchi, H., Nishikawa, T., & Takumi, T. (2021) · Neuroscience Research · doi:10.1016/j.neures.2021.03.005 · Cited by 4 · see citing works
- Authors
- Blumenthal, I., Ragavendran, A., Erdin, S., Klei, L., Sugathan, A., Guide, J. R., Manavalan, P., Zhou, J. Q., Wheeler, V. C., Levin, J. Z., Ernst, C., Roeder, K., Devlin, B., Gusella, J. F., & Talkowski, M. E.
- Affiliations
- Massachusetts General Hospital (US)
- University of Pittsburgh (US)
- Carnegie Mellon University (US)
- Broad Institute (US)
- Douglas Mental Health University Institute (CA)
- Corresponding author
- Talkowski, Michael E.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2014-06
- Volume
- 94
- Issue
- 6
- Pages
- 870-883
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC4121471
- OpenAlex
- W1975606212
- Cited by
- 145
- References
- 75
- Citations by year
- 2026: 7 · 2025: 5 · 2024: 12 · 2023: 17 · 2022: 9 · 2021: 19 · 2020: 14 · 2019: 10 · 2018: 12 · 2017: 12 · 2016: 10 · 2015: 13 · 2014: 4
- FWCI
- 8.54
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Autism Speaks
- National Institute of Mental Health (MH095867, U24MH081810, R37MH057881, R00MH095867, K99MH095867)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Keywords
- 16p11.2 deletion, 16p11.2 duplication, copy number variation, autism spectrum disorder, dosage compensation, position effect, chromosome conformation, 16p11.2 microdeletion, synaptic function, chromatin modification, transcriptional regulation, intellectual disability, FMR1 gene, NRXN1, NRXN3, CHD8, EHMT1, MeCP2, TCF4, SATB2, CEP290, ASD pathogenesis
- MeSH terms
- Animals, Autistic Disorder, Cerebral Cortex, Child, Chromosome Deletion, Chromosomes, Human, Pair 16, Female, Genotype, Humans, Male, Intellectual Disability, Pedigree, Phenotype, Transcription, Genetic, Sequence Analysis, RNA, Mice, Genome-Wide Association Study, DNA Copy Number Variations, Chromosome Duplication
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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