Temporal dynamics and genetic control of transcription in the human prefrontal cortex
Open accessAbstract
Previous investigations have combined transcriptional and genetic analyses in human cell lines, but few have applied these techniques to human neural tissue. To gain a global molecular perspective on the role of the human genome in cortical development, function and ageing, we explore the temporal dynamics and genetic control of transcription in human prefrontal cortex in an extensive series of post-mortem brains from fetal development through ageing. We discover a wave of gene expression changes occurring during fetal development which are reversed in early postnatal life. One half-century later in life, this pattern of reversals is mirrored in ageing and in neurodegeneration. Although we identify thousands of robust associations of individual genetic polymorphisms with gene expression, we also demonstrate that there is no association between the total extent of genetic differences between subjects and the global similarity of their transcriptional profiles. Hence, the human genome produces a consistent molecular architecture in the prefrontal cortex, despite millions of genetic differences across individuals and races. To enable further discovery, this entire data set is freely available (from Gene Expression Omnibus: accession GSE30272; and dbGaP: accession phs000417.v1.p1) and can also be interrogated via a biologist-friendly stand-alone application (http://www.libd.org/braincloud).
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Initial brain-specific functional genomics work provided greater insight but could be enhanced with larger sample sizes.
“Initial work focusing on brain-specific functional genomics has provided greater insight but could be enhanced with larger sample sizes (11, 12).”
From Comprehensive functional genomic resource and integrative model for the human brain (2018) · cites this paper as [12]
Recent studies had analysed transcriptional dynamics during human brain development only in a small number of relatively coarse brain regions.
“Several important recent studies have begun to analyse transcriptional dynamics during human brain development4, 5, although only in a small number of relatively coarse brain regions.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [5]
The high degree of similarity between the two brains is suggestive of a strong underlying common blueprint for the human brain transcriptome and is consistent with other recent studies of human neocortical gene expression.
“this high degree of similarity is suggestive of a strong underlying common blueprint for the human brain transcriptome and is consistent with other recent studies of human neocortical gene expression4, 5”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [5]
Prior studies have examined only a restricted subset of prenatal human brain regions and cortical layers.
“Several recent studies have assayed a limited set of brain structures1,3–5 and layers2 from prenatal human brain.”
From Transcriptional landscape of the prenatal human brain (2014) · cites this paper as [1]
CMC eQTLs captured most eQTLs found in other independent brain samples, with replication π1 values of 0.98 for GTEx v6 and 0.70-0.93 for several microarray datasets.
“Considering microarray-based eQTLs from the Harvard Brain Bank 15, BrainCloud16, NIH17, and the UK Brain Expression Consortium (UKBEC)18, we estimated π1 to be 0.75, 0.70, 0.79, and 0.93, respectively, indicating that our results captured most eQTLs found in other independent samples.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [16]
CommonMind Consortium eQTLs replicate most eQTLs found in other independent samples, with π1 values of 0.98 for GTEx v6, 0.75 for Harvard Brain Bank, 0.70 for BrainCloud, 0.79 for NIH, 0.93 for UKBEC, and 0.77 for HBCC.
“GTEx v6 is the largest public dataset of eQTLs from DLPFC tissue (n = 92) assayed by RNA-seq; its replication in CMC is π1 = 0.98.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [16]
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Common variant at 16p11.2 conferring risk of psychosis
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The dynamic role of genetics on cortical patterning during childhood and adolescence
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Prenatal Expression Patterns of Genes Associated With Neuropsychiatric Disorders
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Self-citationEvolution and development of the mammalian cerebral cortex
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A meta-analysis of gene expression quantitative trait loci in brain
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- Authors
- Colantuoni, C., Lipska, B. K., Ye, T., Hyde, T. M., Tao, R., Leek, J. T., Colantuoni, E. A., Elkahloun, A. G., Herman, M. M., Weinberger, D. R., & Kleinman, J. E.
- Affiliations
- National Institutes of Health (US)
- Johns Hopkins University (US)
- Corresponding author
- Kleinman, Joel E.
- ORCID
- Venue
- Nature
- Published
- 2011-10
- Volume
- 478
- Issue
- 7370
- Pages
- 519-523
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3510670
- OpenAlex
- W2117970703
- Cited by
- 685
- References
- 27
- Citations by year
- 2026: 10 · 2025: 24 · 2024: 16 · 2023: 23 · 2022: 32 · 2021: 39 · 2020: 46 · 2019: 74 · 2018: 56 · 2017: 68 · 2016: 65 · 2015: 53 · 2014: 76 · 2013: 56 · 2012: 42
- FWCI
- 35.44
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of Mental Health
- National Human Genome Research Institute (ZICHG200365)
- National Institute of Child Health and Human Development
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- prefrontal cortex, gene expression, transcriptional dynamics, brain development, brain aging, neurodegeneration, genetic polymorphism, fetal development, postnatal development, transcriptome, postmortem brain, spatiotemporal gene expression
- MeSH terms
- Aging, Autopsy, Fetus, Humans, Time Factors, Genome, Human, Prefrontal Cortex, Gene Expression Regulation, Developmental, Polymorphism, Single Nucleotide, Gene Expression Profiling, Racial Groups, Transcriptome
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