Somatic retrotransposition alters the genetic landscape of the human brain
Open accessAbstract
Retrotransposons are mobile genetic elements that use a germline 'copy-and-paste' mechanism to spread throughout metazoan genomes. At least 50 per cent of the human genome is derived from retrotransposons, with three active families (L1, Alu and SVA) associated with insertional mutagenesis and disease. Epigenetic and post-transcriptional suppression block retrotransposition in somatic cells, excluding early embryo development and some malignancies. Recent reports of L1 expression and copy number variation in the human brain suggest that L1 mobilization may also occur during later development. However, the corresponding integration sites have not been mapped. Here we apply a high-throughput method to identify numerous L1, Alu and SVA germline mutations, as well as 7,743 putative somatic L1 insertions, in the hippocampus and caudate nucleus of three individuals. Surprisingly, we also found 13,692 somatic Alu insertions and 1,350 SVA insertions. Our results demonstrate that retrotransposons mobilize to protein-coding genes differentially expressed and active in the brain. Thus, somatic genome mosaicism driven by retrotransposition may reshape the genetic circuitry that underpins normal and abnormal neurobiological processes.
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Retrotransposition occurs more frequently in the brain, and in particular in the hippocampus and striatum, relative to other somatic tissues such as blood, heart and liver.
“Several other reports have indicated that retrotransposition occurs more frequently in the brain, and in particular in the hippocampus and striatum, relative to other somatic tissues, such as blood, heart and liver45,46.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [45]
The paper’s Abstract reports somatic retrotransposon insertions in the hippocampus and caudate nucleus, a part of the striatum. It does not compare retrotransposition frequency in those regions with blood, heart, or liver, so the claimed higher frequency relative to those tissues is not supported by this copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredSeveral neurological disorders, including Rhett Syndrome, Smith-Magenis syndrome and schizophrenia, are characterized by dysregulation of L1 activity.
“several neurological disorders, including Rhett Syndrome, Smith–Magenis syndrome and schizophrenia are characterized by dysregulation of L1 activity27,45,47.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [45]
The passage on disease implications (page unavailable in our copy) says MeCP2 deletion increases L1 copy number and may affect neuronal maturation in Rett syndrome. Another passage links RAI1 to Smith–Magenis syndrome and schizophrenia, but describes an Alu insertion in that gene—not dysregulated L1 activity in either disorder. The paper therefore does not support the claim for all three disorders. (LLM, conf=0.88)
Experimental — accuracy not yet measuredDe novo insertions of retrotransposons preferentially affect actively transcribed genes in the brain, including dopamine receptors, amino acid transporters and genes regulating synaptic transmission.
“de novo insertions of retrotransposons appear to preferentially affect actively transcribed genes in the brain, including dopamine receptors, amino acid transporters and genes regulating synaptic transmission45.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [45]
When transposable elements, especially retrotransposons, are activated, they mobilize through an RNA intermediate and can cause somatic mutations or large genomic rearrangements via their insertion into random segments of the genome.
“When TEs, especially retrotransposons, are activated, they mobilize through an RNA intermediate and can cause somatic mutations or large genomic rearrangements via their insertion into random segments of the genome [241, 242]”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [241]
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- Authors
- Baillie, J. K., Barnett, M. W., Upton, K. R., Gerhardt, D. J., Richmond, T. A., De Sapio, F., Brennan, P. M., Rizzu, P., Smith, S., Fell, M., Talbot, R. T., Gustincich, S., Freeman, T. C., Mattick, J. S., Hume, D. A., Heutink, P., Carninci, P., Jeddeloh, J. A., & Faulkner, G. J.
- Affiliations
- Roslin Institute (GB)
- Western General Hospital (GB)
- Amsterdam UMC Location Vrije Universiteit Amsterdam (NL)
- Scuola Internazionale Superiore di Studi Avanzati (IT)
- The University of Queensland (AU)
- RIKEN (JP)
- Corresponding author
- Faulkner, Geoffrey J.
- ORCID
- Venue
- Nature
- Published
- 2011-10-30
- Volume
- 479
- Issue
- 7374
- Pages
- 534-537
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3224101
- OpenAlex
- W2032679533
- Cited by
- 684
- References
- 3
- Citations by year
- 2026: 11 · 2025: 27 · 2024: 25 · 2023: 26 · 2022: 36 · 2021: 38 · 2020: 44 · 2019: 34 · 2018: 49 · 2017: 67 · 2016: 62 · 2015: 61 · 2014: 61 · 2013: 73 · 2012: 66
- FWCI
- 78.30
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- SDL (submittedVersion)
- Pure Amsterdam UMC (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Wellcome Trust (090385, 090385/Z/09/Z)
- Biotechnology and Biological Sciences Research Council (BBS/E/D/05191131, BBS/E/D/05191130, BB/H005935/1)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- somatic retrotransposition, LINE-1 retrotransposons, Alu elements, SVA retrotransposon, somatic mosaicism, human brain, hippocampus, caudate nucleus, germline mutations, somatic insertions, copy number variation, brain development, insertional mutagenesis
- MeSH terms
- Base Sequence, Brain, Caudate Nucleus, Epistasis, Genetic, Hippocampus, Humans, Mosaicism, Nerve Tissue Proteins, Organ Specificity, Transcription Factors, Trans-Activators, Genome, Human, Polymerase Chain Reaction, Mutagenesis, Insertional, Germ-Line Mutation, Retroelements, Alu Elements, Histone Deacetylase 1, DNA Copy Number Variations, Clonal Evolution
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