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Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain
Open accessAbstract
A major unanswered question in neuroscience is whether there exists genomic variability between individual neurons of the brain, contributing to functional diversity or to an unexplained burden of neurological disease. To address this question, we developed a method to amplify genomes of single neurons from human brains. Because recent reports suggest frequent LINE-1 (L1) retrotransposition in human brains, we performed genome-wide L1 insertion profiling of 300 single neurons from cerebral cortex and caudate nucleus of three normal individuals, recovering >80% of germline insertions from single neurons. While we find somatic L1 insertions, we estimate <0.6 unique somatic insertions per neuron, and most neurons lack detectable somatic insertions, suggesting that L1 is not a major generator of neuronal diversity in cortex and caudate. We then genotyped single cortical cells to characterize the mosaicism of a somatic AKT3 mutation identified in a child with hemimegalencephaly. Single-neuron sequencing allows systematic assessment of genomic diversity in the human brain.
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“Retrotransposition during development or adulthood would lead to somatic mosaicism, and has been estimated to occur in adult neurons by qPCR or single-cell genomic studies at varying (but generally low) frequencies (events/cell): < 0.04–0.680, 13.781, 0.58–182, 0.283 and 0.63–1.6684.”
From The role of retrotransposable elements in ageing and age-associated diseases (2021) · cites this paper as [80]
In the citing paper
“Reanalysis of their data while filtering these artifacts generates a consensus that retrotransposition does occur in developing brain but at a much lower rate consistent with prior single-cell studies (Evrony et al., 2012; Evrony et al., 2015), thereby constraining the range of possible functional roles for retrotransposition in the brain.”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Evrony et al., 2012
In the citing paper
“These RC-seq somatic insertion rates are quite consistent with rates previously estimated by L1 insertion profiling (L1-IP) in single cortical and caudate neurons (0.07 ± 0.15 (SD); p = 0.54, ANOVA) (Evrony et al., 2012), and using single-neuron whole-genome sequencing (0.18 ± 0.47 (SD); p = 0.37, ANOVA) (Evrony et al., 2015), suggesting a notable consensus by three methods confirming that somatic”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Evrony et al., 2012
In the citing paper
“The 2 remaining cells in which L1 #1 was detected (neurons 2 and 77) (Evrony et al., 2015) were excluded from the rate estimate, because they were a priori chosen for whole-genome sequencing as positive controls known to harbor somatic L1 insertions previously detected by the L1-IP method in Evrony et al. (2012).”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Evrony et al. (2012)
In the citing paper
“Surprisingly, levels of mosaicism as low as 8% are sufficient to disrupt the normal architecture and function of the neocortex in HMG (Evrony et al., 2012; Lee et al., 2012; Poduri et al., 2012; Riviere et al., 2012).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
In the citing paper
“In the human brain, single-cell sequencing has been successfully used to detect somatic mosaicism in HMG and to evaluate the rate of somatic long interspersed nuclear element-1 (LINE1) retrotransposition (Evrony et al., 2012).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
In the citing paper
“Fewer than one unique insertion was detected per neuron, suggesting that LINE1 retrotransposition is not a major generator of neuronal diversity in the brain.”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
In the citing paper
“In the human brain, single-cell sequencing has been successfully used to detect somatic mosaicism in HMG and to evaluate the rate of somatic long interspersed nuclear element-1 (LINE1) retrotransposition (Evrony et al., 2012).”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
In the citing paper
“Fewer than one unique insertion was detected per neuron, suggesting that LINE1 retrotransposition is not a major generator of neuronal diversity in the brain.”
From Genetic Changes Shaping the Human Brain (2015) · cites this paper as Evrony et al., 2012
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Metadata
- Authors
- Evrony, G. D., Cai, X., Lee, E., Hills, L. B., Elhosary, P. C., Lehmann, H. S., Parker, J. J., Atabay, K. D., Gilmore, E. C., Poduri, A., Park, P. J., & Walsh, C. A.
- Affiliations
- Boston Children's Hospital (US)
- Brigham and Women's Hospital (US)
- Case Western Reserve University (US)
- Corresponding author
- Walsh, Christopher A.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-10
- Volume
- 151
- Issue
- 3
- Pages
- 483-496
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3567441
- OpenAlex
- W2123490990
- Cited by
- 548
- References
- 66
- Citations by year
- 2026: 16 · 2025: 26 · 2024: 23 · 2023: 28 · 2022: 29 · 2021: 36 · 2020: 45 · 2019: 41 · 2018: 45 · 2017: 56 · 2016: 49 · 2015: 55 · 2014: 48 · 2013: 47 · 2012: 4
- FWCI
- 29.39
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Manton Center for Orphan Disease Research, Boston Children's Hospital
- National Institute of General Medical Sciences (T32GM007726, T32GM007753)
- National Institute of Neurological Disorders and Stroke (R01NS035129, R01NS079277)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- LINE-1 retrotransposition, somatic mutations, somatic mosaicism, hemimegalencephaly, cerebral cortex, caudate nucleus, single-cell genotyping
- MeSH terms
- Caudate Nucleus, Cerebral Cortex, Child, Chromosomes, Human, Pair 18, Humans, Male, Mosaicism, Mutation, Neurons, Trisomy, Long Interspersed Nucleotide Elements, Proto-Oncogene Proteins c-akt, Malformations of Cortical Development, Genome-Wide Association Study, Single-Cell Analysis
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