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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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Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Clustal W and Clustal X version 2.0
Larkin, M., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., López, R., et al. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm404 · Cited by 28,598
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390
Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Humana Press eBooks · doi:10.1385/1-59259-192-2:365 · Cited by 15,068
Circos: An information aesthetic for comparative genomicsPreprint
Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 11,073
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Goecks, J., Nekrutenko, A., Taylor, J., & The Galaxy Team (2010) · Genome biology · doi:10.1186/gb-2010-11-8-r86 · Cited by 3,539
Tumour evolution inferred by single-cell sequencing
Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L., McIndoo, J., Cook, K., Stepansky, A., Levy, D., Esposito, D., et al. (2011) · Nature · doi:10.1038/nature09807 · Cited by 2,598
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Chromothripsis from DNA damage in micronuclei
Zhang, C., Spektor, A., Cornils, H., Francis, J. M., Jackson, E. K., Liu, S., Meyerson, M. M., & Pellman, D. S. (2015) · Nature · doi:10.1038/nature14493 · Cited by 1,155
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
Cossarizza, A., Chang, H., Radbruch, A., Acs, A., Adam, D., Adam‐Klages, S., Agace, W. W., Aghaeepour, N., Akdiş, M., Allez, M., et al. (2019) · European Journal of Immunology · doi:10.1002/eji.201970107 · Cited by 1,007
Revealing the vectors of cellular identity with single-cell genomics
Wagner, A., Regev, A., & Yosef, N. (2016) · Nature Biotechnology · doi:10.1038/nbt.3711 · Cited by 632
Roles for retrotransposon insertions in human disease
Hancks, D. C., & Kazazian, H. H. (2016) · Mobile DNA · doi:10.1186/s13100-016-0065-9 · Cited by 670
Aging and neurodegeneration are associated with increased mutations in single human neurons
Lodato, M. A., Rodin, R. E., Bohrson, C. L., Coulter, M. E., Barton, A. R., Kwon, M., Sherman, M. A., Vitzthum, C. M., Luquette, L. J., Yandava, C. N., et al. (2018) · Science · doi:10.1126/science.aao4426 · Cited by 635
Self-citationAdvances and Applications of Single-Cell Sequencing Technologies
Wang, Y., & Navin, N. E. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.005 · Cited by 624
Genome-wide inactivation of porcine endogenous retroviruses (PERVs)
Yang, L., Güell, M., Niu, D., George, H., Lesha, E., Grishin, D., Aach, J., Shrock, E. L., Xu, W., Poci, J., et al. (2015) · Science · doi:10.1126/science.aad1191 · Cited by 611
Somatic mutation, genomic variation, and neurological disease
Poduri, A., Evrony, G. D., Cai, X., & Walsh, C. A. (2013) · Science · doi:10.1126/science.1237758 · Cited by 584
Self-citationSomatic mutation in single human neurons tracks developmental and transcriptional history
Lodato, M. A., Woodworth, M. B., Lee, S., Evrony, G. D., Mehta, B. K., Karger, A., Lee, S., Chittenden, T. W., D’Gama, A. M., Cai, X., et al. (2015) · Science · doi:10.1126/science.aab1785 · Cited by 570
Self-citationMosaic Copy Number Variation in Human Neurons
McConnell, M. J., Lindberg, M. R., Brennand, K. J., Piper, J. C., Voet, T., Cowing-Zitron, C., Shumilina, S., Lasken, R. S., Vermeesch, J. R., Hall, I. M., et al. (2013) · Science · doi:10.1126/science.1243472 · Cited by 551
Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)
Cossarizza, A., Chang, H., Radbruch, A., Abrignani, S., Addo, R., Akdis, M., Andrä, I., Andreata, F., Annunziato, F., Arranz, E., et al. (2021) · European Journal of Immunology · doi:10.1002/eji.202170126 · Cited by 531
Integrated genome and transcriptome sequencing of the same cell
Dey, S. S., Kester, L., Spanjaard, B., Bienko, M., & van Oudenaarden, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3129 · Cited by 502
Restricting retrotransposons: a review
Goodier, J. L. (2016) · Mobile DNA · doi:10.1186/s13100-016-0070-z · Cited by 436
The role of retrotransposable elements in ageing and age-associated diseases
Gorbunova, V., Seluanov, A., Mita, P., McKerrow, W., Fenyö, D., Boeke, J. D., Linker, S. B., Gage, F. H., Kreiling, J. A., Petrashen, A. P., et al. (2021) · Nature · doi:10.1038/s41586-021-03542-y · Cited by 446
Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
Tubio, J. M. C., Li, Y., Ju, Y. S., Martincorena, I., Cooke, S. L., Tojo, M., Gundem, G., Pipinikas, C. P., Zamora, J., Raine, K., et al. (2014) · Science · doi:10.1126/science.1251343 · Cited by 412
Mobile DNA in Health and Disease
Kazazian, H. H., & Moran, J. V. (2017) · New England Journal of Medicine · doi:10.1056/nejmra1510092 · Cited by 445
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Reiter, R. J., Rosales‐Corral, S., Tan, D., Acuña-Castroviejo, D., Qin, L., Yang, S., & Xu, K. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18040843 · Cited by 453
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Shukla, R., Upton, K. R., Muñoz-López, M., Gerhardt, D. J., Fisher, M. E., Nguyen, T., Brennan, P. M., Baillie, J. K., Collino, A., Ghisletti, S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.02.032 · Cited by 405
The role of de novo mutations in the genetics of autism spectrum disorders
Ronemus, M., Iossifov, I., Levy, D., & Wigler, M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3585 · Cited by 390
Measuring and interpreting transposable element expression
Lanciano, S., & Cristofari, G. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0251-y · Cited by 415
Single Cell Genomics: Advances and Future Perspectives
Macaulay, I. C., & Voet, T. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004126 · Cited by 384
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biologyPreprint
Gardner, E. J., Lam, V. K. L., Harris, D., Chuang, N. T., Scott, E., Pittard, W. S., Mills, R. E., & Devine, S. E. (2017) · Genome Research · doi:10.1101/gr.218032.116 · Cited by 378
Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues
De Cecco, M., Criscione, S. W., Peterson, A. L., Neretti, N., Sedivy, J. M., & Kreiling, J. A. (2013) · Aging · doi:10.18632/aging.100621 · Cited by 365
Ubiquitous L1 Mosaicism in Hippocampal Neurons
Upton, K. R., Gerhardt, D. J., Jesuadian, J. S., Richardson, S. R., Sánchez-Luque, F. J., Bodea, G. O., Ewing, A. D., Salvador-Palomeque, C., van der Knaap, M. S., Brennan, P. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.03.026 · Cited by 320
Tau Activates Transposable Elements in Alzheimer’s Disease
Guo, C., Jeong, H.-H., Hsieh, Y.-C., Klein, H.-U., Bennett, D. A., De Jager, P. L., Liu, Z., & Shulman, J. M. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.004 · Cited by 315
D’Gama, A. M., Woodworth, M. B., Hossain, A. A., Bizzotto, S., Hatem, N. E., LaCoursiere, C. M., Najm, I., Ying, Z., Yang, E., Barkovich, A. J., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.11.106 · Cited by 333
Self-citationCai, X., Evrony, G. D., Lehmann, H. S., Elhosary, P. C., Mehta, B. K., Poduri, A., & Walsh, C. A. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.043 · Cited by 318
Self-citationMelatonin: an inhibitor of breast cancer
Hill, S. M., Belancio, V. P., Dauchy, R. T., Xiang, S., Brimer, S., Mao, L., Hauch, A. T., Lundberg, P. W., Summers, W. M., Yuan, L., et al. (2015) · Endocrine Related Cancer · doi:10.1530/erc-15-0030 · Cited by 328
The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes
Richardson, S. R., Doucet, A. J., Kopera, H. C., Moldovan, J. B., Garcia-Perez, J. L., & Moran, J. V. (2015) · Microbiology Spectrum · doi:10.1128/microbiolspec.mdna3-0061-2014 · Cited by 338
Somatic mosaicism: implications for disease and transmission genetics
Campbell, I. M., Shaw, C. A., Stankiewicz, P., & Lupski, J. R. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.03.013 · Cited by 296
Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia
Bundo, M., Toyoshima, M., Okada, Y., Akamatsu, W., Ueda, J., Nemoto-Miyauchi, T., Sunaga, F., Toritsuka, M., Ikawa, D., Kakita, A., et al. (2014) · Neuron · doi:10.1016/j.neuron.2013.10.053 · Cited by 321
Interactive analysis and assessment of single-cell copy-number variations
Garvin, T. H., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J. B., Wigler, M. H., & Schatz, M. C. (2015) · Nature Methods · doi:10.1038/nmeth.3578 · Cited by 287
A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancerPreprint
Scott, E., Gardner, E. J., Masood, A., Chuang, N. T., Vertino, P. M., & Devine, S. E. (2016) · Genome Research · doi:10.1101/gr.201814.115 · Cited by 317
Cell lineage analysis in human brain using endogenous retroelements
Evrony, G. D., Lee, E., Mehta, B. K., Benjamini, Y., Johnson, R. M., Cai, X., Yang, L., Haseley, P., Lehmann, H. S., Park, P. J., et al. (2015) · Neuron · doi:10.1016/j.neuron.2014.12.028 · Cited by 269
Self-citationAge-related clonal hematopoiesis
Shlush, L. I. (2018) · Blood · doi:10.1182/blood-2017-07-746453 · Cited by 281
The Developmental Control of Transposable Elements and the Evolution of Higher Species
Friedli, M., & Trono, D. (2015) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100814-125514 · Cited by 274
Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis
Bae, T., Tomasini, L., Mariani, J., Zhou, B., Roychowdhury, T., Franjic, D., Pletikos, M., Pattni, R., Chen, B.-J., Venturini, E., et al. (2017) · Science · doi:10.1126/science.aan8690 · Cited by 267
Building a lineage from single cells: genetic techniques for cell lineage tracking
Woodworth, M. B., Girskis, K. M., & Walsh, C. A. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2016.159 · Cited by 236
Self-citationMobile DNA elements in the generation of diversity and complexity in the brain
Erwin, J. A., Marchetto, M. C., & Gage, F. H. (2014) · Nature reviews. Neuroscience · doi:10.1038/nrn3730 · Cited by 277
Mosaicism in health and disease — clones picking up speed
Forsberg, L. A., Gisselsson, D., & Dumanski, J. P. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.145 · Cited by 261
McConnell, M. J., Moran, J. V., Abyzov, A., Akbarian, S., Bae, T., Cortes-Ciriano, I., Erwin, J. A., Fasching, L., Flasch, D. A., Freed, D., et al. (2017) · Science · doi:10.1126/science.aal1641 · Cited by 262
Self-citationSomatic mosaicism and neurodevelopmental disease
D’Gama, A. M., & Walsh, C. A. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0257-3 · Cited by 249
Self-citationTransposition-Driven Genomic Heterogeneity in the Drosophila Brain
Perrat, P. N., Dasgupta, S., Wang, J., Theurkauf, W. E., Weng, Z., Rosbash, M., & Waddell, S. (2013) · Science · doi:10.1126/science.1231965 · Cited by 245
Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons
Liu, E. Y., Russ, J., Cali, C. P., Phan, J. M., Amlie-Wolf, A., & Lee, E. B. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.003 · Cited by 231
“…from our studies that TDP-43 pathology is associated with retrotransposition per se, although retrotransposition has been observed in neuronal cells (Baillie et al., 2011; Erwin et al., 2016; Evrony et al., 2012, 2015, 2016; Faulkner and Garcia-Perez, 2017; Macia et al., 2017; Up-ton et al., 2015).”
BackgroundSelf-citationSingle-cell transcriptome sequencing: recent advances and remaining challenges
Liu, S., & Trapnell, C. (2016) · F1000Research · doi:10.12688/f1000research.7223.1 · Cited by 230
Somatic genomic changes in single Alzheimer’s disease neurons
Miller, M. B., Huang, A. Y., Kim, J., Zhou, Z., Kirkham, S. L., Maury, E. A., Ziegenfuss, J. S., Reed, H. C., Neil, J. E., Rento, L., et al. (2022) · Nature · doi:10.1038/s41586-022-04640-1 · Cited by 223
L1-associated genomic regions are deleted in somatic cells of the healthy human brain
Erwin, J. A., Paquola, A. C. M., Singer, T., Gallina, I., Novotny, M., Quayle, C., Bedrosian, T. A., Alves, F. I. A., Butcher, C. R., Herdy, J. R., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4388 · Cited by 195
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Mita, P., & Boeke, J. D. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.01.001 · Cited by 217
The impact of transposable elements on mammalian development
Garcia-Perez, J. L., Widmann, T. J., & Adams, I. R. (2016) · Development · doi:10.1242/dev.132639 · Cited by 215
Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS
Krug, L., Chatterjee, N., Borges-Monroy, R., Hearn, S., Liao, W.-W., Morrill, K., Prazak, L., Rozhkov, N., Theodorou, D., Hammell, M., et al. (2017) · PLOS Genetics · doi:10.1371/journal.pgen.1006635 · Cited by 201
Transposable Elements Re-Wire and Fine-Tune the Transcriptome
Cowley, M., & Oakey, R. J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003234 · Cited by 207
Guo, H., Zhu, P., Guo, F., Li, X., Wu, X., Fan, X., Wen, L., & Tang, F. (2015) · Nature Protocols · doi:10.1038/nprot.2015.039 · Cited by 188
Hou, Y., Wu, K., Shi, X., Li, F., Song, L., Wu, H., Dean, M. C., Li, G., Tsang, S. X., Jiang, R., et al. (2015) · GigaScience · doi:10.1186/s13742-015-0068-3 · Cited by 187
LINE-1 Evasion of Epigenetic Repression in Humans
Sanchez-Luque, F. J., Kempen, M.-J. H. C., Gerdes, P., Vargas-Landin, D. B., Richardson, S. R., Troskie, R.-L., Jesuadian, J. S., Cheetham, S. W., Carreira, P. E., Salvador-Palomeque, C., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.024 · Cited by 161
Unravelling cellular relationships during development and regeneration using genetic lineage tracing
Baron, C. S., & van Oudenaarden, A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0186-3 · Cited by 183
Philippe, C., Vargas-Landín, D. B., Doucet, A. J., van Essen, D., Vera‐Otarola, J., Kuciak, M., Corbin, A., Nigumann, P., & Cristofari, G. (2016) · eLife · doi:10.7554/elife.13926 · Cited by 186
Repetitive DNA sequence detection and its role in the human genome
Liao, X., Zhu, W., Zhou, J., Li, H., Xu, X., Zhang, B., & Gao, X. (2023) · Communications Biology · doi:10.1038/s42003-023-05322-y · Cited by 192
Resolving rates of mutation in the brain using single-neuron genomics
Evrony, G. D., Lee, E., Park, P. J., & Walsh, C. A. (2016) · eLife · doi:10.7554/elife.12966 · Cited by 163
Self-citationL1 Retrotransposons and Somatic Mosaicism in the Brain
Richardson, S. R., Morell, S., & Faulkner, G. J. (2014) · Annual Review of Genetics · doi:10.1146/annurev-genet-120213-092412 · Cited by 185
Wang, L., Zhou, K., Fu, Z., Yu, D., Huang, H., Zang, X., & Mo, X. (2017) · Journal of Molecular Neuroscience · doi:10.1007/s12031-016-0872-y · Cited by 172
The Role of Transposable Elements in Health and Diseases of the Central Nervous System
Reilly, M. T., Faulkner, G. J., Dubnau, J., Ponomarev, I., & Gage, F. H. (2013) · The Journal of Neuroscience · doi:10.1523/jneurosci.3369-13.2013 · Cited by 175
The Diverse Genetic Landscape of Neurodevelopmental Disorders
Hu, W. F., Chahrour, M. H., & Walsh, C. A. (2014) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025600 · Cited by 177
Self-citationSeparation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq
Macaulay, I. C., Teng, M. J., Haerty, W., Kumar, P., Ponting, C. P., & Voet, T. (2016) · Nature Protocols · doi:10.1038/nprot.2016.138 · Cited by 170
Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition
Goodier, J. L., Cheung, L. E., & Kazazian, H. H. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt512 · Cited by 180
Transposable elements in the mammalian embryo: pioneers surviving through stealth and service
Gerdes, P., Richardson, S. R., Mager, D. L., & Faulkner, G. J. (2016) · Genome Biology · doi:10.1186/s13059-016-0965-5 · Cited by 156
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D’Gama, A. M., Pochareddy, S., Li, M., Jamuar, S. S., Rodin, R. E., Lam, A.-T. N., Šestan, N., & Walsh, C. A. (2015) · Neuron · doi:10.1016/j.neuron.2015.11.009 · Cited by 153
Self-citationEngineered LINE-1 retrotransposition in nondividing human neuronsPreprint
Macia, Á., Widmann, T. J., Heras, S. R., Ayllón, V., Sánchez, L., Benkaddour-Boumzaouad, M., Muñoz-López, M., Rubio, A., Amador‐Cubero, S., Blanco-Jimenez, E., et al. (2016) · Genome Research · doi:10.1101/gr.206805.116 · Cited by 166
Somatic Mosaicism in the Human Genome
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Saleh, A., Macia, A., & Muotri, A. R. (2019) · Frontiers in Neurology · doi:10.3389/fneur.2019.00894 · Cited by 149
Detecting Somatic Mutations in Normal Cells
Dou, Y., Gold, H. D., Luquette, L. J., & Park, P. J. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.04.003 · Cited by 151
Self-citationLINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma
Doucet-O’Hare, T. T., Rodić, N., Sharma, R., Darbari, I., Abril, G., Choi, J. A., Ahn, J. Y., Cheng, Y., Anders, R. A., Burns, K. H., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1502474112 · Cited by 158
Autophagy supports genomic stability by degrading retrotransposon RNA
Guo, H., Chitiprolu, M., GAGNON, D. R., Meng, L., Perez‐Iratxeta, C., Lagace, D. C., & Gibbings, D. (2014) · Nature Communications · doi:10.1038/ncomms6276 · Cited by 154
TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells
Fasching, L., Kapopoulou, A., Sachdeva, R., Petri, R., Jönsson, M. E., Männe, C., Turelli, P., Jern, P., Cammas, F. M., Trono, D., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.12.004 · Cited by 150
Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma
Rodić, N., Steranka, J. P., Makohon-Moore, A. P., Moyer, A. F., Shen, P., Sharma, R., Kohutek, Z. A., Huang, C. R. L., Ahn, D. H., Mita, P., et al. (2015) · Nature Medicine · doi:10.1038/nm.3919 · Cited by 150
Recent advances in single-cell sequencing technologies
Wen, L., & Tang, F. (2022) · Precision Clinical Medicine · doi:10.1093/pcmedi/pbac002 · Cited by 127
Genetic Changes Shaping the Human Brain
Bae, B.-I., Jayaraman, D., & Walsh, C. A. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.01.035 · Cited by 135
Self-citationSingle-cell paired-end genome sequencing reveals structural variation per cell cycle
Voet, T., Kumar, P., Loo, P. V., Cooke, S. L., Marshall, J., Lin, M., Esteki, M. Z., der Aa, N. V., Mateiu, L. M., McBride, D. J., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt345 · Cited by 149
Transposable elements as genetic regulatory substrates in early development
Gifford, W. D., Pfaff, S. L., & Macfarlan, T. S. (2013) · Trends in Cell Biology · doi:10.1016/j.tcb.2013.01.001 · Cited by 147
Retroelements in human disease
Kaer, K., & Speek, M. (2013) · Gene · doi:10.1016/j.gene.2013.01.008 · Cited by 150
Somatic mutations, genome mosaicism, cancer and aging
Vijg, J. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.04.002 · Cited by 143
Early life experience drives structural variation of neural genomes in mice
Bedrosian, T. A., Quayle, C., Novaresi, N., & Gage, F. H. (2018) · Science · doi:10.1126/science.aah3378 · Cited by 131
Bushman, D. M., Kaeser, G. E., Siddoway, B., Westra, J. W., Rivera, R. R., Rehen, S. K., Yung, Y. C., & Chun, J. (2015) · eLife · doi:10.7554/elife.05116 · Cited by 136
Stress and the dynamic genome: Steroids, epigenetics, and the transposome
Hunter, R. G., Gagnidze, K., McEwen, B. S., & Pfaff, D. W. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1411260111 · Cited by 137
Single-cell omics in ageing: a young and growing field
He, X., Memczak, S., Qu, J. T., Belmonte, J. C. I., & Liu, G. (2020) · Nature Metabolism · doi:10.1038/s42255-020-0196-7 · Cited by 129
Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolutionPreprint
Ewing, A. D., Gacita, A. M., Wood, L. D., Ma, F., Xing, D., Kim, M., Manda, S. S., Abril, G., Pereira, G., Makohon-Moore, A. P., et al. (2015) · Genome Research · doi:10.1101/gr.196238.115 · Cited by 129
Rodin, R. E., Dou, Y., Kwon, M., Sherman, M. A., D’Gama, A. M., Doan, R. N., Rento, L. M., Girskis, K. M., Bohrson, C. L., Kim, S. N., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00765-6 · Cited by 135
Self-citationTransposable Elements: A Common Feature of Neurodevelopmental and Neurodegenerative Disorders
Jönsson, M. E., Garza, R., Johansson, P. A., & Jakobsson, J. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.05.004 · Cited by 122
Baek, S. T., Copeland, B. R., Yun, E.-J., Kwon, S., Guemez‐Gamboa, A., Schaffer, A. E., Kim, S., Kang, H., Song, S., Mathern, G. W., et al. (2015) · Nature Medicine · doi:10.1038/nm.3982 · Cited by 126
Structural variation in 1,019 diverse humans based on long-read sequencing
Schloissnig, S., Pani, S., Ebler, J., Hain, C., Tsapalou, V., Söylev, A., Hüther, P., Ashraf, H., Prodanov, T., Asparuhova, M., et al. (2025) · Nature · doi:10.1038/s41586-025-09290-7 · Cited by 141
Applications of Single-Cell DNA Sequencing
Evrony, G. D., Hinch, A. G., & Luo, C. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111320-090436 · Cited by 129
Self-citationRetrotransposition of gene transcripts leads to structural variation in mammalian genomes
Ewing, A. D., Ballinger, T. J., Earl, D. A., Harris, C. C., Ding, L., Wilson, R. K., & Haussler, D. H. (2013) · Genome biology · doi:10.1186/gb-2013-14-3-r22 · Cited by 118
Single cell analysis of cancer genomes
Loo, P. V., & Voet, T. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.12.004 · Cited by 118
Mosaicism in Human Health and Disease
Thorpe, J., Osei‐Owusu, I., Avigdor, B. E., Tupler, R. G., & Pevsner, J. (2020) · Annual Review of Genetics · doi:10.1146/annurev-genet-041720-093403 · Cited by 121
The Microprocessor controls the activity of mammalian retrotransposons
Heras, S. R., Macías, S., Plass, M., Fernández, N., Cano, D., Eyras, E., Garcia-Perez, J. L., & Cáceres, J. F. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2658 · Cited by 123
Heritable L1 retrotransposition in the mouse primordial germline and early embryoPreprint
Richardson, S. R., Gerdes, P., Gerhardt, D. J., Sanchez-Luque, F. J., Bodea, G. O., Muñoz-López, M., Jesuadian, J. S., Kempen, M.-J. H. C., Carreira, P. E., Jeddeloh, J. A., et al. (2017) · Genome Research · doi:10.1101/gr.219022.116 · Cited by 117
Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging
Zhang, L., & Vijg, J. (2018) · Annual Review of Genetics · doi:10.1146/annurev-genet-120417-031501 · Cited by 108
Jönsson, M. E., Brattås, P. L., Gustafsson, C., Petri, R., Yudovich, D., Pircs, K., Verschuere, S., Madsen, S., Hansson, J., Larsson, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11150-8 · Cited by 119
Calibrating genomic and allelic coverage bias in single-cell sequencing
Zhang, C.-Z., Adalsteinsson, V. A., Francis, J., Cornils, H., Jung, J., Maire, C., Ligon, K. L., Meyerson, M., & Love, J. C. (2015) · Nature Communications · doi:10.1038/ncomms7822 · Cited by 112
Crichton, J. H., Dunican, D. S., MacLennan, M., Meehan, R. R., & Adams, I. R. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1468-0 · Cited by 115
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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