Natural mutagenesis of human genomes by endogenous retrotransposons
Open accessAbstract
Two abundant classes of mobile elements, namely Alu and L1 elements, continue to generate new retrotransposon insertions in human genomes. Estimates suggest that these elements have generated millions of new germline insertions in individual human genomes worldwide. Unfortunately, current technologies are not capable of detecting most of these young insertions, and the true extent of germline mutagenesis by endogenous human retrotransposons has been difficult to examine. Here, we describe technologies for detecting these young retrotransposon insertions and demonstrate that such insertions indeed are abundant in human populations. We also found that new somatic L1 insertions occur at high frequencies in human lung cancer genomes. Genome-wide analysis suggests that altered DNA methylation may be responsible for the high levels of L1 mobilization observed in these tumors. Our data indicate that transposon-mediated mutagenesis is extensive in human genomes and is likely to have a major impact on human biology and diseases.
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L1 retrotransposon activity has been linked to DNA damage, mutagenesis, and deregulation of host gene transcription.
“Long interspersed element 1 (L1) retrotransposon activity, in particular, has been linked to DNA damage5, mutagenesis6,7, and deregulation of host gene transcription8.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [7]
L1 activity has been implicated in a variety of age-related disorders, including cancer and neurodegeneration.
“L1 activity has been implicated in a variety of age-related disorders12, including cancer7,13 and neurodegeneration14,15.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [7]
Most KNR insertions in an individual are heterozygous and present in a single copy per cell.
“This shows that most KNR insertions in an individual are heterozygous and present in a single copy per cell.”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Iskow et al., 2010
The corrected RC-seq retrotransposition rate is consistent with the absence of significant somatic L1 insertions in brain tumors.
“and is consistent with the absence of significant somatic L1 insertions in brain tumors (Helman et al., 2014; Iskow et al., 2010; Lee et al., 2012).”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Iskow et al., 2010
Most germline KNR insertions (~75%) are present in a single copy per cell.
“Most germline KNR insertions (~75%) are present in a single copy per cell as well, since most are in the heterozygous state in individuals of the population.”
From Resolving rates of mutation in the brain using single-neuron genomics (2016) · cites this paper as Iskow et al., 2010
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- Authors
- Iskow, R. C., McCabe, M. T., Mills, R. E., Torene, S., Pittard, W. S., Neuwald, A. F., Van Meir, E. G., Vertino, P. M., & Devine, S. E.
- Affiliations
- Emory University (US)
- University of Maryland, Baltimore (US)
- Corresponding author
- Devine, Scott E.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2010-06
- Volume
- 141
- Issue
- 7
- Pages
- 1253-1261
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC2943760
- OpenAlex
- W2146892790
- Cited by
- 551
- References
- 49
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- FWCI
- 73.65
- Type
- journal article
- Language
- en
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- bronze
- doi.org
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- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- American Cancer Society
- National Human Genome Research Institute (F32HG004207, R01HG002898)
- National Cancer Institute (R01CA132065, P01CA116676, R01CA116804, R01CA086335)
- National Institute of General Medical Sciences (T32GM008490, R01GM078541)
- 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
- retrotransposons, Alu elements, LINE-1 retrotransposons, somatic insertions, DNA methylation, lung cancer, human genome
- MeSH terms
- Brain Neoplasms, Humans, Lung Neoplasms, Methylation, Genome, Human, Mutagenesis, Sequence Analysis, DNA, Long Interspersed Nucleotide Elements, Alu Elements
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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