Many LINE1 elements contribute to the transcriptome of human somatic cells
Open accessAbstract
BACKGROUND: While LINE1 (L1) retroelements comprise nearly 20% of the human genome, the majority are thought to have been rendered transcriptionally inactive, due to either mutation or epigenetic suppression. How many L1 elements 'escape' these forms of repression and contribute to the transcriptome of human somatic cells? We have cloned out expressed sequence tags corresponding to the 5' and 3' flanks of L1 elements in order to characterize the population of elements that are being actively transcribed. We also examined expression of a select number of elements in different individuals. RESULTS: We isolated expressed sequence tags from human lymphoblastoid cell lines corresponding to 692 distinct L1 element sites, including 410 full-length elements. Four of the expression tagged sites corresponding to full-length elements from the human specific L1Hs subfamily were examined in European-American individuals and found to be differentially expressed in different family members. CONCLUSIONS: A large number of different L1 element sites are expressed in human somatic tissues, and this expression varies among different individuals. Paradoxically, few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels. Based on our preliminary expression studies of a limited number of elements in a single family, we predict a significant degree of inter-individual transcript-level polymorphism in this class of sequence.
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The initiation of L1 transcription is imprecise, with the majority of start sites occurring +/−50 bp of the consensus start site, and a subset as far down as +180 bp.
“The initiation of L1 transcription is known to be imprecise, with the majority of start sites occurring +/−50 bp of the consensus start site, and a subset as far down as +180 bp68.”
From L1 drives IFN in senescent cells and promotes age-associated inflammation (2019) · cites this paper as [68]
The Results section on L1 expression tags reports variable 5′ start sites, with 50% (170) within ±50 nucleotides of the consensus start—not a majority. The Results and Discussion describe other starts more than 100 nucleotides upstream, but do not establish a subset starting at +180 bp. The paper’s 182-nucleotide figure concerns transcript termination beyond the 3′ end, not initiation. (LLM, conf=0.88)
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Additional file 5 of Exploratory analysis of L1 retrotransposons expression in autism
Spirito, G., Filosi, M., Domenici, E., Mangoni, D., Gustincich, S., & Sanges, R. (2024) · Figshare · doi:10.6084/m9.figshare.26600515
Additional file 3 of Exploratory analysis of L1 retrotransposons expression in autism
Spirito, G., Filosi, M., Domenici, E., Mangoni, D., Gustincich, S., & Sanges, R. (2024) · Figshare · doi:10.6084/m9.figshare.26600509
Additional file 1 of Exploratory analysis of L1 retrotransposons expression in autism
Spirito, G., Filosi, M., Domenici, E., Mangoni, D., Gustincich, S., & Sanges, R. (2024) · Figshare · doi:10.6084/m9.figshare.26600503
Additional file 4 of Exploratory analysis of L1 retrotransposons expression in autism
Spirito, G., Filosi, M., Domenici, E., Mangoni, D., Gustincich, S., & Sanges, R. (2024) · Figshare · doi:10.6084/m9.figshare.26600512
Additional file 2 of Exploratory analysis of L1 retrotransposons expression in autism
Spirito, G., Filosi, M., Domenici, E., Mangoni, D., Gustincich, S., & Sanges, R. (2024) · Figshare · doi:10.6084/m9.figshare.26600506
Additional file 6 of Exploratory analysis of L1 retrotransposons expression in autism
Spirito, G., Filosi, M., Domenici, E., Mangoni, D., Gustincich, S., & Sanges, R. (2024) · Figshare · doi:10.6084/m9.figshare.26600518
- Authors
- Rangwala, S. H., Zhang, L., & Kazazian, H. H.
- Affiliations
- University of Pennsylvania (US)
- Corresponding author
- Kazazian, Haig H
- Venue
- Genome Biology
- Published
- 2009-09-22
- Volume
- 10
- Issue
- 9
- Pages
- R100-R100
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC2768975
- OpenAlex
- W2107950128
- Cited by
- 102
- References
- 70
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 7 · 2023: 3 · 2022: 6 · 2021: 6 · 2020: 5 · 2019: 8 · 2018: 1 · 2017: 4 · 2016: 9 · 2015: 2 · 2014: 6 · 2013: 9 · 2012: 10
- FWCI
- 10.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- University of Pennsylvania
- National Institutes of Health
- 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 › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- somatic cells, expressed sequence tags, lymphoblastoid cell lines, epigenetic silencing, human genome
- MeSH terms
- Binding Sites, Cell Line, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 13, Chromosomes, Human, Pair 4, Chromosomes, Human, Pair 6, Gene Expression Regulation, Humans, Lymphocytes, Transcription, Genetic, Genome, Human, Sequence Analysis, DNA, DNA, Complementary, Long Interspersed Nucleotide Elements, Reverse Transcriptase Polymerase Chain Reaction, Expressed Sequence Tags, Gene Expression Profiling
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