Cited by 489Chromosomal and Genetic VariationsGenomics and Chromatin DynamicsRNA Research and Splicing

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Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes

Han, Jeffrey S., Szak, Suzanne T., Boeke, Jef D.·2004·Nature

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Abstract

LINE-1 (L1) elements are the most abundant autonomous retrotransposons in the human genome, accounting for about 17% of human DNA. The L1 retrotransposon encodes two proteins, open reading frame (ORF)1 and the ORF2 endonuclease/reverse transcriptase. L1 RNA and ORF2 protein are difficult to detect in mammalian cells, even in the context of overexpression systems. Here we show that inserting L1 sequences on a transcript significantly decreases RNA expression and therefore protein expression. This decreased RNA concentration does not result from major effects on the transcription initiation rate or RNA stability. Rather, the poor L1 expression is primarily due to inadequate transcriptional elongation. Because L1 is an abundant and broadly distributed mobile element, the inhibition of transcriptional elongation by L1 might profoundly affect expression of endogenous human genes. We propose a model in which L1 affects gene expression genome-wide by acting as a 'molecular rheostat' of target genes. Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome.

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Additional file 2 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
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Additional file 5 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2024) · Figshare · doi:10.6084/m9.figshare.26647566
Additional file 4 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2024) · Figshare · doi:10.6084/m9.figshare.26647563
Additional file 7 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2024) · Figshare · doi:10.6084/m9.figshare.26647572
Additional file 9 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2024) · Figshare · doi:10.6084/m9.figshare.26647578
Additional file 4 of Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons
Ruggiero, R. P., & Boissinot, S. (2020) · Figshare · doi:10.6084/m9.figshare.12096807
Additional file 8 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2024) · Figshare · doi:10.6084/m9.figshare.26647575
Additional file 2 of Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons
Ruggiero, R. P., & Boissinot, S. (2020) · Figshare · doi:10.6084/m9.figshare.12096798
Additional file 3 of Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons
Ruggiero, R. P., & Boissinot, S. (2020) · Figshare · doi:10.6084/m9.figshare.12096801
Additional file 6 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2024) · Figshare · doi:10.6084/m9.figshare.26647569
Additional file 2 of RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
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Additional file 1 of RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
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Additional file 3 of Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
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Additional file 4 of RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
Briggs, E. M., McKerrow, W., Mita, P., Boeke, J. D., Logan, S. K., & Fenyö, D. (2021) · Figshare · doi:10.6084/m9.figshare.13843928
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Additional file 1 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2023) · Figshare · doi:10.6084/m9.figshare.24709060
Additional file 3 of RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs
Briggs, E. M., McKerrow, W., Mita, P., Boeke, J. D., Logan, S. K., & Fenyö, D. (2021) · Figshare · doi:10.6084/m9.figshare.13843922
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Additional file 3 of An intronic LINE-1 regulates IFNAR1 expression in human immune cells
Buttler, C. A., Ramirez, D., Dowell, R. D., & Chuong, E. B. (2024) · Figshare · doi:10.6084/m9.figshare.26647560
Additional file 6 of Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons
Ruggiero, R. P., & Boissinot, S. (2020) · Figshare · doi:10.6084/m9.figshare.12096816
Additional file 5 of Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons
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Lee, M.-G. (2026) · Research Square · doi:10.21203/rs.3.rs-10975043/v1
Revisiting the impact of synthetic ORF sequences on engineered LINE-1 retrotransposition
Chan, D. L.-K., Workman, S., Smits, N., Carleton, A. L., Gerdes, P., Han, J. S., Boeke, J. D., Faulkner, G. J., & Richardson, S. R. (2026) · PLoS Genetics · doi:10.1371/journal.pgen.1012340 · Cited by 5
Self-citation

Authors: Han, J. S., Szak, S. T., & Boeke, J. D.
Affiliations: Johns Hopkins University (US)
Biogen (United States) (US)
Corresponding author: Boeke, Jef D.
ORCID: Han, Jeffrey S.
Boeke, Jef D.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2004-05
Volume: 429
Issue: 6989
Pages: 268-274
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature02536
OpenAlex: W1981262837
Cited by: 484
References: 52
Citations by year: 2026: 5 · 2025: 7 · 2024: 12 · 2023: 18 · 2022: 13 · 2021: 24 · 2020: 18 · 2019: 12 · 2018: 21 · 2017: 21 · 2016: 22 · 2015: 15 · 2014: 22 · 2013: 25 · 2012: 34
FWCI: 48.86
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords: LINE-1 retrotransposons, transcription elongation, ORF1, retrotransposon expression, gene expression regulation, human transcriptome, transposable elements, RNA stability, transcription initiation
MeSH terms: Animals, Base Sequence, Cell Line, Endonucleases, Half-Life, Humans, Mammals, Models, Genetic, RNA-Directed DNA Polymerase, RNA Polymerase III, RNA, Messenger, Transcription, Genetic, Down-Regulation, Open Reading Frames, Evolution, Molecular, Computational Biology, Long Interspersed Nucleotide Elements, RNA Stability, Feedback, Physiological, Mice

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Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes

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