The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
Molecular archeology of L1 insertions in the human genome
Open accessAbstract
BACKGROUND: As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. In particular, L1 elements exhibit a variety of sequence structures after insertion into the human genome that are amenable to computational analysis. We carried out a detailed analysis of the anatomy and distribution of L1 elements in the human genome using a new computer program, TSDfinder, designed to identify transposon boundaries precisely. RESULTS: Structural variants of L1 elements shared similar trends in the length and quality of their target site duplications (TSDs) and poly(A) tails. Furthermore, we found no correlation between the composition and genomic location of the pre-insertion locus and the resulting anatomy of the L1 insertion. We verified that L1 insertions with TSDs have the 5'-TTAAAA-3' cleavage site associated with L1 endonuclease activity. In addition, the second target DNA cut required for L1 insertion weakly matches the consensus pattern TTAAAA. On the other hand, the L1-internal breakpoints of deleted and inverted L1 elements do not resemble L1 endonuclease cleavage sites. Finally, the genome sequence data indicate that whereas singly inverted elements are common, doubly inverted elements are almost never found. CONCLUSIONS: The sequence data give no indication that the creation of L1 structural variants depends on characteristics of the insertion locus. In addition, the formation of 5' truncated and 5' inverted L1s are probably not due to the action of the L1 endonuclease.
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“As the vast majority of L1s in the human genome are 5′ truncated (average L1 length is approximately 900bp, 90-95% of all L1s are 5′trunctated), this analysis was unsurprisingly skewed towards the 3′ end of L1s.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [53]
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · cited 1×
“The BLASTX program [45] was used to translate our set of full-length L1 DNA sequences in all three reading frames and compare them to the L1.”
MethodInitial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Sequence logos: a new way to display consensus sequences
Schneider, T. D., & Stephens, R. M. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.20.6097 · Cited by 3,354 · cited 1×
“DNA sequence logos [59] of TSDs were generated using binary code downloaded from the site [60].”
MethodBLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
Tatusova, T. A., & Madden, T. L. (1999) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1999.tb13575.x · Cited by 1,789
The Sequence of the Human Genome
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“L1 poly(A) tails During the process of TPRT, whereby a copy of an L1 is inserted into the genome, reverse transcription is believed to be primed on the poly(A) tail of the L1 transcript [12,14,17,27].”
BackgroundHuman L1 retrotransposon encodes a conserved endonuclease required for retrotransposition
Feng, Q., Moran, J. V., Kazazian, H. H., & Boeke, J. D. (1996) · Cell · doi:10.1016/s0092-8674(00)81997-2 · Cited by 1,139 · cited 7×
“The functional significance of ORF1 is not clear, whereas ORF2 contains three domains critical for L1 propagation: endonuclease [12], reverse transcriptase [7,13], and a 3 ́-terminal Zn finger-like domain [14].”
BackgroundResultInfluentialSelf-citationHigh frequency retrotransposition in cultured mammalian cells
Moran, J. V., Holmes, S. E., Naas, T. P., DeBerardinis, R. J., Boeke, J. D., & Kazazian, H. H. (1996) · Cell · doi:10.1016/s0092-8674(00)81998-4 · Cited by 1,022 · cited 10×
“The functional significance of ORF1 is not clear, whereas ORF2 contains three domains critical for L1 propagation: endonuclease [12], reverse transcriptase [7,13], and a 3 ́-terminal Zn finger-like domain [14].”
BackgroundInfluentialSelf-citationFour Evolutionary Strata on the Human X Chromosome
Lahn, B. T., & Page, D. C. (1999) · Science · doi:10.1126/science.286.5441.964 · Cited by 1,010 · cited 1×
“Furthermore, the concentration of L1s with TSDs on the p arm of the X chromosome is lower than that on the q arm (Figure 8). Lahn and Page [ 52 ] have hypothesized that the distal p arm is the site of the youngest evolutionary strata on the X chromosome, indicating that the X and Y chromosomes actively recombined at t…”
Background
Research works printed but not linked: 4
- Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, Boeke JD: Human L1 retrotransposition is associated with genetic instability in vivo. Cell. 2002, 110: 327-338. · DOI
- Pickeral OK: Bioinformatics of human retrotransposons. PhD dissertation. Edited by: Baltimore MD. 2000, The Johns Hopkins University
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- BLAST 2 Sequences. [http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html]
Cited by
Sorted by citations
The impact of retrotransposons on human genome evolution
Cordaux, R., & Batzer, M. A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2640 · Cited by 1,692
“Indeed, as a result of TPRT and decay over time, most L1 copies are inactivated by truncations, internal rearrangements and mutation”
Ten things you should know about transposable elements
Bourque, G., Burns, K. H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin, H. L., Macfarlan, T. S., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1577-z · Cited by 1,430
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
“Most LINE-1 s in the human genome are grossly truncated at their 5′-end [6, 36, 37].”
BackgroundInfluentialActive human retrotransposons: variation and disease
Hancks, D. C., & Kazazian, H. H. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.02.006 · Cited by 592
Human L1 element target‐primed reverse transcription in vitro
Cost, G. J., Feng, Q., Jacquier, A., & Boeke, J. D. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf592 · Cited by 519
Self-citation
Metadata
- Authors
- Szak, S. T., Pickeral, O. K., Makalowski, W., Boguski, M. S., Landsman, D., & Boeke, J. D.
- Affiliations
- National Institutes of Health (US)
- Human Genome Sciences (United States) (US)
- Johns Hopkins University (US)
- Corresponding author
- Boeke, Jef D
- Venue
- Genome Biology
- Published
- 2002-09-19
- Volume
- 3
- Issue
- 10
- Pages
- research0052-research0052
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC134481
- OpenAlex
- W2139253234
- Cited by
- 230
- References
- 55
- Citations by year
- 2026: 8 · 2025: 12 · 2024: 6 · 2023: 10 · 2022: 9 · 2021: 9 · 2020: 2 · 2019: 4 · 2018: 7 · 2017: 10 · 2016: 10 · 2015: 12 · 2014: 17 · 2013: 9 · 2012: 6
- FWCI
- 12.67
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (CA-16519, P01CA016519)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › 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
- LINE-1 retrotransposons, human genome, transposon insertion, target site duplication, poly(A) tail, structural variants
- MeSH terms
- Algorithms, Base Sequence, Binding Sites, Humans, Poly A, Recombination, Genetic, Genome, Human, Mutagenesis, Insertional, Retroelements, Computational Biology
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