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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
Venter, J. C., Smith, H. O., & Adams, M. D. (2015) · Clinical Chemistry · doi:10.1373/clinchem.2014.237016 · Cited by 1,665
Luan, D. D., Korman, M. H., Jakubczak, J. L., & Eickbush, T. H. (1993) · Cell · doi:10.1016/0092-8674(93)90078-5 · Cited by 1,173 · cited 2×
“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
- NCBI Computational Biology Branch: David Landsman's group. [http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/]
- BLAST 2 Sequences. [http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html]
Cited by
Sorted by citations
Items 101–200 of 238
Gallus, S., Hallström, B. M., Kumar, V., Dodt, W. G., Janke, A., Schumann, G. G., & Nilsson, M. A. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv017 · Cited by 27
“Additional sequencing problems come from homopolymeric poly(A) stretches which are located, for instance, at the 30-ends of younger L1 insertions and range from 10–85 nt (Szak et al. 2002).”
BackgroundTransposable elements as instructors of the immune system
Schmidleithner, L., Stüve, P., & Feuerer, M. (2025) · Nature reviews. Immunology · doi:10.1038/s41577-025-01172-3 · Cited by 35
“Although TEs are still relatively active in many lower organisms, such as bacteria, they have been mostly inactivated over time in the human genome due to accumulated mutations or active silencing by the host organism (Box 1) and are consequently no longer as mobile 5,6 .”
Adney, E. M., Ochmann, M. T., Sil, S., Truong, D. M., Mita, P., Wang, X., Kahler, D. J., Fenyö, D., Holt, L. J., & Boeke, J. D. (2019) · Genetics · doi:10.1534/genetics.119.302601 · Cited by 27
Self-citationHedges, D. J., & Belancio, V. P. (2011) · Advances in genetics · doi:10.1016/b978-0-12-380860-8.00006-9 · Cited by 21
Lock, F. E., Babaian, A., Zhang, Y., Gagnier, L., Kuah, S., Weberling, A., Karimi, M. M., & Mager, D. L. (2017) · PLoS ONE · doi:10.1371/journal.pone.0180659 · Cited by 24
Gentles, A. J., Kohany, O., & Jurka, J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi188 · Cited by 23
“The second consensus nicking signal (5#-ANTNTN-AA) weakly resembles the first nicking signal (5#-TTTT-AA), as previously suggested (Szak et al. 2002).”
BackgroundThe Changing Tails of a Novel Short Interspersed Element in Aedes aegypti
Tu, Z. J., Li, S., & Mao, C. (2004) · Genetics · doi:10.1534/genetics.104.032045 · Cited by 23
Transposable Element Annotation in Completely Sequenced Eukaryote Genomes
Flutre, T., Permal, E., & Quesneville, H. (2012) · Topics in current genetics · doi:10.1007/978-3-642-31842-9_2 · Cited by 22
“TSDfinder (Szak et al. 2002) is based on the L1 TE insertion signature which is constituted in part by two Target Site Duplications (TSDs) and a polyA tail.”
BackgroundTanaka, A., Nakatani, Y., Hamada, N., Jinno‐Oue, A., Shimizu, N., Wada, S., Funayama, T., Mori, T., Islam, S., Hoque, S. A., et al. (2012) · Mutagenesis · doi:10.1093/mutage/ges025 · Cited by 23
The Flow of the Gibbon LAVA Element Is Facilitated by the LINE-1 Retrotransposition Machinery
Meyer, T. J., Held, U., Nevonen, K. A., Jung‐Klawitter, S., Pirzer, T., Carbone, L., & Schumann, G. G. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw224 · Cited by 22
“Subfamily LAVA_B consists of a large and diverse expansion of ten small and midsized subfamilies that evolved between 12 and 18 mya.”
BackgroundLINEs of evidence: noncanonical DNA replication as an epigenetic determinant
Belan, E. (2013) · Biology Direct · doi:10.1186/1745-6150-8-22 · Cited by 22
“The fact that “synthetic” and endogenous L1s target the same consensus sequence [127,134], but”
BackgroundLine-1: Implications in the etiology of cancer, clinical applications, and pharmacologic targets
Khalid, M., Bojang, P., Hassanin, A. A. I., Bowers, E. C., Reyes‐Reyes, E. M., Ramos, I. N., & Ramos, K. S. (2018) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2018.09.003 · Cited by 21
Internal priming: An opportunistic pathway for L1 and Alu retrotransposition in hominins
Srikanta, D., Sen, S. K., Conlin, E. M., & Batzer, M. A. (2009) · Gene · doi:10.1016/j.gene.2009.05.014 · Cited by 20
“To explore that a similar integration mechanism is active in vivo, we scanned the human genome for truncated Alu and L1 elements with TSDs≥6 bp (Szak et al., 2002).”
InfluentialCheng, L., Pai, T., & Li, L. (2011) · Steroids · doi:10.1016/j.steroids.2011.10.010 · Cited by 20
Grechishnikova, D., & Poptsova, M. S. (2016) · BMC Genomics · doi:10.1186/s12864-016-3344-4 · Cited by 20
“Most of L1s found in the human genome are 5′-end truncated or damaged and therefore have lost the retrotransposition ability [2].”
BackgroundInfluentialMechanism of Alu integration into the human genome
Chen, J., Férec, C., & Cooper, D. N. (2007) · Genomic Medicine · doi:10.1007/s11568-007-9002-9 · Cited by 18
“Studies of recently inserted genomic L1 elements in the human genome (Myers et al. 2002; Pavlicek et al. 2002; Szak et al. 2002; Boissinot et al. 2004), pathological L1 direct insertions (Chen et al.”
BackgroundLaha, T., Kewgrai, N., Loukas, A. C., & Brindley, P. J. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-154 · Cited by 19
“For the L1 elements in the human genome, a new L1 insertion is usually flanked by short direct repeats derived from the target DNA locus upon L1 integration [32,36].”
BackgroundInfluentialAn abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris
Wenke, T., Holtgräwe, D., Horn, A. V., Weißhaar, B., & Schmidt, T. (2009) · Plant Molecular Biology · doi:10.1007/s11103-009-9542-6 · Cited by 18
“The population of 50 truncated L1 copies in human shows also correlation between reverse transcript length and copy number (Szak et al. 2002).”
BackgroundRamos, K. S., Bojang, P., & Bowers, E. C. (2021) · Experimental Biology and Medicine · doi:10.1177/15353702211031247 · Cited by 19
Recent Advances in Double-Strand Break-Free Kilobase-Scale Genome Editing Technologies
Tou, C. J., & Kleinstiver, B. P. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00311 · Cited by 17
An update on post‐transcriptional regulation of retrotransposons
Warkocki, Z. (2022) · FEBS Letters · doi:10.1002/1873-3468.14551 · Cited by 19
High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements
Lee, J., Mun, S., Meyer, T. J., & Han, K. (2012) · Comparative and Functional Genomics · doi:10.1155/2012/129416 · Cited by 17
“Most previous studies of human-specific L1s focused on the 3′ UTRs rather than the 5′ UTRs because over 90% of L1 elements are 5′ truncated [19, 20], a result of the termination of reverse transcription, for unknown reasons, before the”
Singh, D. K., & Rath, P. C. (2012) · RNA Biology · doi:10.4161/rna.22402 · Cited by 17
“, in the human X chromosome.(12,13) Distribution of L1s in the genome differs with respect to their size and evolutionary age.”
BackgroundMonti, V., Serafini, C., Manicardi, G. C., & Mandrioli, M. (2013) · Journal of Heredity · doi:10.1093/jhered/est017 · Cited by 17
Spliced integrated retrotransposed element (SpIRE) formation in the human genome
Larson, P. A., Moldovan, J. B., Jasti, N., Kidd, J. M., Beck, C. R., & Moran, J. V. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2003067 · Cited by 20
Molecular and Temporal Characteristics of Human Retropseudogenes
Devor, E. J., & Moffat-Wilson, K. A. (2003) · Human Biology · doi:10.1353/hub.2003.0075 · Cited by 16
“The prevailing model of retroelement, or retroposon, mobilization involves endogenous retrotranscription of an RNA species (cf. Maestre et al. 1995) followed by enzymatically mediated retroposition (Sassaman et al. 1997; Jurka 1997; Cost and Boeke 1998; Szak et al. 2002).”
BackgroundInfluentialLINE-1 activation and epigenetic silencing of suppressor genes in cancer
Tufarelli, C., Cruickshanks, H. A., & Meehan, R. R. (2013) · Mobile Genetic Elements · doi:10.4161/mge.26832 · Cited by 17
mRNA Retrotransposition Coupled with 5' Inversion as a Possible Source of New Genes
Kojima, K. K., & Okada, N. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp050 · Cited by 15
Wang, C., & Liang, C. (2022) · Scientific Reports · doi:10.1038/s41598-021-04208-5 · Cited by 14
Discovery of short pseudogenes derived from messenger RNAs
Terai, G., Yoshizawa, A., Okida, H., Asai, K., & Mitsuyama, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1098 · Cited by 13
“Comparison of TSDscan with existing methods of identifying retrotransposed elements Two other software packages, RTanalyzer (30) and TSDfinder (27), are available to detect retrotransposed elements.”
BackgroundMethodInfluentialSOX ‐11 regulates LINE ‐1 retrotransposon activity during neuronal differentiation
Orqueda, A. J., Gatti, C. R., Ogara, M. F., & Falzone, T. L. (2018) · FEBS Letters · doi:10.1002/1873-3468.13260 · Cited by 15
Heads or tails: L1 insertion-associated 5' homopolymeric sequences
Meyer, T. J., Srikanta, D., Conlin, E. M., & Batzer, M. A. (2010) · Mobile DNA · doi:10.1186/1759-8753-1-7 · Cited by 11
“Top strand cleavage, integration of the cDNA, and synthesis of a top strand complement to the cDNA complete the insertion, leaving the structural hallmarks of classical TPRT: intact target site duplications (TSDs), a typical EN cleavage site motif, and a variable length poly(A) tail [17,20,23,24].”
BackgroundVondrak, T., de Oliveira, L. C., Novák, P., Koblížková, A., Neumann, P., & Macas, J. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.04.011 · Cited by 12
“These two insertion sites had consensus sequences of 5 0 -TTCTA-3 0 and 5 0 -TTTCAA-3 0 , similar to the cannonical cleavage site of mammalian L1 elements (5 0 -TTTTAA-3 0 ) [47] .”
BackgroundDiscovery of a new repeat family in the Callithrix jacchus genomePreprint
Konkel, M. K., Ullmer, B., Arceneaux, E. L., Sanampudi, S., Brantley, S. A., Hubley, R., Smit, A. F. A., & Batzer, M. A. (2016) · Genome Research · doi:10.1101/gr.199075.115 · Cited by 12
Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons
Nishiyama, E., & Ohshima, K. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy098 · Cited by 11
“The sequence of an Oryzias RTE of medaka fish (clone OlRTE-a03; GenBank: AB021490) was obtained from Zupunski et al. (2001), and the sequence of a lizard RTE of green anole (clone AcRTE-a01; GenBank: AAWZ01014759) was obtained from Tay et al. (2010).”
BackgroundMethodInfluentialUnbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9
Briggs, E. M., Mita, P., Sun, X., Ha, S., Vasilyev, N., Leopold, Z., Nudler, E., Boeke, J. D., & Logan, S. K. (2021) · Mobile DNA · doi:10.1186/s13100-021-00249-9 · Cited by 13
“These nonfunctional sequences are predominantly ancestral LINE-1 sequences, including subfamilies L1PA2-L1PA7, which can no longer mobilize [1, 4, 5].”
BackgroundSelf-citationMarsano, R. M., Marconi, S., Moschetti, R., Barsanti, P., Caggese, C., & Caizzi, R. (2003) · Molecular Genetics and Genomics · doi:10.1007/s00438-003-0947-7 · Cited by 11
“In addition, the development of new in silico approaches (Bao and Eddy 2002; Szak et al. 2002) and better criteria for the analysis of genomic databases (Berezikov et al. 2000; Bowen and McDonald 2001;Kaminker et al. 2002) has permitted the discovery of TE families that had previously escaped…”
BackgroundThe Potential Regulation of L1 Mobility by RNA Interference
Horman, S. R., Svoboda, P., & Prak, E. T. L. (2006) · BioMed Research International · doi:10.1155/jbb/2006/32713 · Cited by 10
“A high copy number of L1 sequences in mammalian genomes increases the likelihood of generating inverted repeats either by genome rearrangements or by insertions of L1 elements into or near themselves [44].”
BackgroundEvolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome
Yang, L., Metzger, G. A., Valle, R. P. D., Rubalcaba, D. D., & McLaughlin, R. N. (2023) · The EMBO Journal · doi:10.1038/s44318-023-00007-y · Cited by 11
“…widely applied approach to approximate the in vivo fi tness of LINE-1s is counting the number of 3 ’ transductions generated by speci fi c LINE-1s (Szak et al, 2002), but is limited by the small proportion of LINE-1 retrotranspositions that carry 3 ’ transductions - approximately 15% (Szak et al,…”
InfluentialThe Regulation and Immune Signature of Retrotransposons in Cancer
Alkailani, M. I., & Gibbings, D. (2023) · Cancers · doi:10.3390/cancers15174340 · Cited by 10
Marsano, R. M., & Caizzi, R. (2005) · Gene · doi:10.1016/j.gene.2005.06.010 · Cited by 10
Nuclear dualism without extensive DNA elimination in the ciliate Loxodes magnus
Seah, B. K. B., Singh, A. D., Vetter, D. E., Emmerich, C., Peters, M. A., Soltys, V., Hüettel, B., & Swart, E. C. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2400503121 · Cited by 9
Mangoni, D., Mazzetti, A., Ansaloni, F., Simi, A., Tartaglia, G. G., Pandolfini, L., Gustincich, S., & Sanges, R. (2024) · BioEssays · doi:10.1002/bies.202400125 · Cited by 9
The 5′ truncation of retrotransposon L1: a process of genome integrity
Levin, H. L., Lee, S., & Anand, A. (2025) · Genetics · doi:10.1093/genetics/iyaf202 · Cited by 13
Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies
Nguyen, A. K., Blacksmith, M. S., & Kidd, J. M. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae142 · Cited by 10
“We additionally investigated how many retrocopies retained the signature hallmarks of retrotransposition, which are the presence of target-site duplications (TSDs) and poly(A) tails (Szak et al. 2002; Fig.”
BackgroundTarget site analysis of RTE1_LA and its AfroSINE partner in the elephant genome
Gilbert, C., Pace, J. K., & Waters, P. D. (2008) · Gene · doi:10.1016/j.gene.2008.08.013 · Cited by 9
Solovyov, A., Behr, J. M., Hoyos, D., Banks, E., Drong, A., Zhong, J. Z., Garcia-Rivera, E., McKerrow, W., Chu, C., Zaller, D. M., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.11.539471 · Cited by 9
Identification of novel LTR retrotransposons in the genome of Aedes aegypti
Minervini, C. F., Viggiano, L., Caizzi, R., & Marsano, R. M. (2009) · Gene · doi:10.1016/j.gene.2009.03.021 · Cited by 8
“This strategy has been successfully applied to the identification of L1 insertions in the human genome (Szak et al., 2002), LTR retrotransposons insertions in A.”
MethodKhan, M., Shah, S., Lv, B., Lv, Z., Ji, N., Song, Z., Wu, P., Wang, X., & Mehmood, A. (2022) · Ocular Immunology and Inflammation · doi:10.1080/09273948.2022.2112238 · Cited by 8
Zhang, J., Tang, J., Li, G., Li, N., Wang, J., Yao, R., & Yu, T. (2023) · Journal of Thrombosis and Haemostasis · doi:10.1016/j.jtha.2023.08.012 · Cited by 8
L1 Regulation in Mouse and Human Germ Cells
Newkirk, S. J., & An, W. (2017) · Springer eBooks · doi:10.1007/978-3-319-48344-3_2 · Cited by 9
“, 5′ truncations, inversions, substitutions, INDELs, and any other types of debilitating mutations) render the elements incompetent (Szak et al. 2002).”
BackgroundLee, H., Min, J. W., Mun, S., & Han, K. (2022) · Life · doi:10.3390/life12101583 · Cited by 9
“Newly inserted L1 elements have hallmark features of 2~20 base pairs flanking target site duplications (TSDs) [1,42].”
BackgroundRegulation of mammalian LINE1 retrotransposon transcription
Fedorov, A. V. (2009) · Cell and Tissue Biology · doi:10.1134/s1990519x09010015 · Cited by 7
“This hypoth- 6 CELL AND TISSUE BIOLOGY Vol. 3 No. 1 2009 FEDOROV esis is supported by computer assay data, which demonstrated that L1 fragments are present in both sense and antisense orientation in introns and nontranslated regions of 9% human genes (Szak et al., 2002).”
BackgroundMethodZhang, K., Fan, W., Deininger, P. L., Edwards, A., Xu, Z., & Zhu, D. (2009) · International Journal of Computational Biology and Drug Design · doi:10.1504/ijcbdd.2009.030763 · Cited by 7
“It is worth noting that, for both sets of PAI sequences, we only consider those from Alu Y family and of the perfect TSDs, that is, the 5′ TSD exactly matches the 3′ TSD. TSDs are indentified by applying TSDFinder (Szak et al., 2002) to the annotated human and chimpanzee genomes available at UCSC Genome Browser (http:…”
BackgroundMethodInfluentialRetrotransposable genetic elements causing neutrophil defects
Roos, D., & de Boer, M. (2018) · European Journal of Clinical Investigation · doi:10.1111/eci.12953 · Cited by 8
Laha, T., Kewgrai, N., Loukas, A. C., & Brindley, P. J. (2006) · Experimental Parasitology · doi:10.1016/j.exppara.2005.12.018 · Cited by 7
“By way of comparison, L1 elements apparently integrate at numerous sites in the human genome because EN of L1 preferably cleaves DNA at the short consensus sequence, 5 -TTTT/A-3 (where/designates the cleavage site) (Szak et al., 2002).”
BackgroundLINE‐1 Retrotransposition: Impact on Genome Stabilityand Diversity and Human Disease
Prak, N. L., & Haoudi, A. (2006) · BioMed Research International · doi:10.1155/jbb/2006/37049 · Cited by 7
Intragenic L1 Insertion: One Possibility of Brain Disorder
Son, J.-H., Do, H., & Han, J. (2022) · Life · doi:10.3390/life12091425 · Cited by 6
“The ssDNA works as the primer that allows ORF2p to initiate reverse transcription of L1 RNAs.”
BackgroundInfluentialRamos, K. S., Teneng, I., Montoya-Durango, D. E., Bojang, P., Haeberle, M. T., Ramos, I. N., Stribinskis, V., & Kalbfleisch, T. (2013) · Epigenetics and human health · doi:10.1007/978-3-642-23380-7_6 · Cited by 6
Insights into the DNA cleavage mechanism of human LINE‐1 retrotransposon endonuclease
Repanas, K., Fuentes, G., Cohen, S. X., Bonvin, A. M. J. J., & Anastassis Perrakis, A. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22201 · Cited by 6
Characterization of LINE-1 transposons in a human genome at allelic resolutionPreprint
Yang, L., Metzger, G. A., & McLaughlin, R. N. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/594200 · Cited by 6
“expected from the often abortive 3’-5’ target-primed reverse transcription of LINE-1s (Szak et al. 2002).”
BackgroundStructural features of somatic and germline retrotransposition events in humans
Sulo, P., Cajuso, T., Norri, T., Taira, A., Kuisma, H., Välimäki, N., Lepistö, A., Renkonen‐Sinisalo, L., Koskensalo, S., Seppälä, T. T., et al. (2025) · Mobile DNA · doi:10.1186/s13100-025-00357-w · Cited by 6
“We investigated whether we could identify EN cut sites, however no additional EN motifs or recurrent patterns were present, consistent with the findings reported in Szak et al. [48].”
InfluentialHarrington, A. W., & Steiniger, M. (2016) · Fly · doi:10.1080/19336934.2016.1165372 · Cited by 5
Rajagopalan, M., Balasubramanian, S., & Ramaswamy, A. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.07.002 · Cited by 5
“to recognize the flexible T-A sequence at the DNA minor groove for phosphodiester hydrolysis [35].”
BackgroundA comprehensive analysis of gorilla-specific LINE-1 retrotransposons
Jeon, S., Kim, S., Oh, M. H., Liang, P., Tang, W., & Han, K. (2021) · Genes & Genomics · doi:10.1007/s13258-021-01146-4 · Cited by 5
Li, T. D., Toohill, K., & Modzelewski, A. J. (2025) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.70022 · Cited by 5
“Reverse transcription is an inefficient process that often leads to insertions being significantly truncated at their 5′ ends, reducing their 5′ un-translated regions (UTRs) and thus their own regulatory capacity (Ghanim et al. 2025; Kazazian and Moran 2017; Szak et al. 2002).”
Neural Transposition in the Drosophila Brain
Waddell, S., Barnstedt, O., & Treiber, C. D. (2014) · Advances in genetics · doi:10.1016/b978-0-12-800222-3.00004-8 · Cited by 5
“Reinserted elements are also frequently truncated, especially at the 5′ end of non-LTR elements (Szak et al., 2002).”
BackgroundPaulat, N. S., McGuire, E., Subramanian, K., Osmanski, A. B., Moreno-Santillán, D. D., Ray, D. A., & Xing, J. (2022) · Life · doi:10.3390/life12081190 · Cited by 4
“This is expected given that most LTR elements are solo-LTRs [44], while most LINEs are truncated [45].”
BackgroundKim, Y., Sung, H., Shin, H. S., Kim, M. J., Lee, J.-S., Park, S. S., & Seong, M. (2021) · Journal of Human Genetics · doi:10.1038/s10038-021-00967-1 · Cited by 5
A LINE-1 Element Insertion in the 5′-Noncoding Region of Caprine Growth Hormone Receptor Gene
Maj, A., & Zwierzchowski, L. (2005) · Biochemical Genetics · doi:10.1007/s10528-005-8162-3 · Cited by 4
“The TTAAAA sequence is identical to a consensus for LINE-1 endonucleases (Szak et al., 2002).”
MethodSela, N., Stern, A., Makałowski, W., Pupko, T., & Ast, G. (2008) · Biology Direct · doi:10.1186/1745-6150-3-41 · Cited by 4
“This may result in gene duplication or exon shuffling, subsequently enriching the protein repertoire [10-13].”
BackgroundNovel trends in genetics: transposable elements and their application in medicine.
Vand‐Rajabpour, F., Raoofian, R., Habibi, L., Akrami, S. M., & Tabrizi, M. H. (2014) · PubMed · Cited by 3
Identification of human-specific AluS elements through comparative genomics
Lee, J., Kim, Y., Mun, S., Kim, H., & Han, K. (2014) · Gene · doi:10.1016/j.gene.2014.11.005 · Cited by 3
Rangwala, S. H., & Richards, E. J. (2010) · Mobile DNA · doi:10.1186/1759-8753-1-10 · Cited by 3
“In mammals, the consensus for the LINE 5’ endonuclease cleavage site contains two thymines, whereas the duplicated target site often starts with a string of four adenines [14-16].”
Background[Dacron and polytetrafluoroethylene aorto-bifemoral grafts].
Davidovic, L. B., Lotina, S. I., Kostic, D. M., Cinara, I., Cvetkovic, S. D., Stojanović, P. L., Velimirović, L. B., Markovic, D. M., Pejkić, S., & Pavlović, G. (1997) · PubMed · Cited by 3
Mammalian small nucleolar RNAs are mobile genetic elements
Weber, M. J. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0020205.eor · Cited by 4
Repeat in Genomes: How and Why You Should Consider Them in Genome Analyses?
Lerat, E. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20227-6 · Cited by 3
“The identification of non-LTR retrotransposons has been the goal of some programs like TSDfinder (Szak et al. 2002) and SINEDR (Tu et al. 2004).”
MethodFourth-generation gene editors: Integration-based genome engineering
Kincaid, A. E., Hewitt, A. W., & Rajendra, K. C. (2026) · Molecular Therapy Advances · doi:10.1016/j.omta.2026.201753 · Cited by 2
“82,84 R2 retrotransposons R2 retrotransposons are a type of non-LTR retrotransposons that encode their own reverse transcriptase and endonuclease protein for site-specific integration.”
Comparative genomics reveals LINE-1 recombination with diverse RNAs
Law, C., & Burns, K. H. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101165 · Cited by 5
The evolutionary history and genomic impact of mammalian DNA transposons
Pace, J. K. (2009) · UTA ResearchCommons (University of Texas Arlington) · Cited by 2
Long Interspersed Nuclear Element (LINE-1/L1)
Ramos, K. S., & Bojang, P. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.01922-x · Cited by 2
LINE-1 Retrotransposons and Their Role in Cancer
Rahbari, R., Habibi, L., García-Puche, J. L., Badge, R. M., & Garcia-Perez, J. L. (2015) · Springer eBooks · doi:10.1007/978-94-017-9639-2_3 · Cited by 2
Bolger, I., Shaw, R., Tam, O. H., Roque, C. G., Jackson, C. A., O’Neill, K., Smith, C. M., Phatnani, H. P., Natarajan, K., & Hammell, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.09.698641 · Cited by 4
“Many TE copies in the genome represent fragments due to recombination, structural variation, and truncation during aborted transposition attempts 51,52 .”
The Computational Tools to Identify DNA Repeats and Motifs: A Systematic Review
Singh, K., Srivastava, S., Prabhu, A. A., & Kaur, N. (2024) · Current Topics in Medicinal Chemistry · doi:10.2174/0115680266331305241113172257 · Cited by 1
Cuarenta, A. (2025) · Neurobiology of Stress · doi:10.1016/j.ynstr.2025.100709 · Cited by 1
Regulatory roles of transposable elements on autism molecular neuropathology
Techaniyom, P., Korsirikoon, C., Chitta, P., & Sae‐Lee, C. (2025) · Epigenomics · doi:10.1080/17501911.2025.2501520 · Cited by 3
ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements
Travers, S. L., Khansa, A., & Ellison, C. E. (2025) · Mobile DNA · doi:10.1186/s13100-025-00389-2 · Cited by 2
“For instance, a common difficulty arises from the poorly defined 5 ′ boundaries of LINEs, which are frequently truncated during insertion [44].”
Suntsova, M., Modestov, A., Rabushko, E., Komarov, N., Gaziev, I., Novosadskaya, A., Barysionak, A., Захарова, Г. С., Shaban, N., Khristichenko, A., et al. (2026) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2026.111541 · Cited by 1
Devor, E. J. (2004) · Journal of Heredity · doi:10.1093/jhered/esh034 · Cited by 1
“Retropseudogenes are reverse transcribed from mature mRNAs using an endogenous reverse transcriptase (Maestre et al. 1995) and then mobilized for retroposition by L1 retroposon-encoded enzymes acting in trans (Cost and Boeke 1998; Esnault et al. 2000; Szak et al. 2001 ).”
Transposon regulation upon dynamic loss of DNA methylation
Walter, M. (2015) · HAL · doi:10.13140/rg.2.2.18747.21286 · Cited by 1
AGO2 slicing restrains RTL1 to prevent vascular defects and lethal neonatal muscle failurePreprint
Kumar, M., Maria, A. G., Moses, A., Prajapat, M., Clements, J., Kitazawa, M., Shiura, H., Fukuda, K., & Vidigal, J. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.02.646793 · Cited by 2
Dinámica evolutiva de los retrotransposones ALU en el genoma humano
Hackenberg, M. (2011) · Institutional Repository of the University of Granada (University of Granada)
Bandyopadhyay, N., Settles, A. M., & Kahveci, T. (2010) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/1854776.1854794
“The TSDfinder [27], refines the coordinates of the L1 insertions that are detected by RepeatMasker.”
MethodExamining Selective Pressures Shaping Retrotransposon Distribution Within Genes
Linker, S. B. (2014)
Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
Bojang, P., & Ramos, K. S. (2016) · Journal of Visualized Experiments · doi:10.3791/53753
LINE-1 Retrotransposable Elem ent DNA Accumulates in HIV-1-
Jones, R. B., Song, H., Xu, Y., Garrison, K. E., Buzdin, A. A., Anwar, N. M., Hunter, D. V., Mujib, S., Mihajlovic, V., Martin, E. S., et al. (2013)
Retrotransposon Contribution to Genomic Plasticity
Doucet-O’Hare, T. T., & Kazazian, H. H. (2017) · Springer eBooks · doi:10.1007/978-3-319-48344-3_3
Zhuang, J. (2015) · The Journal of the American Medical Association (JAMA) Network (American Medical Association) · doi:10.13028/m2q30p
“4a), which is consistent with previous findings about the L1 element in the human genome (Lee et al., 2012; Szak et al., 2002).”
ResultInterruptional Activity and Simulation of Transposable Elements
Jin, L. (2017) · University Library - University of Saskatchewan (University of Saskatchewan)
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
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 ›
Are you an author, or do you see a problem with this page? Request a review
