Molecular archeology of L1 insertions in the human genome.

Suzanne T. Szak, Oxana K. Pickeral, Wojciech Makalowski, Mark S. Boguski, David Landsman, Jef D. Boeke

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
JournalGenome Biology
Volume3
Issue number10
StatePublished - Sep 19 2002
Externally publishedYes

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Long Interspersed Nucleotide Elements
Archaeology
Human Genome
archaeology
Endonucleases
genome
Anatomy
transposons
anatomy
cleavage
Genome
Computational Biology
loci
bioinformatics
messenger RNA
Software
genomics
Messenger RNA
DNA
software

ASJC Scopus subject areas

  • Genetics

Cite this

Szak, S. T., Pickeral, O. K., Makalowski, W., Boguski, M. S., Landsman, D., & Boeke, J. D. (2002). Molecular archeology of L1 insertions in the human genome. Genome Biology, 3(10).

Molecular archeology of L1 insertions in the human genome. / Szak, Suzanne T.; Pickeral, Oxana K.; Makalowski, Wojciech; Boguski, Mark S.; Landsman, David; Boeke, Jef D.

In: Genome Biology, Vol. 3, No. 10, 19.09.2002.

Research output: Contribution to journalArticle

Szak, ST, Pickeral, OK, Makalowski, W, Boguski, MS, Landsman, D & Boeke, JD 2002, 'Molecular archeology of L1 insertions in the human genome.', Genome Biology, vol. 3, no. 10.
Szak ST, Pickeral OK, Makalowski W, Boguski MS, Landsman D, Boeke JD. Molecular archeology of L1 insertions in the human genome. Genome Biology. 2002 Sep 19;3(10).
Szak, Suzanne T. ; Pickeral, Oxana K. ; Makalowski, Wojciech ; Boguski, Mark S. ; Landsman, David ; Boeke, Jef D. / Molecular archeology of L1 insertions in the human genome. In: Genome Biology. 2002 ; Vol. 3, No. 10.
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