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Developing informatic resources for LINE-1 retrotransposons

By Robert Kevin Hastings

Abstract

The human genome contains vast numbers of sequences that have copied themselves to new genomic locations by retrotransposition. Long Interspersed Nuclear Element-1 (LINE-1 or L1) is the only sequence in the human genome still capable of autonomous retrotransposition. L1 elements have contributed to the evolution of the human genome via insertional mutagenesis, pseudogene formation, sequence transduction, and recombination events (producing insertions, deletions and inversions). Currently general and L1- specific sequence databases do not reflect the true level of Full Length Human Specific L1 (FL-L1HS) variation, due to the polymorphic nature of these elements and the way the databases were compiled.\ud Methods to identify FL-L1HS were applied to three sequence assemblies (Reference, Celera and HuRef) and the nucleotide accession database from NCBI. A non-redundant set of 533 FL-L1HS was discovered in these four sources, of which 164 resided in genes. The trace archives from Ensembl were also searched and a further 48 potential FL-L1HS were found. Computational analyses showed 154 FL-L1HS were potentially capable of retrotransposition, including 54 that resided in genes. Alongside these analyses a Target Site Duplication (TSD) detection and analysis tool, TSDmapper was developed to automatically detect TSDs in FL-L1HS sequences and provide annotation on sequence transduction. TSDmapper was used to predict the pre-insertion sequence of all 533 unique L1s, which facilitated in-silico genotyping.\ud A new informatic resource, baseLINE (http://baseline.gene.le.ac.uk), was created to display and enable searching of all the L1 annotation information generated. Data can be viewed in a genomic context in chromosome ideograms or can be exported via the Distributed Annotation Service (DAS) on to the Ensembl genome browser. TSDmapper is also provided as a web application at baseline for users to perform TSD annotation of their sequences of interest

Publisher: University of Leicester
Year: 2009
OAI identifier: oai:lra.le.ac.uk:2381/8218

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  1. (2002). A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3’ terminus of l1. doi
  2. (1998). Allelic heterogeneity in LINE-1 retrotransposition activity.
  3. (1990). An Alu insert as the cause of a severe form of hemophilia A. doi
  4. (1993). Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable element. doi
  5. (2006). dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. doi
  6. (2004). Finishing the euchromatic sequence of the human genome. doi
  7. (2006). Fitness cost of LINE-1 (L1) activity in humans.
  8. (1999). Full-length human L1 insertions retain the capacity for high frequency retrotransposition in cultured cells. doi
  9. (1999). Hereditary desmoid disease in a family with a germline Alu I repeat mutation of the APC gene. Human Heredity, doi
  10. (2003). Hot L1s account for the bulk of retrotransposition in the human population. doi
  11. (2002). Human l1 retrotransposition is associated with genetic instability in vivo. doi
  12. (1990). Identification of a novel large F9 gene mutation-an insertion of an Alu repeated DNA element in exon e of the factor 9 gene. Human Mutation, doi
  13. (1988). Improved tools for biological sequence comparison. doi
  14. (2008). Nucleic Acids Research, 36(Database issue), doi
  15. (1996). RepeatMasker Open-3.0. URL: http://www.repeatmasker.org 44, 78,
  16. (1993). Reverse transcriptase encoded by a human transposable element. doi
  17. (1995). RNA polymerase III dependence of the human L1 promoter and possible participation of the RNA polymerase II factor YY1 in the RNA polymerase III transcription system. doi
  18. (1950). The desoxyribose nucleic acid content of animal nuclei. doi
  19. (2008). The diploid genome sequence of an Asian individual.
  20. (2003). The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. doi
  21. (2001). The sequence of the human genome. doi
  22. (2005). The structures of mouse and human L1 elements reflect their insertion mechanism. doi
  23. (2003). Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. doi
  24. (1990). Unconventional translation of mammalian LINE-1 retrotransposons.
  25. (1995). Wholegenome random sequencing and assembly of Haemophilus influenzae Rd. doi

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