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Title: EGASP: the human ENCODE Genome Annotation Assessment Project
Author: Guigó Serra, Roderic
Flicek, Paul
Abril Ferrando, Josep Francesc, 1970-
Reymond, Alexandre
Lagarde, Julien
Denoeud, France
Antonarakis, Stylianos E.
Ashburner, Michael
Bajic, Vladimir B.
Birney, Ewan
Castelo, Robert
Eyras, Eduardo
Ucla, Catherine
Gingeras, Thomas R.
Harrow, Jennifer
Hubbard, Tim
Lewis, Suzanna E.
Reese, Martin G.
Keywords: Genoma humà
Human genome
DNA Sequence Analysis
Issue Date: 2006
Publisher: BioMed Central
Abstract: Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.
Note: Reproducció del document publicat a
It is part of: Genome Biology, 2006, vol. 7, Suppl. 1:S2
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ISSN: 1465-6914
Appears in Collections:Articles publicats en revistes (Genètica, Microbiologia i Estadística)

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