The contribution of transposable elements to Bos taurus gene structure

Almeida, Luciane Madureira; Silva, Israel Tojal da; Silva, Wilson A.; Castro, Juliana P.; Riggs, Penny K.; Carareto, Claudia M. A.; Amaral, M. E. J.

doi:10.1016/j.gene.2006.10.012

Cited by 33 publications

(38 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As in a previous study (Almeida et al, 2007), we retrieved the Bos taurus draft assembly (based on Btau_3.1) entries from GenBank and converted them to FASTA-formatted sequence files using the BioPerl toolkit (Stajich et al, 2002). These multifasta files contained exonic regions from 22,805 nuclear genes.…”

Section: Data Collection and Detection Of Transposable Elementsmentioning

confidence: 99%

“…However, nowadays, several segments derived from TEs have been found in coding regions of host genes (Nekrutenko and Li, 2001;Ganko et al, 2003;Britten, 2004;Lipatov et al, 2005;Iwashita et al, 2003Iwashita et al, , 2006Cordaux et al, 2006;Gotea and Makalowski, 2006;Sakai et al, 2007;Almeida et al, 2007). Although the most common event probably is the elimination of the TE sequence before translation by several post-transcriptional mechanisms, these sequences are in some cases required for proper expression and functionality of proteins (Gotea and Makalowski, 2006 This result was obtained using the RepeatMasker program.…”

Section: Evolutionary Significance Of Transposable Elements In Exonsmentioning

confidence: 99%

“…Recently, molecular and computational analyses have shown sequences of functional genes derived entirely from mobile element sequences (Britten, 2004;Mallet et al, 2004;Brandt et al, 2005;Iwashita et. al., 2006;Cordaux et al, 2006;Gotea and Makalowski, 2006;Volff, 2006;Sakai et al, 2006;Almeida et al, 2007). Iwashita et al (2003Iwashita et al ( , 2006 reported that bucentaur gene (bcnt 97 ), which encodes the craniofacial developmental protein1, recruited an AP-END of BovB/RTE as a coding exon, and Almeida et al (2007) observed that zinc finger 452 gene, involved in various cellular functions including cell proliferation, differentiation and apoptosis, recruited a Charlie 10 DNA transposon entirely as an exon.…”

Section: Introductionmentioning

confidence: 99%

“…al., 2006;Cordaux et al, 2006;Gotea and Makalowski, 2006;Volff, 2006;Sakai et al, 2006;Almeida et al, 2007). Iwashita et al (2003Iwashita et al ( , 2006 reported that bucentaur gene (bcnt 97 ), which encodes the craniofacial developmental protein1, recruited an AP-END of BovB/RTE as a coding exon, and Almeida et al (2007) observed that zinc finger 452 gene, involved in various cellular functions including cell proliferation, differentiation and apoptosis, recruited a Charlie 10 DNA transposon entirely as an exon. In this paper, we report a TE fragment as part of an exon of the bovine FAST kinase domains 3 (FASTKD3) gene, reinforcing that TE-derived sequences have been acquired or gene expression and function.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Report of a chimeric origin of transposable elements in a bovine-coding gene

Almeida¹,

Amaral²,

Silva³

et al. 2008

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ~85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage.

show abstract

Section: Data Collection and Detection Of Transposable Elementsmentioning

confidence: 99%

Section: Evolutionary Significance Of Transposable Elements In Exonsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Report of a chimeric origin of transposable elements in a bovine-coding gene

Almeida¹,

Amaral²,

Silva³

et al. 2008

Genet. Mol. Res.

View full text Add to dashboard Cite

show abstract

“…Transposable elements (TEs) are important components of genomes (Almeidaa et al 2007). TEs can constitute up to half of the genome mass in vertebrates (Zamudio & Bourc'his 2010).…”

Section: Introductionmentioning

confidence: 99%

The application of microarray technology to the identification of Tc1-like element sequences in fish genomes

Wenne

Handschuh

Poćwierz-Kotus

et al. 2011

Marine Biology Research

View full text Add to dashboard Cite

The phylogenetic relationships between Tc1 transposable elements have previously been reported for the genomes of some fish species. However, research in this field has been hindered by the low number of fish genome sequences available in databases. The application of a DNA microarray as a universal tool for Tc1 transposon sequence analysis in fish genomes is described here. A prototype oligonucleotide microarray was constructed and used to compare samples of genomic DNA isolated from selected fish species. These results, combined with earlier reported molecular analysis of Tc1 showed the usefulness of DNA microarray in the screening of transposon sequences.

show abstract

Bovine Genome Architecture

Adelson

2012

Bovine Genomics

View full text Add to dashboard Cite

The contribution of transposable elements to Bos taurus gene structure

Cited by 33 publications

References 82 publications

Report of a chimeric origin of transposable elements in a bovine-coding gene

Report of a chimeric origin of transposable elements in a bovine-coding gene

The application of microarray technology to the identification of Tc1-like element sequences in fish genomes

Bovine Genome Architecture

Contact Info

Product

Resources

About