Genome-wide distribution and potential regulatory functions of AtATE, a novel family of miniature inverted-repeat transposable elements in Arabidopsis thaliana.
A study of transgenic promoter::beta-glucuronidase lines showed that the promoters of the two Arabidopsis ARGININE DECARBOXYLASE paralogues, ADC1 and ADC2, exhibited extremely different patterns of activity. One major feature of the promoter of ADC1 was the presence of a novel transposable element, which was shown to possess all of the characteristics of Miniature Inverted-repeat Transposable Elements (MITEs), and to be present in 26 full-length copies and 1617 partial copies and fragments distributed throughout the Arabidopsis genome. TRANSFAC analysis showed that this transposable element possesses a significant number of transcription-factor binding motifs. A bioinformatics approach based on a suffix-tree compilation was used to obtain an exhaustive description of exact copy numbers and positions of the element in the Arabidopsis genome. The distribution among the chromosomes was non-random, and a significant number of copies were found in regions flanking genes. Full-length copies of the transposable element were detected in the immediate vicinity of 22 genes, either upstream or downstream.
Centre National de la Recherche Scientifique, Université de Rennes 1, UMR 6553, Campus de Beaulieu, Bâtiment 14, 263 Avenue du Général Leclerc, 35042 Rennes Cedex, France. Abdelhak.Elamrani@univ-rennes1.fr
A
A
El Amrani
L
L
Marie
A
A
Aïnouche
J
J
Nicolas
I
I
Couée
D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics*; D001483:Base Sequence; D002262:Carboxy-Lyases / Q000235:genetics; D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D020440:Gene Duplication; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D005966:Glucuronidase / Q000235:genetics; D007527:Isoenzymes / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid
D004251:DNA Transposable Elements; D018744:DNA, Plant; D007527:Isoenzymes; D005966:Glucuronidase; D002262:Carboxy-Lyases; C019722:arginine decarboxylase