Plant Transposable Elements

Abstract

Genomic programs are yielding tremendous amounts of data about plant genomes and their expression. In order to exploit and understand this data it will be necessary to determine the mechanisms leading to natural variation of patterns of gene expression. The ability to understand how gene expression varies among populations (and not only within the population used in the genomics program) and following the exposure of plants to various stress conditions will be fundamental to progress in the post-genomics phase. Transposable elements (TEs) make up nearly half of the total amount of DNA in many plant genomes, so definition of their influence on genome structure and gene expression is of clear significance to the understanding of global genome regulation and phenotype variations. We describe here the different types of plant TEs and recent examples on how they contribute to structure, evolution and genetic control architecture of plant genomes.

Mechanisms of Transposable Element Evolution in Plants and Their Effects on Gene Expression

“…In general, class I TEs tend to be distributed farther from genes than are class II TEs [35]. Although some LTR retrotransposons show no insertional preference [107], TE families with a preference towards euchromatic regions include miniature inverted repeat elements (MITEs), SINEs, helitrons, CACTAs, and MULEs [19,96,[108][109][110][111]. Likewise, the Ds/Spm family preferentially inserts in GC-rich regions around translational initiation sites [112], with a similar insertion pattern noted for the BraSto MITE family in Brassica species [113].…”

“…Approximately 8-10 % of A. thaliana and rice genes harbor TE fragments, with En/Spm-like and Copialike TEs and kinase genes overrepresented in A. thaliana [189,190]. Some TE-gene chimeras retain DNA-binding ability in the form of transcription factors [19]. Given the specificity of transposase for binding sites within TEs, this means that domesticated TE transcription factors could be targeted to transposed TEs in such a way that both the DNA sequence and the encoded DNA-binding protein are effectively "co-domesticated," forming new regulatory networks [19].…”

“…The most common family of TEs in plants is the long terminal repeat (LTR) retrotransposons, with the LTRs defining the transcriptional direction and boundaries of the TE [16][17][18]. Other class I retrotransposons include autonomous long interspersed elements (LINEs) and nonautonomous short interspersed elements (SINEs) that are derived from transfer RNAs (tRNAs) [19]. …”

Seleção deprimerspara análise deinter simple sequence repeatsna cultivar ‘Itália’ deVitis viníferaL.

“…Elementos transponíveis (TES) são relatados como os maiores contribuintes para estimular a variabilidade do genoma e, em particular, para promover mutações somáticas (Collier e Largaespada, 2007;Deragon et al, 2008). Benjak et al (2009) descreveram um alto número de elementos transponíveis, e estes possuem sequências genômicas transduplicadas e amplificadas, incluindo sequências de genes e fragmentos de outros elementos móveis.…”

Mosquitoes LTR Retrotransposons: A Deeper View into the Genomic Sequence of Culex quinquefasciatus

“…Class I elements can be further categorized in LTR- and non-LTR retrotransposons depending on the presence or absence of direct terminal repeats. Retrotransposons are major components of eukaryotic genomes; they are among the strongest evolutionary driving force acting on the genomes [5], and are potentially able to change gene expression patterns [6] [7]. Their ability to inflate eukaryotic genome size [8] is also at the basis for their use as molecular markers in organisms of socio-economic interest [9].…”