CÉLULAS DE SILICIO POLICRISTALINO

Throughout the history of their study, transposons have been defined as parasitic DNA (ORGEL AND

CRICK 1980; SABOT AND SCHULMAN 2006; GIRARD AND HANNON 2008). Yet increasingly, examples have

been found which may justify the ubiquitous preservation of TEs within genotypes.

Maintenance of chromosome structure

Transposons constitute the majority of pericentromeric and telomeric heterochromatin in most

genomes (SLOTKIN AND MARTIENSSEN 2007). Sequence data show that the centromeric retrotransposon

(CR) lineage of Ty3-Gypsy retrotransposons, and their typical association with centromeric satellite

repeats, pre-date the divergence of the monocots and eudicots (DU et al. 2010). Aside from acting as

functional constituents of these chromosomal structures, it appears that TEs throughout the genome may be associated with maintaining the constitutive heterochromatin in a condensed state. In

Arabidopsis, 24-nucleotide siRNAs produced by TEs have been associated with centromere methylation and those produced by centromeric satellite repeats have likewise been linked to TE silencing (MAY et al. 2005).

The non-coding telomeres, which lie at the end of eukaryotic chromosomes, are thought to protect the euchromatic regions from erosion. They are composed of tandemly repetitive DNA, added via the reverse transcription of RNA templates by the enzyme telomerase. The similarity of telomerase in both structure and mechanism to the reverse transcriptase genes of non-LTR retrotransposons is

thought to be due to their descent from a common ancestral sequence (LINGNER et al. 1997). In fact,

in Drosophila, which does not have a telomerase homologue, the function of telomerase is replaced

by two non-LTR retrotransposons HeT-A and TART, which accumulate at the chromosome ends in a

developmentally controlled manner (PARDUE AND DEBARYSHE 2011).

Gene creation

By transporting fragments of endogenous genes during their mobilisation, TEs rearrange the genome, shuffling exon fragments and creating new ORFs. New sequence arrangements are subject

to selective pressures, those that persist contribute to genome evolution (KAZAZIAN 2004; FESCHOTTE

AND PRITHAM 2007).

An analysis of Mutator-like elements in rice revealed the ability of some of these elements to capture and transport portions of host genes throughout the genome as they transpose. Approximately one- fifth of over 3000 of these so-called Pack-MULEs were found to be carrying exons from multiple genome locations. Regions of over a thousand genes appear to have been mobilised in this way (JIANG et al. 2004). Pack-MULEs have since also been found in the genomes of maize and Arabidopsis,

and a comparison of these elements across the three genomes reveals the preferential capture of

CG-rich gene fragments (FERGUSON AND JIANG 2011).

Helitrons, unlike most class II TEs, are not flanked by TIRs and are therefore difficult to detect in sequence data. Their specific sequence type is associated with an unusual form of rolling-circle transposition, however. Over successive rounds of ‘cut-and-paste’ mobilisation, these elements collect small regions from ORFs at their insertion sites. Transcripts of both pack-MULES and Helitrons

have been observed that consist of captured exons correctly spliced together (BENNETZEN 2005). It is

therefore highly likely that these TE types contribute directly to new gene creation.

Similar genomic restructuring has occurred in grapevine through the activity of MITEs (BENJAK et al.

2009). One element family, mPifvine-3.1, is particularly common in the 3’ untranslated region (UTR)

of genes. The authors that identified this family propose that this location bias is due to an unknown selective advantage conferred by the elements, rather than insertion site specificity.

Gene regulation

Sequence motifs within retrotransposon LTRs regulate mRNA synthesis from the transcription start sits (TSS) within the 5’LTR (see Figure 2.2). Being identical in sequence, the 3’LTR can drive the formation of mRNA transcripts from sequence downstream of the TE insertion, potentially placing genes under the regulatory control of the TE. Sequence similarity between the CREs of an active

tobacco Tto1 retrotransposon and a plant defence gene (AoPR1) indicate that an ancient Tto1

insertion may possibly have contributed some stress-response regulatory motifs to the promoter of

this gene (TAKEDA et al. 1999). As much as one quarter of all promoter regions in the human genome

contain TE-derived sequences, including regulatory motifs (JORDAN et al. 2003).

Ito and colleagues (2011) showed that heat shock activation of the Arabidopsis retrotransposon

ONSEN results in new insertions in plants deficient of siRNA biogenesis. Genes neighbouring new

ONSEN insertions also became heat responsive. A study by Naito and colleagues (2009) has even shown the preferential insertion of the stress-activated rice DNA transposon mPing into gene promoters, resulting in a large proportion of genes at insertion loci coming under stress-responsive transcriptional regulation. Through selection, therefore, TE-derived sequences become domesticated as functional and necessary parts of the eukaryotic genomes.

TE ‘immunity’

As described (see 2.2.4), TEs that are transcriptionally dormant as a result of epigenetic modifications are still capable of contributing siRNAs. In this way, TEs maintain asymmetrical DNA methylation patterns and provide a trigger for silencing new insertions. The maintenance of a diverse library of TE types within the genome therefore facilitates the rapid identification and silencing of new potentially

mutagenic elements. In addition to a collection of reference elements, it is possible that RDR proteins are involved in the maintenance of a pool of dsRNA, enabling an even swifter response to the

reactivation of dormant transposons.

Active TE demethylation

Plants lacking the systems required to maintain epigenetic modifications lose DNA methylation at

each replication cycle, in a process known as passive demethylation (TEIXEIRA AND COLOT 2010). A

subfamily of DNA glycosylases have been identified in Arabidopsis, however, which actively remove

methylated cytosine bases from the DNA, leaving a gap which is filled with unmethylated cytosine (ZHU 2009).

One of these enzymes in particular, DEMETER (DME), is specifically expressed during plant female gametogenesis in the central cell, which gives rise to the triploid endosperm following fertilisation (CHOI et al. 2002). An increase in DME expression leads to genome-wide demethylation and a non-CG hypermethylation at siRNA-targeted loci. In contrast, the DNA of the embryo itself is

hypermethylated, with a particularly high CHH methylation across transposable elements. The authors propose that transposon methylation may be removed in the non-gametic endosperm in order to allow the activation of transposons and a consequent accumulation of TE-targeting siRNAs. Trafficking of these siRNAs to the embryo may be responsible for enhanced silencing of mobile elements (HSIEH et al. 2009).

Slotkin and colleagues (2009) drew the same conclusions about the mechanism for TE silencing in

gametes after studying male gametogenesis in Arabidopsis. Their experiments showed an apparent

downregulation of the DDM1 gene in vegetative nucleus of pollen, accompanied by reactivation of certain TEs. The same TEs are hypermethylated in adjacent sperm cells, where siRNAs corresponding to the specific TEs abound.