Transposable elements (TEs) occupy a significant proportion of the genomes of higher plants. The activation of TEs can have a range of effects, including alteration in gene expression and chromosome rearrangements as the elements mobilize within the genome. These mutations are usually deleterious. Therefore, inactivation of TEs can be crucial for survival of the host organisms. Because TEs encode enzymes required for their own maintenance and jumping, suppressing these gene products at a transcriptional or post-transcriptional level are effective ways to inactivate TEs. In the November 6, 2001 issue of Trends in Plant Science (11:527-534), H. Okamoto and H. Hirochika (Molecular Genetics Department, Institute of Agrobiological Sciences, Ibaraki, Japan) review the current understanding of TE silencing in eukaryotes.
The abundance of TEs varies greatly in plant genomes. TEs comprise 14 percent of the Arabidopsis genome and 50-80% of the maize genome. The highly methylated heterochromatin region in the centromere in Arabidopsis is rich in TEs. In maize, these elements are also confined to the methylated heterochromatin region, where they exist in high copy numbers. DNA TEs exist in two structural forms: autonomous elements carrying a transposase gene and non-autonomous elements requiring transposase proteins for their transposition.
There are two processes by which TEs are inactivated. Silencing may be accomplished by transcriptional gene silencing (TGS), by post-transcriptional gene silencing (PTGS), or by both methods. In transcriptional gene silencing (TGS), transcription of the element is blocked, and often the process is associated with methylation of promoters of silenced genes. The TGS process begins with a DNA-DNA interaction between homologous regions of TEs located at different positions. In Drosophilia, polycomb (PC) proteins mediate these types of DNA pairings. DNA-DNA pairing is also considered to initiate the process of methylation and silencing in plants. Chromation remodeling occurs by action of DDM1 (Decreased DNA Methylation), and is followed by methylation of target regions by DNA methylases such as MET1 or CMT3. Further chromatin remodelling may occur through action of MOM1 (Manifestation of Maximum), which condenses nucleosomes to result in repressive chromatin.
Post-translational gene silencing (PTGS), by contrast, involves degradation of TE transcripts. Like TGS, PTGS also involves suppression through methylation and/or chromatin remodeling. However, the PTGS process is initiated by double-stranded RNA (dsRNA) or aberrant RNA which cleaved by an RNase complex called Dicer. This generates small RNA molecules of 21-22 nucleotides. This small RNAs (sRNA) is thought to act as a guide for RNA degradation by an RNase complex or for methylation of target genomic regions. The identification of 21-22 nucleotide-long RNAs originating from a tobacco LTR transposon indicate that the plant TEs are also silenced by PTGS.
Both TGS and PTGS may involve DNA methylation of silenced regions as a common feature. Methylation does seem to be conserved in plants. Drosophila and C. elegans lack major DNA methylation, but still are capable of executing TGS, suggesting that chromatin remodeling and modification may play a more major role during TGS in these organisms.
Endogenous genes other than TEs may also be targets for silencing. Allelic DNA-DNA interaction and repetitive DNA structures are associated with repression of gene expression in some cases. For example, in maize, paramutation is a phenomena in which a heritable change in gene expression is caused by the coexistence of distinct alleles. This event involves DNA-DNA pairing and has similarity to the trans-sensing phenomena that has been described in Drosophila. In Arabidopsis, silencing of the phosphoribosyl anthranilate isomerase ( PAI ) locus is similar to paramutation. The PAI genes are silenced in the ecotype Wassilewskija, but not in Columbia. The dispersed in both ecotypes, but one of the unlinked sites exists as an inverted repeat in the Ws ecotype. Silenced PAI genes may be reactivated in a ddm1 background, suggesting that methylation is involved in inactivation. Other recent studies with have indicated that inverted repeats, direct repeats or repetitive sequences might be targets for epigenetic regulation by methylation in Arabidopsis.
Although there is a good deal of similarity between transgene silencing and transposable element silencing, there are a number of major differences. Firstly, insertion of transgenes in the chromosomes occurs at random locations, whereas target site specificities exist for TE integration. The distribution of TEs may have implications for chromatin remodeling and thus silencing events. Secondly, single-copy transgenes are sometimes methylated and silenced, TE silencing is thought to have arisen as a genome defense response to limit the proliferation of multicopy elements. In Arabidopsis, however, many single or low-copy number TEs are methylated and silenced, leading the authors to suggest that silencing of single copy transgenes and TEs could have common mechanistic elements.
Genome size varies greatly in plant species, and TEs and retroelements are critical in determining this size. Arabidopsis, which is relatively poor in TEs and retroelements, has a the genome of 125 Mb, while the maize genome is 2400 Mb. Differences have been observed between plant species in the ability to silence retroelements. For example, the retrosposon Tto1 is silenced in Arabidopsis when its copy number is increased to 10-15, but remains active in tobacco plants, were it is present in 30 copies, and cultured tobacco cells, which contain 300 copies.
The authors state that recent advances in gene silencing and epigenetic events have led to increased understanding of the mechanisms of these processes. They propose that TEs that result in dsRNA or aberrant RNA are silenced by PTGS, while actively transposing multicopy TEs are silenced by TGS. In conclusion, the authors reiterate that intensive investigation needs to be carried out at biochemical and molecular levels in order to understand fully mechanisms of gene silencing more fully.