MITEs, Miniature Elements with a Major Role in Plant Genome Evolution

Guermonprez, Hélène; Hénaff, Elizabeth; Cifuentes, Marta; Casacuberta, Josep

doi:10.1007/978-3-642-31842-9_7

Cited by 7 publications

(6 citation statements)

References 65 publications

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“…Together with LTR retrotransposons, and TRIMs ( Gao et al. 2016 ) MITEs are the most prevalent type of TEs in plants were they are frequently found in the gene-rich euchromatic regions of the chromosomes ( Casacuberta and Santiago 2003 ; Guermonprez et al. 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)

Morata

Marín

Payet³

et al. 2018

Genome Biology and Evolution

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Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. Transposons have been show to contain transcription factor binding sites that can be mobilized upon transposition with the potential to integrate new genes into transcriptional networks. Miniature inverted-repeat transposable elements (MITEs) are a type of noncoding DNA transposons that could be particularly suited as a vector to mobilize transcription factor binding sites and modify transcriptional networks during evolution. MITEs are small in comparison to other transposons and can be excised, which should make them less mutagenic when inserting into promoters. On the other hand, in spite of their cut-and-paste mechanisms of transposition, they can reach very high copy numbers in genomes. We have previously shown that MITEs have amplified and redistributed the binding motif of the E2F transcription factor in different Brassicas. Here, we show that MITEs have amplified and mobilized the binding motifs of the bZIP60 and PIF3 transcription factors in peach and Prunus mume, and the TCP15/23 binding motif in tomato. Our results suggest that MITEs could have rewired new genes into transcriptional regulatory networks that are responsible for important adaptive responses and breeding traits in plants, such as stress responses, flowering time, or fruit ripening. The results presented here therefore suggest a general impact of MITEs in the evolution of transcriptional regulatory networks in plants.

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Section: Introductionmentioning

confidence: 99%

Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)

Morata

Marín

Payet³

et al. 2018

Genome Biology and Evolution

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“…Indeed, on one hand, mini-satellites can easily expand, increasing the number of tandemly repeated motifs (Richard et al, 2008), and, on the other hand, MITEs are present as large families of elements (Guermonprez et al, 2012). Most MITEs are thought to be the result of amplification of deletion derivatives of DNA transposons by an unknown amplification mechanism (Guermonprez et al, 2012). According to this scenario, acquisition of an E2F BS by a single DNA transposon may give rise to an entire MITE family containing the E2F BS, which, if present in a mini-satellite structure, may also increase its copy number within each MITE.…”

Section: Various Te Families Have Amplified the E2f Bsmentioning

confidence: 99%

“…retrotransposons) and that therefore contain a functional promoter that may in some case be co-opted as an alternative promoter (Testori et al, 2012). MITEs are defective class II elements that transpose by a cut-and-paste mechanism that does not involve transcription of the MITE itself (Guermonprez et al, 2012). Therefore, in contrast to most cases reported so far, the TFBSs contained in the MITEs reported here may have an effect on transcriptional regulation of endogenous genes without having a previous role in expression of the TE itself.…”

Section: Various Te Families Have Amplified the E2f Bsmentioning

confidence: 99%

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution of Brassica species

et al. 2014

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SUMMARYTransposable elements (TEs) are major players in genome evolution. The effects of their movement vary from gene knockouts to more subtle effects such as changes in gene expression. It has recently been shown that TEs may contain transcription factor binding sites (TFBSs), and it has been proposed that they may rewire new genes into existing transcriptional networks. However, little is known about the dynamics of this process and its effect on transcription factor binding. Here we show that TEs have extensively amplified the number of sequences that match the E2F TFBS during Brassica speciation, and, as a result, as many as 85% of the sequences that fit the E2F TFBS consensus are within TEs in some Brassica species. We show that these sequences found within TEs bind E2Fa in vivo, which indicates a direct effect of these TEs on E2F-mediated gene regulation. Our results suggest that the TEs located close to genes may directly participate in gene promoters, whereas those located far from genes may have an indirect effect by diluting the effective amount of E2F protein able to bind to its cognate promoters. These results illustrate an extreme case of the effect of TEs in TFBS evolution, and suggest a singular way by which they affect host genes by modulating essential transcriptional networks.

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“…Besides stress activation, strategies used by TEs to avoid silencing include [85]: (i) Inserting in regions close to genes which decreases but not fully eliminates silencing [43]; (ii) capturing gene fragments to resemble normal genes-a strategy used by pack-MULEs (MUtator-Like Elements) [86]; (iii) non-autonomous replication (e.g., MITES) to increase copy number [87]; and (iv) the generation of micro RNAs to suppress genes involved in epigenetic control. It could be argued that when TEs become part of the genome as controllers of transcription or when they donate partial or full reading frames to normal plant genes during exaptation events [44,58], they also escape host control.…”

Section: Can Tes Escape Epigenetic Control?mentioning

confidence: 99%

“…Since miRNAs can be produced from processing stem-loop RNA structures, MITEs are ideal TE candidates for miRNA production. Most of these elements have lost their transposase and have inverted repeats that can form the desired hairpins with a double RNA stretch that can be processed into a miRNA [87]. However, similar TEs inserted in tandem and opposite direction are also suitable for the generation of TE-derived miRNAs in plants, animals and fungi [89].…”

Section: Can Tes Escape Epigenetic Control?mentioning

confidence: 99%

Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation

2018

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In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition.

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MITEs, Miniature Elements with a Major Role in Plant Genome Evolution

Cited by 7 publications

References 65 publications

Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)

Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution of Brassica species

Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation

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