Fact sheet 4: TEs and mobilomes

Panpan Zhang

In this chapter, we will study transposable elements (TEs) in plants which includes structure and type of TEs in eukaryotes, composition and differences of TEs in plant genomes, epigenetic regulation of TEs in plants and regulation of TEs in plant genome.

A TE is a piece of DNA that can be replicated or fragmented from a chromosomal DNA, and then inserted into another site, thereby affecting gene regulation at the insertion site [1,2]. According to the transposition mechanism of TEs, TEs can be divided into two categories: RNA-type transposons and DNA-type transposons [3]. RNA-type transposons are also called retrotransposons. The splicing is first transcribed into RNA, and then transposed into DNA by reverse transcription. The whole process is transposed in the form of "DNA-RNA-DNA", so the RNA-based transposon is "copy-paste". The DNA type of the transposon "cut-paste" forms the transposition, which is cut from one position and inserted into another position under the action of a transposase [3,4].

Although TEs are abundant in plant species and account for greater than 50% of some genomes [5], epigenetic modifications are involved in maintaining their silent state [6]. Among them, DNA methylation, histone modification and small RNA are important ways to inhibit transposition, usually in transcription or post-level transcription silencing [6]. The quantitative expansion and contraction of TEs are accompanied by the defense mechanism of the host genome, thereby not only changing the overall structure of the genome, but also causing changes in gene expression and function [7,8]. The effects of TEs on the insertion site genes are mainly characterized by mutations in the gene's own functions and new functionalization, genetic structural variations, reprogramming of nucleic acid sequences and epigenetic modifications, which may ultimately result in phenotypic variations [9].

With the deepening of epigenetic research, people have a clearer understanding of the role of TEs in eukaryotes: from the initial structural features, transposition mechanisms to subsequent apparent inhibition modifications and further understanding of their regulation of gene expression. In higher plants, due to these characteristics of TEs, we can see them as hubs linking genomic variation and epigenomic variation, that is, they will also carry modification information while being subjected to apparent inhibition. Passing to adjacent regions induces the formation of epiallele, which can be further transmitted in the offspring , being a treasure for studying plant epigenetics [10].

1. Rebollo, Rita, Mark T. Romanish, and Dixie L. Mager. "Transposable elements: an abundant and natural source of regulatory sequences for host genes." Annual review of genetics46 (2012): 21-42.

2. Lisch, Damon. "How important are transposons for plant evolution?." Nature Reviews Genetics 14.1 (2013): 49.

3. Wicker, Thomas, et al. "A unified classification system for eukaryotic transposable elements." Nature Reviews Genetics8.12 (2007): 973.

4. Lee, Sung-Il, and Nam-Soo Kim. "Transposable elements and genome size variations in plants." Genomics & informatics 12.3 (2014): 87-97.

5. Tenaillon, Maud I., Jesse D. Hollister, and Brandon S. Gaut. "A triptych of the evolution of plant transposable elements." Trends in plant science 15.8 (2010): 471-478.

6. Lisch, Damon. "Epigenetic regulation of transposable elements in plants." Annual review of plant biology 60 (2009): 43-66.

7. Chuong, Edward B., Nels C. Elde, and CĂ©dric Feschotte. "Regulatory activities of transposable elements: from conflicts to benefits." Nature Reviews Genetics 18.2 (2017): 71.

8. Rebollo, Rita, Mark T. Romanish, and Dixie L. Mager. "Transposable elements: an abundant and natural source of regulatory sequences for host genes." Annual review of genetics46 (2012): 21-42.

9. Cui, Xiekui, and Xiaofeng Cao. "Epigenetic regulation and functional exaptation of transposable elements in higher plants." Current opinion in plant biology 21 (2014): 83-88.

10. Mirouze, Marie, and Clémentine Vitte. "Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes." Journal of experimental botany 65.10 (2014): 2801-2812.