Abstract
BackgroundmPing is an endogenous MITE in the rice genome, which is quiescent under normal conditions but can be induced towards mobilization under various stresses. The cellular mechanism responsible for modulating the activity of mPing remains unknown. Cytosine methylation is a major epigenetic modification in most eukaryotes, and the primary function of which is to serve as a genome defense system including taming activity of transposable elements (TEs). Given that tissue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes, it provides a tractable system to investigate the possible relationship between the two phenomena.ResultsmPing transposition and cytosine methylation alteration were measured in callus and regenerated plants in three rice (ssp. indica) genotypes, V14, V27 and R09. All three genotypes showed transposition of mPing, though at various frequencies. Cytosine methylation alteration occurred both at the mPing-flanks and at random loci sampled globally in callus and regenerated plants of all three genotypes. However, a sharp difference in the changing patterns was noted between the mPing-flanks and random genomic loci, with a particular type of methylation modification, i.e., CNG hypermethylation, occurred predominantly at the mPing-flanks. Pearson's test on pairwise correlations indicated that mPing activity is positively correlated with specific patterns of methylation alteration at random genomic loci, while the element's immobility is positively correlated with methylation levels of the mPing's 5'-flanks. Bisulfite sequencing of two mPing-containing loci showed that whereas for the immobile locus loss of CG methylation in the 5'-flank was accompanied by an increase in CHG methylation, together with an overall increase in methylation of all three types (CG, CHG and CHH) in the mPing-body region, for the active locus erasure of CG methylation in the 5'-flank was not followed by such a change.ConclusionOur results documented that tissue culture-induced mPing activity in rice ssp. indica is correlated with alteration in cytosine methylation patterns at both random genomic loci and the elements' flanks, while the stability of mPing positively correlates with enhanced methylation levels of both the flanks and probably the elements per se. Thus, our results implicate a possible role of cytosine methylation in maintaining mPing stability under normal conditions, and in releasing the element's activity as a consequence of epigenetic perturbation in a locus-specific manner under certain stress conditions.
Highlights
MPing is an endogenous miniature inverted-repeat transposable elements (TEs) (MITEs) in the rice genome, which is quiescent under normal conditions but can be induced towards mobilization under various stresses
We have shown in this study that various types of cytosine methylation alteration occurred in calli and their regenerants in all three studied rice genotypes, which included both hypo- and hyper-methylation that occurred at CG or CHG sites
Given the relationship between the mPing activity and alteration in cytosine methylation at globally sampled random genomic loci, discussed above, it is pertinent to ask two questions: (1) Are the genomic regions immediately flanking the mPing copies underwent methylation alteration? (2) Are the methylation states of the mPing immediate flanking regions important for the element's stability? To answer these two questions, we performed transposon (mPing)-methylation display (TMD) analysis targeting at the various immobile mPing copies in the calli and regenerants from each of the three rice genotypes. We found that both the 5'- and 3'mPing flanks underwent extensive methylation alteration that could be classified into four types as in the case of random genomic loci detected by methylation-sensitive amplified polymorphism (MSAP)
Summary
MPing is an endogenous MITE in the rice genome, which is quiescent under normal conditions but can be induced towards mobilization under various stresses. Cytosine methylation is a major epigenetic modification in most eukaryotes, and the primary function of which is to serve as a genome defense system including taming activity of transposable elements (TEs). Given that tissue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes, it provides a tractable system to investigate the possible relationship between the two phenomena. Transposable elements (TEs) are sequences capable of changing their physical locations in their host genomes [1,2]. Whereas retrotransposons usually reach very high copy numbers, DNA transposons often retain low copies [5]. One exception to this general rule is the miniature inverted-repeat TEs (MITEs), which are DNA transposons, yet they can reach high copy numbers in the range of thousands [3]
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have