Genomic asymmetric epigenetic modification of transposable elements is involved in gene expression regulation of allopolyploid Brassica napus

Abstract

SUMMARYPolyploids are common and have a wide geographical distribution and environmental adaptability. Allopolyploidy may lead to the activation of transposable elements (TE). However, the mechanism of epigenetic modification of TEs in the establishment and evolution of allopolyploids remains to be explored. We focused on the TEs of model allopolyploid Brassica napus (AnAnCnCn), exploring the TE characteristics of the genome, epigenetic modifications of TEs during allopolyploidization, and regulation of gene expression by TE methylation. In B. napus, approximately 50% of the genome was composed of TEs. TEs increased with proximity to genes, especially DNA transposons. TE methylation levels were negatively correlated with gene expression, and changes in TE methylation levels were able to regulate the expression of neighboring genes related to responses to light intensity and stress, which promoted powerful adaptation of allopolyploids to new environments. TEs can be synergistically regulated by RNA‐directed DNA methylation pathways and histone modifications. The epigenetic modification levels of TEs tended to be similar to those of the diploid parents during the genome evolution of B. napus. The TEs of the An subgenome were more likely to be modified, and the imbalance in TE number and epigenetic modification level in the An and Cn subgenomes may lead to the establishment of subgenome dominance. Our study analyzed the characteristics of TE location, DNA methylation, siRNA, and histone modification in B. napus and highlighted the importance of TE epigenetic modifications during the allopolyploidy process, providing support for revealing the mechanism of allopolyploid formation and evolution.

High- or Low-Yielding F2 Progeny of Wheat Is Result of Specific TaCKX Gene Coexpression Patterns in Association with Grain Yield in Paternal Parent

“…As reviewed in the introduction, any deviations from the non-Mendelian inheritance of a parent-of-origin expression pattern might be the effect of epigenetic regulation. The main factors of this epigenetic regulation are the balance of gene dosage [ 28 ], small interfering RNAs [ 36 , 41 ], noncoding RNAs [ 44 , 45 ], or cis - and/or trans -regulatory elements [ 34 , 35 , 36 , 37 , 38 ]. All of them might be involved in the regulation of these epigenetic types of expression patterns, especially in polyploid species.…”

“…Such nonadditive gene expression levels associated with phenotypic heterosis in F 1 plants have already been reported and reviewed [ 29 , 30 , 31 , 32 , 33 ]. These deviations from the general role are the result of different factors, such as epigenetic regulation by transcription factors [ 34 , 35 , 36 , 37 , 38 ], the balance of gene dosage [ 39 , 40 ], small interfering RNAs (sRNA) [ 36 , 41 ], histone modifications [ 42 ], R-loop formation [ 43 ], or distally acting factors [ 31 ]. Furthermore, noncoding RNAs have been described as regulators of the development of shoots and grains in barley [ 44 ] and dominant epigenetic regulators of early meiotic stages in wheat, ensuring reproductive success [ 45 ].…”