Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa)

Abstract

Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.

Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii

“…LTR/Gypsy with distal HSs carried a higher number of chromatin states 12/13 and H3K9ac modification was increased significantly at distal HSs (Figure 6b,d), implying that these distal TEs may carry activated enhancer elements in the HSs. Further, the open signals on TEs in the proximal promoters were correlated with gene expression (Figure 6a), consistent with the gene expression induced by open promoters in rice [65]. Interestingly, our study revealed that genes with TE neighbors carrying HSs showed higher levels of expression compared with genes carrying TE neighbors without HSs (Figure 6a), indicating a positive significance of TE opening near genes.…”

Annotation of the Turnera subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner

“…Transposable elements (TE) are one of the driving forces of evolution, altering gene expression patterns [ 46 , 47 , 48 ], chromatin accessibility [ 45 , 49 , 50 ], and gene duplication and evolution [ 26 , 47 ]. It has been proposed that TEs may be the main driving force for genome evolution in several species, including Moso bamboo [ 51 ], Pinus tabuliformis [ 52 ], and Allium fistulosum [ 53 ].…”