Fig. 8

Pol II is essential for transcription of TE-overlapped lncRNA. a Venn diagrams illustrating the proportion of lncRNAs with reads mapped against mRNA Seq library prepared with poly(A) enrichment (poly(A)+). Poly(A)− represents the unmapped lncRNAs. b Enrichment of Pol II signals at lncRNA and PCG sites. The heatmap reads are clustered according to the enrichment profile of Pol II and mock. c Heatmap showing the dynamics of Pol II binding efficiency difference in equal and up- and downregulated lncRNAs in the F₁ hybrid. The left panel of the heatmap indicates the annotation of lncRNA overlapped with Gypsy, LINE, and TE. d Schematic model of lncRNA origination within TE regions during genome shock of hybridization and polyploidization. d Transposon elements (TEs) are generally suppressed by siRNA and DNA methylation. During hybridization and polyploidization, de novo DNA methylation mediated by small RNA introduces dynamic RNA transcription. Based on our analysis, the reprogramming of DNA methylation during hybridization gives rise to novel lncRNAs from LINEs