RT Journal Article SR Electronic T1 Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.09.21.507229 DO 10.1101/2022.09.21.507229 A1 Jérémy Berthelier A1 Leonardo Furci A1 Shuta Asai A1 Munissa Sadykova A1 Tomoe Shimazaki A1 Ken Shirasu A1 Hidetoshi Saze YR 2022 UL http://biorxiv.org/content/early/2022/09/21/2022.09.21.507229.abstract AB Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also cotranscribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, “ParasiTE”, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides novel insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.Competing Interest StatementThe authors have declared no competing interest.