Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

被引：17

作者：

Berthelier, Jeremy ^{[1
]}

Furci, Leonardo ^{[1
]}

Asai, Shuta ^{[2
]}

Sadykova, Munissa ^{[1
]}

Shimazaki, Tomoe ^{[1
]}

Shirasu, Ken ^{[2
]}

Saze, Hidetoshi ^{[1
]}

机构：

[1] Okinawa Inst Sci & Technol Grad Univ OIST, Plant Epigenet Unit, 1919-1 Tancha, Onna, Okinawa 9040495, Japan

[2] RIKEN, Ctr Sustainable Resource Sci, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan

来源：

NATURE COMMUNICATIONS | 2023年 / 14卷 / 01期

关键词：

DNA METHYLATION; DISEASE RESISTANCE; JMJC DOMAIN; ELEMENTS; PROTEIN; COMPLEX; EXPRESSION; PLANTS; HETEROCHROMATIN; IDENTIFICATION;

D O I：

10.1038/s41467-023-38954-z

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 co-transcribed 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 insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.

引用

页数：19

共 122 条

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