PacBio full-length transcriptome analysis reveals the role of tRNA-like structures in RNA processing

Yanping Hu; Shuangyong Yan; Haohao Yan; Jingping Su; Zhongqiu Cui; Junling Li; Shengjun Wang; Yue Sun; Wenjing Li; Shan Gao

doi:10.1016/j.cellsig.2024.111515

PacBio full-length transcriptome analysis reveals the role of tRNA-like structures in RNA processing

Cell Signal. 2024 Nov 19:111515. doi: 10.1016/j.cellsig.2024.111515. Online ahead of print.

Authors

Yanping Hu¹, Shuangyong Yan², Haohao Yan³, Jingping Su², Zhongqiu Cui², Junling Li², Shengjun Wang², Yue Sun², Wenjing Li⁴, Shan Gao⁵

Affiliations

¹ College of Life Sciences, Nankai University, Tianjin 300071, China; Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China.
² Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China.
³ College of Life Sciences, Nankai University, Tianjin 300071, China.
⁴ Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China. Electronic address: wjli@nwipb.cas.cn.
⁵ College of Life Sciences, Nankai University, Tianjin 300071, China. Electronic address: gao_shan@mail.nankai.edu.cn.

PMID: 39571702
DOI: 10.1016/j.cellsig.2024.111515

Abstract

Background: Mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) are distinct from nuclear DNA (nuDNA) in a eukaryotic cell. Animal mitochondria transcribe a single primary transcript that carries all genes from a DNA strand; In contrast, plant mitochondria and chloroplasts produce multiple primary transcripts, with each transcript carrying several genes. How primary transcripts of plant mtDNA and cpDNA are processed into mature RNAs is still unknown.

Results: In the present study, we employed PacBio's full-length transcriptome data to characterize the transcription of Arabidopsis thaliana mtDNA, providing a more comprehensive and precise understanding. The primary findings included 20 novel mitochondrial (mt) RNAs of A. thaliana, transcripts carrying single introns or exons, long mt and chloroplast (cp) tRNAs with intricate secondary structures, and the role of tRNA-like structures in RNA processing. The gene of No. 20 novel mt RNA and its paralog on chromosome 2 of A. thaliana were assigned locus IDs ATMG01335 and AT2G07811.

Conclusions: According to our upgraded "mitochondrial cleavage" model, tRNA-like structures serve as "punctuation" marks for RNA processing, akin to the role of tRNAs. Both tRNA-like structures and tRNAs collaborate for RNA processing in plant mitochondria and chloroplasts.

Keywords: Inverted repeat; TIS; TTS; polyA-like site; tRNA-like site.