Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Reddy, Anireddy S. N.; Huang, Jie; Syed, Naeem H.; Ben-Hur, Asa; Dong, Suomeng; Gu, Lianfeng

doi:10.1042/bst20190492

Title: Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Journal Article · Mon Nov 16 00:00:00 EST 2020 · Biochemical Society Transactions

DOI:https://doi.org/10.1042/bst20190492· OSTI ID:1851428

^[1]; Huang, Jie ^[2]; Syed, Naeem H. ^[3]; Ben-Hur, Asa ^[4]; Dong, Suomeng ^[2]; Gu, Lianfeng ^[5]

Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, U.S.A.
Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
School of Human and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, U.K.
Computer Science Department, Colorado State University, Fort Collins, CO 80523, U.S.A
Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China

Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.

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Research Organization:: Colorado State Univ., Fort Collins, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0010733

OSTI ID:: 1851428

Journal Information:: Biochemical Society Transactions, Vol. 48, Issue 6; ISSN 0300-5127

Publisher:: Portland Press

Country of Publication:: United States

Language:: English

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