Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Syed, N. 2020. Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochemical Society Transactions.
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-/posttranscriptional 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 these 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
Although the mechanisms by which developmental cues and different stresses regulate co-/posttranscriptional splicing are largely unknown, a few recent studies are beginning to provide some insights into these mechanisms. These 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.
|Keywords||Abiotic stresses; Biotic stresses; Drought; Co-transcriptional processing; Epitranscriptome; Gene regulation; Nanopore direct RNA sequencing; Post-transcriptional gene regulation; RNA splicing.|
|Journal||Biochemical Society Transactions|
|Publication process dates|
|Accepted||22 Oct 2020|
|Deposited||29 Oct 2020|
|Accepted author manuscript|
File Access Level
|Output status||In press|
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