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

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.

Analysis of a large number of plant transcriptomes using high-throughput short and long reads under different conditions has established that diverse abiotic and biotic stresses and environmental cues such as light, which regulates many aspects of plant growth and development, have a profound impact on gene expression at the co-/post-transcriptional level.

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 eliciting appropriate responses for optimal growth and plant survival under adverse conditions.

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.