Alternative Splicing as a Regulator of Early Plant Development

Abstract

Most plant genes are interrupted by introns and the corresponding transcripts need to undergo pre-mRNA splicing to remove these intervening sequences. Alternative splicing (AS) is an important posttranscriptional process that creates multiple mRNA variants from a single pre-mRNA molecule, thereby enhancing the coding and regulatory potential of genomes. In plants, this mechanism has been implicated in the response to environmental cues, including abiotic and biotic stresses, in the regulation of key developmental processes such as flowering, and in circadian timekeeping. The early plant development steps – from embryo formation and seed germination to skoto- and photomorphogenesis – are critical to both execute the correct body plan and initiate a new reproductive cycle. We review here the available evidence for the involvement of AS and various splicing factors in the initial stages of plant development, while highlighting recent findings as well as potential future challenges.

Delay of Germination-1 (DOG1): A Key to Understanding Seed Dormancy

“…This major form, named ε, excludes the third exon and incorporates a part of the second. The nascent mRNA-ε is formed by alternative polyadenylation and not by differential splicing [3,47]. The level of DOG1 transcripts is strongly decreased throughout the final part of seed maturation, though the abundance of DOG1 protein does not diminish [10].…”

“…However, more research is still required to clarify the exact role of the different DOG1 protein isoforms in plants. Finally, and given that DOG1 is extensively regulated [1,3,9,13,25,42,47], recent relevant evidence demonstrated that asDOG1, a long non-coding antisense RNA from DOG1 in Arabidopsis, suppresses DOG1 expression during seed maturation in cis and promotes germination [16,23]. This DOG1 antisense partner originates close to the DOG1 proximal polyadenylation.…”

“…The critical role of ABA in the induction of PD is currently unquestionable [33]. ABA and DOG1 seem to act in concert to carry out the PD, a striking event during seed development [10,47,48]. The action of DOG1 in regulating PD is ABA-coordinated [10].…”

Splice-site Strength Estimation: A simple yet powerful approach to analyse RNA splicing

“…During mRNA formation, certain sections of the transcribed RNA (introns) are removed with joining of the adjacent regions (exons) in a process known as splicing. Splicing is a fundamental process in eukaryotic gene regulation [6][7][8] . Introns removed during the splicing process typically harbour canonical sequences at the 5' beginning (GT) and the 3' end (AG), which facilitate their identification as splice sites [9][10][11] .…”

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

“…Transcriptomes consist of complex populations of transcripts produced through the co-ordinated transcription and post-transcriptional processing of precursor messenger RNAs (pre-mRNAs). Alternative splicing (AS) of pre-mRNA transcripts is the main source of different transcript isoforms that are generated through regulated differential selection of alternative splice sites on the pre-mRNA and up to 60-70% intron-containing plant genes undergo AS Mastrangelo et al, 2012;Staiger and Brown, 2013;Carvalho et al, 2013;Chamala et al, 2015;Filichkin et al, 2015;Capovilla et al, 2015;Calixto et al, 2016;Laloum et al, 2018;Szakonyi & Duque, 2018). The two main functions of AS are to increase protein diversity and regulate expression levels of specific transcripts by producing AS isoforms that are degraded by nonsense mediated decay (NMD) (Nilsen and Gravely, 2010;Kalyna et al, 2012;Reddy et al, 2013;Staiger and Brown, 2013;Lee and Rio, 2015).…”