Maria Kalyna

Alternative Splicing Landscape in Plants

Alternative splicing is a key mechanism to increase the diversity of expressed information in eukaryotic genomes. In many eukaryotic genes, protein information embedded in regions called exons is interrupted by introns. Introns have to be removed and exons spliced together to yield a mature protein-coding transcript (mRNA). During alternative splicing, differential inclusion of exons and introns or their parts in mRNAs results in multiple transcript and protein variants with different fates and functions from a single gene. In the model plant Arabidopsis, an important role of alternative splicing is evidenced by ~60% of multi-exon genes undergoing alternative splicing (Marquez et al., 2012; Zhang et al., 2017). The question remains to what extent alternative splicing contributes to regulation of gene expression and proteome diversity and what are the biological functions of alternative splicing.

Cover illustration (Marquez et al., 2015) by Dr. Maria Kalyna gives a kaleidoscopic view of the proteome, reflecting the diversity generated by alternative splicing.

Regulation of Alternative Splicing

Production of transcript variants is tightly regulated. It changes in different tissues and cell types, during development, and in response to environmental cues. For example, light regulates alternative splicing by retrograde signals from chloroplasts (Petrillo et al., 2014). Serine/arginine-rich (SR) proteins are major regulators of alternative splicing and are themselves regulated via alternative splicing. Chloroplasts signal the nucleus to modulate alternative splicing of SR genes. Regulation of some plant SR genes by alternative splicing is evolutionarily conserved over up to a billion years, from single-celled green alga Chlamydomonas reinhardtii and moss Physcomitrella patens to Arabidopsis and rice (Kalyna et al., 2006), suggesting ancient role of this regulation. SR proteins play important roles in various aspects of plant growth and response to environment, including the DNA damage response. Elucidating regulation and molecular functions of SR proteins is essential for understanding how they modulate gene expression and biological processes during plant development and adaptation.

Interplay between Alternative Splicing and Different Post-Transcriptional Processes

Exitrons: Hidden Alternative Splicing within Protein-Coding Exons

Closer examination of alternative splicing in Arabidopsis led to the discovery of unusual alternative splicing events present also in humans that involve introns with features of both introns and protein-coding exons. These introns, named exitrons, allow alternative splicing of the internal parts of annotated protein-coding exons. Exitron splicing occurs in at least 6.6% Arabidopsis and 3.7% human protein-coding genes (Marquez et al., 2015; Zhang et al., 2017). Majority of exitrons have sizes of multiples of three nucleotides. Splicing of these exitrons results in internally deleted protein isoforms and affects protein domains, disordered regions, and various types of post-translational modifications, thus broadly influencing protein function. Exitron splicing is regulated across tissues, in response to stress, and in carcinogenesis. Exitrons originate from ancestral coding exons. We propose a "splicing memory" hypothesis whereby upon intron loss imprints of former exon borders defined by vestigial splicing regulatory elements could drive the evolution of exitron splicing (Marquez et al., 2012; Marquez et al., 2015). Intriguingly, exitrons exhibit distinctive nucleosome positioning pattern compared to other alternatively spliced regions, and nucleosome patterns differ between exitrons and retained introns, pointing to their distinct regulation (Jabre et al., 2020).