Light-regulated pre-mRNA splicing in plants

Abstract

Light signal perceived by the red/far-red absorbing phytochrome (phy) family of photoreceptors regulates plant growth and development throughout the life cycle. Phytochromes regulate the light-triggered physiological responses by controlling gene expression both at the transcriptional and post-transcriptional levels. Recent large-scale RNA-seq studies have demonstrated the roles of phys in altering the global transcript diversity by modulating the pre-mRNA splicing in response to light. Moreover, several phy-interacting splicing factors/regulators from different species have been identified using forward genetics and protein-protein interaction studies, which modulate the light-regulated pre-mRNA splicing. In this article, we summarize our current understanding of the role of phys in the light-mediated pre-mRNA splicing and how that contributes to the regulation of gene expression to promote photomorphogenesis.

Keywords: Arabidopsis; Photomorphogenesis; Phytochrome signaling; Pre-mRNA splicing; Splicing factor.

Figure 1.. Schematics of pre-mRNA splicing and major types of alternative splicing (AS)

(A) Majority of the pre-mRNAs contain one or more introns flanking the exons on either side and consensus sequences defining the 5’-splice site (5’-SS) with a conserved GU, 3’-SS with a conserved AG, a branched point (BP) adenine (A) 18 to 40 nucleotide upstream of the 3’-SS, and a poly-pyrimidine tract (PPT) following the BP. Majority of the exons and introns contain regulatory cis-acting elements including, exonic/intronic splicing enhancers (ESE/ISE), exonic/intronic splicing silencers (ESS/ISS). Trans-acting regulators such as serine/arginine-rich (SR) proteins bind to the ESE/ISEs to promote splicing, while heterogeneous nuclear ribonucleoproteins (hnRNPs) bind to the ESS/ISS and repress the splicing. U1-small nuclear ribonucleoproteins (U1-snRNPs) target the 5’-SS, while the U2-snRNPs and U2- associated factors target the 3’-SS. Appropriate exon-intron junction and the splicing is determined by the core spliceosome assembly and the corresponding cis-acting elements bound by the trans-acting regulators interacting with the U1 and/or U2-snRNPs. (B) Drawings show constitutive splicing and different forms of alternative splicing common in plants such as exon skipping, intron retention, mutually exclusive exons, alternative 5’-SS and 3’-SS selection. Black lines denote introns and different colored rectangles indicate exons.

Figure 2.. Model shows phytochrome-modulated pre-mRNA splicing in Arabidopsis

SFPS and RRC1 are two known splicing factors that directly interact with phytochrome B (phyB) and regulate phytochrome-modulated pre-mRNA splicing in Arabidopsis. In the dark (left panel), SFPS and RRC1 interact with each other and also form complexes with U2-snRNP/U2-AF and target hundreds of co-regulated pre-mRNAs for splicing. Moreover, SFPS and RRC1 independently target a large number of distinct pre-mRNAs for splicing in both dark and light conditions. When plants are exposed to light (right panel), activated phyB interacts with SFPS/RRC1 complex in nucleoplasm and photobodies, which might lead to the targeting of different sets of pre-mRNAs for splicing and/or prevention of splicing by unknown mechanism. Because SFPS/RRC1 can associate with U2AFs, and the U2AFs associate with U2 snRNP, it is still unclear whether phyB remains in the nucleoplasm and photobodies or phyB also directly participates on the spliceosome complex throughout the process of target identification and splicing. It is also possible that upon interaction with the SFPS/RRC1 complex, phyB induces biochemical changes to the SFPS and RRC1 proteins, and releases the complex for appropriate target selection and subsequent splicing.

Figure 3.. Model shows phytochrome-modulated pre-mRNA splicing in Physcomitrella patens

PphnRNP-H1 and PphnRNP-F1 are the two splicing regulators known to modulate phytochrome-dependent pre-mRNA splicing in P. patens. In the dark (left panel), U1-snRNP/U1C/PRP39 associated spliceosome complex promotes the AS in hundreds of target pre-mRNAs in a phytochrome-independent manner. In response to light irradiation (right panel), activated phytochromes interact with PphnRNP-H1/PphnRNP-F1. Phytochromes also promote the high-affinity interaction between PphnRNP-H1 and PRP39, due to which PRP39 dissociates from U1snRNP/U1C complex. This might lead to the reduced activity of U1-snRNP/U1C complex and intron retention in target pre-mRNAs. Moreover, a purine-rich GAA motif is one of the bona fide exonic splicing silencer (ESS), which recruits hnRNP-F1 to promote intron retention in affected transcripts.