Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association

Abstract

RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.

Figure 1

RZ-1C controls co-transcriptional splicing. A, Summary of main features of RZ-1C binding. The number of crosslink sites (XLS) and genes associated with RZ-1C determined by eCLIP (Zhu et al., 2020). Enriched binding motifs found among XLS and preferred bound genomic regions are shown as a scheme. B, Proposed working model for the role of RZ-1C in promoting co-transcriptional splicing exemplified at the FLC locus. RZ-1C inhibits transcription of FLC. On the other side, binding during transcription enhances co-transcriptional splicing by interacting with splicing-related proteins. Full-length FLC mRNA is translated to protein to repress flowering. Boxes denote exons and lines denote introns.

Figure 2

The role of HLP1 in polyadenylation control. A, Summary of main features of HLP1 binding. Number of crosslink sites (XLS) and genes associated with HLP1 determined by iCLIP (Zhang et al., 2015). Enriched binding motifs found among XLS and preferred bound genomic regions are shown as a scheme. B, Proposed working model for the role of HLP1 binding to the FCA transcript to control alternative polyadenylation. When the proximal poly(A) site is used, the non-functional FCA-β isoform is produced. When distal poly(A) sites are favored, the full-length FCA protein FCA-γ can repress FLC to promote flowering. Boxes denote exons and lines denote introns.

Figure 3

Binding of the m⁶A reader ECT2 to the RR(m⁶A)CH motif. A, Summary of main features of ECT2 binding. Number of crosslink sites (XLS) and genes associated with ECT2 determined by iCLIP (Arribas-Hernandez et al., 2021). Enriched binding motifs found among target RNAs are depicted. Two sets of motifs were found, binding to the YTH domain or the IDR domain of ECT2, as observed with full-length ECT2-mCherry but not with YTH domain-mCherry. The preferred bound genomic region is shown as a scheme. B, Proposed working model for the role of ECT2 in binding m⁶A modification through the YTH domain exemplified at the PPA1 transcript.

Figure 4

RBPs and phase separation. A, Summary of main features of ALBA5 binding. Number of crosslink sites (XLS) and genes associated with ALBA5 determined by eCLIP (Tong et al., 2022). The preferred bound genomic region is shown as a scheme. B, Proposed working model for the function of ALBA4, ALBA5, and ALBA6 in LLPS mediating heat stress responses. ALBAs can bind RNA from several heat-shock-transcription factors (HSFs) during heat and deliver them into SGs via LLPS to protect them from EXORIBONUCLEASE 4 (XRN4) mediated degradation. This process is reversible. Lack of ALBAs allows HSF degradation by XRN4 and plants become sensitive to heat.