Global spatial analysis of Arabidopsis natural variants implicates 5′UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature

Abstract

How plants perceive and respond to temperature remains an important question in the plant sciences. Temperature perception and signal transduction may occur through temperature‐sensitive intramolecular folding of primary mRNA transcripts. Recent studies suggested a role for retention of the first intron in the 5′UTR of the clock component LATE ELONGATED HYPOCOTYL (LHY) in response to changes in temperature. Here, we identified a set of haplotypes in the LHY 5′UTR, examined their global spatial distribution, and obtained evidence that haplotype can affect temperature‐dependent splicing of LHY transcripts. Correlations of haplotype spatial distributions with global bioclimatic variables and altitude point to associations with annual mean temperature and temperature fluctuation. Relatively rare relict type accessions correlate with lower mean temperature and greater temperature fluctuation and the spatial distribution of other haplotypes may be informative of evolutionary processes driving colonization of ecosystems. We propose that haplotypes may possess distinct 5′UTR pre‐mRNA folding thermodynamics and/or specific biological stabilities based around the binding of trans‐acting RNA splicing factors, a consequence of which is scalable splicing sensitivity of a central clock component that is likely tuned to specific temperature environments.

How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY)

“…Second, three different types of transient AS events have been observed (exon skipping in PRR7, use of an alternative 3′ splice site in PRR5, and intron retention in TOC1 as well as in LHY; James, Syed, Bordage, et al, 2012). It is also possible that temperature-dependent remodelling of the structure of LHY pre-mRNA contributes to the changes in the abundance of LHY I1R on cooling (James, Sullivan, & Nimmo, 2018), but whether this could account for transient effects is less clear.…”

An ecological history of the relict genetic lineage of Arabidopsis thaliana

“…For example, genomic analysis of the self-incompatibility locus (S-locus) showed that only relict accessions from northern Africa carry all known major haplogroups, suggesting that the selfing ability of A. thaliana evolved in this region from multiple independent inactivation alleles (Tsuchimatsu et al, 2017;Durvasula et al, 2017). Furthermore, some flowering time genes have also revealed differentiation of relict accessions for the frequency of natural polymorphisms affecting gene function, such as a very low frequency of early loss-of-function alleles of FRIGIDA and multiple functional polymorphisms at FLC, FT, FLM, PHYB, PHYC and LHY genes (Mendez-Vigo et al, 2011;Brennan et al, 2014;Liu et al, 2014;Lutz et al, 2017;de Montaigu and Coupland, 2017;James et al, 2018). In addition, other genes have been detected by phenotypic and environmental genome wide-association (GWA) analyses, like the flowering promoters TSF and SOC1, the transcription factors LUG and SLK1 involved in flower development, or the stress regulator EIN2 (The 1001 Genomes Consortium, 2016; Lee et al 2017;Tabas-Madrid et al, 2018).…”

A Musashi Splice Variant and Its Interaction Partners Influence Temperature Acclimation in Chlamydomonas

“…A putative splice regulator, Porcupine, was identified recently as a temperature-specific regulator of development in Arabidopsis (Capovilla et al, 2018). Also, the central clock component Late Elongated Hypocotyl is subject to temperature-dependent splicing of its transcripts within the 5′ UTR (James et al, 2018). In silico analyses also have found that alternative splicing occurs in C. reinhardtii, whereby the most prominent splicing event was intron retention (Labadorf et al, 2010;Raj-Kumar et al, 2017).…”