Impact of the sickle mutant and temperature on the structure of transcripts and RNAs from Arabidopsis thaliana

Abstract

Objectives The objective of this data set was to identify how interaction between temperature and the sickle-3 (sic-3) mutant alters the global messenger RNA (mRNA) content of Arabidopsis thaliana seedlings. The motivation was discovery of atypical mRNA splice variants in sic-3 that differed with seedling growth temperature. The expected outcome was identification of mRNA splice variants altered by sic-3, temperature, or the combination of temperature and genotype. Data description The data set is RNAseq profiling of Arabidopsis (Col-0 ecotype) wild type and sic-3 seedlings under 16 °C or 28 °C. A comprehensive view of global mRNA sequences and their content was captured by deep sequencing of RNA pools made from sets of seedlings sampled every 4 h over 20 h. This data set contains sequences representing the spectrum of mRNA splice variants from individual genes, as well as from mRNA-related sequences like spliced introns. This data set enables detection of significant changes in gene-level expression and relative levels of mRNA splice variants caused by the different growth temperatures, the sic-3 mutation or both factors. This data set is useful to study production of mRNA splice variants and other mRNA-related RNAs in a range of plant species because Arabidopsis is a model plant.

Lariat debranching by RNA DEBRANCHING ENZYME 1 depends on SICKLE inArabidopsis thaliana

“…Previous work showed that sic-3 accumulates high levels of splice variants for several circadian clock-associated transcripts, a phenotype exacerbated by exposure to 16°C (Marshall et al, 2016). To understand the global impact of sic-3 on transcript splicing at 16°C, we performed the RNAseq experiment described in SFigure 1A (Marshall & Harmon, 2022) and calculated differential usage of exons or introns in sic-3 relative to wild-type Columbia-0 (Col-0) with the ASpli computational pipeline (Mancini et al, 2021) (Supplementary Methods). The ASpli approach divides genes into subgenic exon and intron features based on existing annotations and then tests for differential usage of these features.…”