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Research Project: Conserved Genes and Signaling Networks that Control Environmental Responses of C4 Grain Crops

Location: Plant Gene Expression Center

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

item MARSHALL, CARINE - University Of California
item Harmon, Frank

Submitted to: BMC Research Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2022
Publication Date: 3/22/2022
Citation: Marshall, C.M., Harmon, F.G. 2022. Impact of the sickle mutant and temperature on the structure of transcripts and RNAs from Arabidopsis thaliana. BMC Research Notes. 15. Article 110.

Interpretive Summary: This publication describes 12 next generation sequencing files, known as FASTQ files, publicly released to the National Center for Biotechnology Information Short Read Archive. This is an open access database for data sharing in the scientific community. Collectively, this set of FASTQ files reports on RNA products from gene expression activity in the model plant Arabidopsis thaliana, analyzed with a method known as RNAseq transcriptome profiling. The reason these data were generated was to identify how the combination of exon sequences in messenger RNA (mRNA) molecules changes when Arabidopsis seedlings have weaker SICKLE gene function and/or are exposed to a warm (28°C) or cool (16°C) temperature. This work was motivated by prior studies indicating this mutant produces atypical mRNA splice variants and the exact types of mRNA splice variants present depend on the growth temperature of the plants. The released files are RNAseq transcriptome profiling of pooled RNA samples, made by combining RNA extracted from seedlings collected at 4-hour intervals over 20 hours while plants were under continuous white lighting and either 28°C or 16°C. Pooling allowed screening for messenger RNAs with time-specific accumulation within the temporal window of sample collection. This data set is useful for investigation of the factors that shape the makeup of the global mRNA pool in Arabidopsis and other plants including crop species. It is mRNAs that ultimately define the traits of all plants.

Technical 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 in sic-3 of atypical mRNA splice variants 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 of Arabidopsis (Col-0 ecotype) wild type or sic-3 seedlings exposed to 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 hours over 20 hours. 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.