Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress

Abstract

Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.

Assessing Transcriptomic Responses to Oxidative Stress: Contrasting Wild-Type Arabidopsis Seedlings with dss1(I) and dss1(V) Gene Knockout Mutants

“…It is considerably downregulated in dss1(V) mutants. According to different studies, this gene is involved in the removal of H 2 O 2 , the biosynthesis and degradation of lignin, the response to environmental stresses, pathogen attack, and oxidative stress [ 40 ]. However, it remains unproven whether the regulation of PRX70 enzyme transcription could be directly influenced by DSS1(V).…”

The Role of lncRNAs in Pig Muscle in Response to Cold Exposure

“…It has been demonstrated that low temperature alters the expression of lncRNAs and mRNAs in plants and animals [24][25][26][27]. When Enshi black pigs were exposed to low temperatures, acute cold stress-induced more DElncRNAs and response pathways compared to cold acclimation.…”

Is winter coming? Impact of the changing climate on plant responses to cold temperature

“…For instance, 135 differentially expressed lncRNAs have been identified in the early stages of cold treatment in Arabidopsis (Calixto et al, 2019). Applying more rigorous filtering for noncoding potential, another recent study identified 114 novel lncRNAs on 86 loci (Liu, Cai, et al, 2022). While it remains to be tested how many of (Heo & Sung, 2011;Kim & Sung, 2017;Swiezewski et al, 2009).…”

“…Perception of cold, both as a stress and cue for development, triggers signalling cascades that converge in the nucleus in a dynamic reprogramming of the plant transcriptome. Interestingly, numerous A. thaliana genes are either responsive to short‐term (timescale of hours) or long‐term (timescale of months) cold treatments (Calixto et al, 2018; Fowler & Thomashow, 2002; Li et al, 2021; Liu, Cai, et al, 2022; Xi et al, 2020). Although most transcriptomic studies have so far measured steady‐state RNA (messenger RNA [mRNA]) levels, recent developments are allowing monitoring of the dynamics of the nascent transcriptome in response to cold (Kindgren et al, 2019).…”

“…For instance, 135 differentially expressed lncRNAs have been identified in the early stages of cold treatment in Arabidopsis (Calixto et al, 2019). Applying more rigorous filtering for noncoding potential, another recent study identified 114 novel lncRNAs on 86 loci (Liu, Cai, et al, 2022). While it remains to be tested how many of these loci are indeed required for cold responses, a number of Arabidopsis examples are relatively well‐characterized, namely, asCBF1 and SVALKA (Kindgren et al, 2018), COLD‐INDUCED LONG ANTISENSE INTRAGENIC RNA ( COOLAIR ), COLD ASSISTED INTRONIC NONCODING RNA ( COLDAIR ) and COLD OF WINTER‐INDUCED NONCODING RNA FROM THE PROMOTER ( COLDWRAP ) (Heo & Sung, 2011; Kim & Sung, 2017; Swiezewski et al, 2009).…”