ArticleBMC plant biology2020
Identification of small RNAs during cold acclimation in Arabidopsis thaliana.
Article in BMC plant biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.International journal of molecular sciences · 2022Pooled it
- High-throughput sequencing and analysis of target genes uncover microRNA-mediated responses to low-temperature stress in Medicago falcata.BMC genomics · 2026Article
- Identification of miRNAs Responsive to a Defined Period of Iron Deficiency and Resupply inPlants (Basel, Switzerland) · 2026Article
- The Emerging Role of the Salt Tolerance-Related Protein in the Abiotic Stress Response ofPlants (Basel, Switzerland) · 2025Review
- Identification and characterization of DICER-LIKE genes and their roles in Marchantia polymorpha development and salt stress response.The Plant journal : for cell and molecular biology · 2025Article
- Molecular Mechanisms Underlying Freezing Tolerance in Plants: Implications for Cryopreservation.International journal of molecular sciences · 2024Review
- Research progress on the physiological response and molecular mechanism of cold response in plants.Frontiers in plant science · 2024Review
- Variations in DNA methylation and the role of regulatory factors in rice (Frontiers in plant science · 2024Article
- Current status for utilization of cold resistance genes and strategies in wheat breeding program.Frontiers in genetics · 2024Review
- Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought.Frontiers in plant science · 2023Article
- Research progress on plant noncoding RNAs in response to low-temperature stress.Plant signaling & behavior · 2022Review
- The Identification ofGenes · 2022Article
- Fine-Tuning Cold Stress Response Through Regulated Cellular Abundance and Mechanistic Actions of Transcription Factors.Frontiers in plant science · 2022Review
- tRNA derived small RNAs-Small players with big roles.Frontiers in genetics · 2022Review
- Review
- Identification of Small RNAs During High Light Acclimation inFrontiers in plant science · 2021Article
- Identification of MicroRNAs inBioMed research international · 2021Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundCold stress causes dynamic changes in gene expression that are partially caused by small non-coding RNAs since they regulate protein coding transcripts and act in epigenetic gene silencing pathways. Thus, a detailed analysis of transcriptional changes of small RNAs (sRNAs) belonging to all known sRNA classes such as microRNAs (miRNA) and small interfering RNA (siRNAs) in response to cold contributes to an understanding of cold-related transcriptome changes.
resultWe subjected A. thaliana plants to cold acclimation conditions (4 °C) and analyzed the sRNA transcriptomes after 3 h, 6 h and 2 d. We found 93 cold responsive differentially expressed miRNAs and only 14 of these were previously shown to be cold responsive. We performed miRNA target prediction for all differentially expressed miRNAs and a GO analysis revealed the overrepresentation of miRNA-targeted transcripts that code for proteins acting in transcriptional regulation. We also identified a large number of differentially expressed cis- and trans-nat-siRNAs, as well as sRNAs that are derived from long non-coding RNAs. By combining the results of sRNA and mRNA profiling with miRNA target predictions and publicly available information on transcription factors, we reconstructed a cold-specific, miRNA and transcription factor dependent gene regulatory network. We verified the validity of links in the network by testing its ability to predict target gene expression under cold acclimation.
conclusionIn A. thaliana, miRNAs and sRNAs derived from cis- and trans-NAT gene pairs and sRNAs derived from lncRNAs play an important role in regulating gene expression in cold acclimation conditions. This study provides a fundamental database to deepen our knowledge and understanding of regulatory networks in cold acclimation.
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