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Transcriptomic profiling of Arabidopsis primary root tips of brl3 mutant exposed to DNA damaging agent zeocin [RNA-seq]

ABSTRACT: Brassinosteroids (BRs) are steroid hormones involved in multiple processes of plant growth and development, and the adaptation to the environment. Some of the processes regulated by BRs are meristem activity and stem cell divisions. At the core of the root stem cell niche, it is placed the quiescent center (QC), that act as a cell reservoir. QC cells only trigger their divisions when need to replenish the stem cells, for example, after a DNA damage. BR signaling is in charge of triggering these QC divisions, but the exact mechanisms of how this process is regulated is still unknown. Here, we use an interdisciplinary approach, using Arabidopsis thaliana as a model system, including molecular genetics, physiology and bioinformatics to decipher the role of BR receptors upon DNA damage regulating the QC divisions. The results uncover novel roles for the BR-receptor kinase BRL3 (BRI1-like 3) receptor in DNA damage response (DDR) in plants, by modulating the DNA repair and the cell-cycle progression. We identified candidate tissue-specific transcriptional regulator, specifically expressed in the QC cells, the RNR2A (RIBONUCLEOTIDE REDUCTASE 2A), in charge of maintaining dNTPs (deoxynucleotide triphosphates) supply during DNA synthesis that is modulated by BRL3 downstream signaling events. Considering the importance of plant stem cells and their tissues for biomass accumulation and constantly exposed to adverse environmental stresses that can cause DNA damage or cell-cycle arrest in the RAM, here we stablished the mechanism linking root meristematic activity to the DDR through the cell-specific steroid receptor kinase BRL3.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE199741 | GEO | 2022/04/02

REPOSITORIES: GEO

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Project description:Brassinosteroids (BRs) are a class of class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined. Small RNA libraries were constructed from control and epibrassinolide-treated seedlings. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes. In results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudo genes and others. Of these, a transgene, BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs while BRI1 mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a-5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However, SPL3, a target of BR-inducible miR156g, is down-regulated by BRs. BR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.

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Transcriptomic profiling of Arabidopsis primary root tips of brl3 mutant exposed to DNA damaging agent zeocin [RNA-seq]

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