Identification of small RNAs during cold acclimation in Arabidopsis thaliana

Tiwari, Bhavika; Habermann, Kristin; Arif, Muhammad; Weil, Heinrich Lukas; Garcia‐Molina, Antoni; Kleine, Tatjana; Mühlhaus, Timo; Frank, Wolfgang

doi:10.1186/s12870-020-02511-3

Cited by 33 publications

(25 citation statements)

References 153 publications

(197 reference statements)

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“…Recently published work indicates that retrograde signalling modulates nuclear gene expression not only by triggering differential transcript accumulation, but also by altering splicing patterns (Petrillo et al ., 2014), read‐through events (Crisp et al ., 2018) and microRNA biogenesis (Fang et al ., 2019). Accordingly, our consortium has identified specific small RNAs (sRNAs) that respond to GUN signals (Habermann et al ., 2020) or exposure to cold (Tiwari et al ., 2020), and we have constructed a cold‐specific miRNA and transcription factor‐dependent gene regulatory network.…”

Section: Ra3 Signalling: Coordination Of Different Acclimation Respomentioning

confidence: 99%

Acclimation in plants – the Green Hub consortium

et al. 2021

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Summary Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to ‘smart breeding’ methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast‐related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.

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Section: Ra3 Signalling: Coordination Of Different Acclimation Respomentioning

confidence: 99%

Acclimation in plants – the Green Hub consortium

et al. 2021

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“…However, the functions of DEmiRs in loranthus seeds under cold stress require further experiments to be explored. miR408 is a highly conserved miRNA in plants and has been recognized to be induced by cold and other abiotic stresses [3]. It has the potential of regulating the genes encoding phytocyanin family proteins (e.g., cupredoxin, plantacyanin, and uclacyanin) [26] and phytophenol oxidases (laccases) [27], which are oxidize flavonoids during seed development and environmental stress [28].…”

Section: Discussionmentioning

confidence: 99%

“…MicroRNAs (miRNA) are a class of endogenous small noncoding RNAs (18~24 nt) that regulate protein expression on the posttranscriptional level via messenger RNA (mRNA) cleavage or translational repression [ 2 , 3 ]. In plants, miRNA primary transcripts are stabilized by DAWDLE and processed to the miRNA : miRNA ∗ duplexes by DCL1, HYL1, SE, and nuclear CBC in D-bodies [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

“…For example, miR168, miR397, miR164, and miR1029 were differentially expressed in wheat genotype C-306 under cold stress [ 7 ]. In Arabidopsis, Tiwari et al identified 93 cold-responsive differentially expressed miRNAs (e.g., miR160, miR169, miR408, and miR779.1) and identified that the target genes of these miRNAs encoded proteins acting in the transcriptional regulation [ 3 ]. To understand the miRNA functions under cold stress in Populus tomentosa , Chen et al compared the miRNA expression profiles of plantlets treated or not with cold conditions (4°C for 8 h) and identified 30 differentially regulated miRNAs from 11 miRNA families, including miR167, miR395, and miR1450 [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

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Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress

Wan

Song

et al. 2021

BioMed Research International

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Taxillus chinensis (DC.) Danser, a parasitic plant that belongs to the Loranthaceae family, has a long history of being used in the Chinese medicine. We observed that the loranthus seeds were sensitive to temperature and could lose viability below 0°C quickly. Thus, we performed small RNA sequencing to study the microRNA (miRNA) regulation in the loranthus seeds under cold stress. In total, we identified 600 miRNAs, for the first time, in the loranthus seeds under cold stress. Then, we detected 224, 229, and 223 miRNAs ( TPM > 1 ) in A0 (control), A1 (cold treatment for 12 h at 0°C), and A2 (cold treatment for 36 h at 0°C), respectively. We next identified 103 differentially expressed miRNAs (DEmiRs) in the loranthus seeds in response to cold. Notably, miR408 was upregulated during the cold treatment, which can regulate genes encoding phytocyanin family proteins and phytophenol oxidases. Some DEmiRs were specific to A1 and may function in early response to cold, such as gma-miR393b-3p, miR946, ath-miR779.2-3p, miR398, and miR9662. It is interesting that ICE3, IAA13, and multiple transcription factors (e.g., WRKY and CRF4 and TCP4) regulated by the DEmiRs have been reported to respond cold in other plants. We further identified 4, 3, and 4 DEmiRs involved in the pathways “responding to cold,” “responding to abiotic stimulus,” and “seed development/germination,” respectively. qRT-PCR was used to confirm the expression changes of DEmiRs and their targets in the loranthus seeds during the cold treatment. This is the first time to study cold-responsive miRNAs in loranthus, and our findings provide a valuable resource for future studies.

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“…The mRNA and sRNA sequencing data of untreated control samples obtained after 3 h, 6 h, and 2 days time points have been already published in our previous study ( Tiwari et al, 2020 ). The mRNA sequencing data of high light treated biological triplicates obtained after 3 h and 2 days have been reported previously ( Garcia-Molina et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana

et al. 2021

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The biological significance of non-coding RNAs (ncRNAs) has been firmly established to be important for the regulation of genes involved in stress acclimation. Light plays an important role for the growth of plants providing the energy for photosynthesis; however, excessive light conditions can also cause substantial defects. Small RNAs (sRNAs) are a class of non-coding RNAs that regulate transcript levels of protein-coding genes and mediate epigenetic silencing. Next generation sequencing facilitates the identification of small non-coding RNA classes such as miRNAs (microRNAs) and small-interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), but changes in the ncRNA transcriptome in response to high light are poorly understood. We subjected Arabidopsis plants to high light conditions and performed a temporal in-depth study of the transcriptome data after 3 h, 6 h, and 2 days of high light treatment. We identified a large number of high light responsive miRNAs and sRNAs derived from NAT gene pairs, lncRNAs and TAS transcripts. We performed target predictions for differentially expressed miRNAs and correlated their expression levels through mRNA sequencing data. GO analysis of the targets revealed an overrepresentation of genes involved in transcriptional regulation. In A. thaliana, sRNA-mediated regulation of gene expression in response to high light treatment is mainly carried out by miRNAs and sRNAs derived from NAT gene pairs, and from lncRNAs. This study provides a deeper understanding of sRNA-dependent regulatory networks in high light acclimation.

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Identification of small RNAs during cold acclimation in Arabidopsis thaliana

Cited by 33 publications

References 153 publications

Acclimation in plants – the Green Hub consortium

Acclimation in plants – the Green Hub consortium

Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress

Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana

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