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Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

ABSTRACT: Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

PROVIDER: PRJNA514040 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8424680.fastq.gz	Fastqsanger.gz
	SRR8424690.fastq.gz	Fastqsanger.gz
	SRR8424700.fastq.gz	Fastqsanger.gz
	SRR8424681.fastq.gz	Fastqsanger.gz
	SRR8424691.fastq.gz	Fastqsanger.gz

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Tissue-specific structurome changes in the RNA structurome mediate salt salinity response in Arabidopsis

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Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis.

Project description:Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base-pairing or protection. Salt stress refolded transcripts differentially in root versus shoot, evincing tissue specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stress-related mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5'UTR, CDS, and 3'UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name "concordancy." Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.

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Physiological and transcriptional reprogramming in adaptation to salinity stress in endangered mangrove associate Hernandia nymphaeifolia

Project description:Hernandia nymphaeifolia is an endangered mangrove associate with high ecological, ornamental, and medicinal values. Its special combination of glycophytic and halophytic characteristics provides an ideal system for investigating salt-responsive mechanisms that may be easily extended to genetic improvement of crops with high salt tolerance. However, little is known regarding salt-responsive mechanisms in H. nymphaeifolia. In this study, we posed gradient salt treatments on H. nymphaeifolia seedlings and investigated their physiological and transcriptional reprogramming in response to salinity stress. The results revealed that hyper-salinity stress posed more adverse impacts on leaf growth, cell integrity and photosynthetic performance of H. nymphaeifolia seedlings compared to those in growing in fresh water or low salt condition, mirroring its nature as a mangrove associate. Genes associated with osmolarity sensor and regulator, ROS scavenging and ion homeostasis were differentially expressed accordingly to alleviate the destructive effects. Furthermore, our results unraveled some pivotal kinases and proteins that regulate the synergistic expression of salt-responsive genes, which may act a key role in regulating the transcriptional remodeling upon salinity stress. These findings enrich our knowledge on the molecular mechanisms underlying the phenotypic plasticity of mangrove associates, and also provide valuable genetic resources for mangrove’s conservation and potential bioengineering application in agricultural field.

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