Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

Kim, Hee Eun; Kim, Wanhui; Lee, Ae Ree; Jin, Suhyun; Abe, Jun; Kim, Nak Kyoon; Lee, Joon‐Hwa; Ahn, Ji Hoon

doi:10.1016/j.bbrc.2017.01.185

Cited by 4 publications

(8 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It was predicted that the miRNA targets whose exogenous NO is down-regulated may play a positive regulatory role in drought stress response. mi156a are important miRNA for plant for abiotic stress responses, growth, and development [57]. miR156 can regulate plant stress tolerance by modulating SQUAMOSA promoter-binding-like protein (SPL) genes that function in anthocyanin biosynthesis [36].…”

Section: Discussionmentioning

confidence: 99%

Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Zhao

Wei

et al. 2019

Genes

View full text Add to dashboard Cite

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

show abstract

Section: Discussionmentioning

confidence: 99%

Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Zhao

Wei

et al. 2019

Genes

View full text Add to dashboard Cite

show abstract

“…There are at least two major processing mechanisms found in plant miRNAs (loop-to-base and base-to-loop processing), where the upper stem, lower stem, and bulges are the structural determinants that are important for the accuracy and efficiency of miRNA hairpin processing [ 121 , 123 , 124 , 125 , 126 , 127 ]. Indeed, mutations in the lower stem, upper stem, and bulges of pri-miR156a affect the production of miR156, thus altering the flowering time [ 121 , 128 , 129 ]. Interestingly, although the majority of the mutations in the upper stem and lower stem reduce the efficiency of miR156 formation at both lower and higher ambient temperatures, the effect of the disruption of base pairing in upper stem 2 (S2) was extraordinarily severe at lower temperature, suggesting the importance of S2 in the regulation of temperature-mediated flowering time [ 121 , 128 , 129 ].…”

Section: Non-coding Rnasmentioning

confidence: 99%

“…Indeed, mutations in the lower stem, upper stem, and bulges of pri-miR156a affect the production of miR156, thus altering the flowering time [ 121 , 128 , 129 ]. Interestingly, although the majority of the mutations in the upper stem and lower stem reduce the efficiency of miR156 formation at both lower and higher ambient temperatures, the effect of the disruption of base pairing in upper stem 2 (S2) was extraordinarily severe at lower temperature, suggesting the importance of S2 in the regulation of temperature-mediated flowering time [ 121 , 128 , 129 ]. Therefore, the S2 region likely acts as a structural determinant for temperature-responsive miR156 hairpin processing [ 121 ].…”

Section: Non-coding Rnasmentioning

confidence: 99%

See 1 more Smart Citation

Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time

Susila

Nasim

Ahn

2018

IJMS

View full text Add to dashboard Cite

In plants, environmental conditions such as temperature affect survival, growth, and fitness, particularly during key stages such as seedling growth and reproduction. To survive and thrive in changing conditions, plants have evolved adaptive responses that tightly regulate developmental processes such as hypocotyl elongation and flowering time in response to environmental temperature changes. Increases in temperature, coupled with increasing fluctuations in local climate and weather, severely affect our agricultural systems; therefore, understanding the mechanisms by which plants perceive and respond to temperature is critical for agricultural sustainability. In this review, we summarize recent findings on the molecular mechanisms of ambient temperature perception as well as possible temperature sensing components in plants. Based on recent publications, we highlight several temperature response mechanisms, including the deposition and eviction of histone variants, DNA methylation, alternative splicing, protein degradation, and protein localization. We discuss roles of each proposed temperature-sensing mechanism that affects plant development, with an emphasis on flowering time. Studies of plant ambient temperature responses are advancing rapidly, and this review provides insights for future research aimed at understanding the mechanisms of temperature perception and responses in plants.

show abstract

“…The opening ( k op ) and closing ( k cl ) rate constants and/or equilibrium constant for base-pair opening ( K op = k op / k cl ) can be determined by measuring the exchange using an external catalyst. These experiments have been used to probe base-pair opening in various DNA duplexes [[3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18]], DNAs containing modified base such as 5-flurourasil, N6-methyl adenine, or modified guanine [[19], [20], [21]], UV-induced photoadduct-containing DNA [22], IHF-complexed DNA [23], interstrand cross-linked DNA [24], i-motif structure formed by the complementary C-rich DNA [25,26], various RNAs [15,[27], [28], [29], [30], [31], [32], [33], [34], [35], [36]], peptide nucleic acids (PNAs) [37,38], and threose nucleic acid (TNA) [39]. NMR exchange and single molecule FRET experiments could be used to study the protonation/deprotonation of adenine bases and formation of A + ·C wobble pair [[40], [41], [42], [43], [44]].…”

Section: Introductionmentioning

confidence: 99%

Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function

Choi

Kim

Jin

et al. 2019

Computational and Structural Biotechnology Journal

Self Cite

View full text Add to dashboard Cite

Base-pair opening is a conformational transition that is required for proper biological function of nucleic acids. Hydrogen exchange, observed by NMR spectroscopic experiments, is a widely used method to study the thermodynamics and kinetics of base-pair opening in nucleic acids. The hydrogen exchange data of imino protons are analyzed based on a two-state (open/closed) model for the base-pair, where hydrogen exchange only occurs from the open state. In this review, we discuss examples of how hydrogen exchange data provide insight into several interesting biological processes involving functional interactions of nucleic acids: i ) selective recognition of DNA by proteins; ii ) regulation of RNA cleavage by site-specific mutations; iii ) intermolecular interaction of proteins with their target DNA or RNA; iv ) formation of PNA:DNA hybrid duplexes.

show abstract

Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

Cited by 4 publications

References 24 publications

Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time

Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function

Contact Info

Product

Resources

About