Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana

The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

(2023) Meenakshi Mittal et al.   Plant Genome

Intronic microRNA‐directed regulation of mitochondrial reactive oxygen species enhances plant stress tolerance in Arabidopsis

(2023) Wei‐Bo Xu et al.   NEW PHYTOLOGIST

Mitochondrial retrograde signaling through UCP1-mediated inhibition of the plant oxygen-sensing pathway

(2022) Pedro Barreto et al.   CURRENT BIOLOGY

The Evolution and Functional Roles of miR408 and Its Targets in Plants

(2022) Yu Gao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

microRNAs and Their Roles in Plant Development

(2022) Qingkun Dong et al.   Frontiers in Plant Science

MicroRNA Mediated Plant Responses to Nutrient Stress

(2022) Waqar Islam et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Role of Sugars in Plant Responses to Stress and Their Regulatory Function during Development

(2022) Philippe Jeandet et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ORANGE negatively regulates flowering time in Arabidopsis thaliana

(2022) Qi Wang et al.   JOURNAL OF PLANT PHYSIOLOGY

The miR408a-BBP-LAC3/CSD1 module regulates anthocyanin biosynthesis mediated by crosstalk between copper homeostasis and ROS homeostasis during light induction in Malus plants

(2022) Yujing Hu et al.   Journal of Advanced Research

Abiotic stress‐induced anthocyanins in plants: Their role in tolerance to abiotic stresses

(2021) Aung Htay Naing et al.   PHYSIOLOGIA PLANTARUM

Superoxide is promoted by sucrose and affects amplitude of circadian rhythms in the evening

(2021) Ángela Román et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent advances in the regulation of plant miRNA biogenesis

(2021) Mu Li et al.   RNA Biology

sRNAanno—a database repository of uniformly annotated small RNAs in plants

(2021) Chengjie Chen et al.   Horticulture Research

Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination

(2021) Yu Wu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The miR169n-NF-YA8 regulation module involved in drought resistance in Brassica napus L

(2021) Jian Li et al.   PLANT SCIENCE

Overexpression of the rice ORANGE gene OsOR negatively regulates carotenoid accumulation, leads to higher tiller numbers and decreases stress tolerance in Nipponbare rice

(2021) Yang Yu et al.   PLANT SCIENCE

Dynamic regulation of small RNAs in anthocyanin accumulation during blueberry fruit maturation

(2021) Xiaobai Li et al.   Scientific Reports

Glucose- and sucrose-signaling modules regulate the Arabidopsis juvenile-to-adult phase transition

(2021) Lai-Sheng Meng et al.   Cell Reports

Over-expression of Arabidopsis ORANGE gene enhances drought stress tolerance through ABA-dependent pathway in Arabidopsis thaliana

(2021) Yong-Jie Shan et al.   PLANT GROWTH REGULATION

Identification of an Allelic Variant of the CsOr Gene Controlling Fruit Endocarp Color in Cucumber (Cucumis sativus L.) Using Genotyping-By-Sequencing (GBS) and Whole-Genome Sequencing

(2021) D. S. Kishor et al.   Frontiers in Plant Science

MdMYB8 is associated with flavonol biosynthesis via the activation of the MdFLS promoter in the fruits of Malus crabapple

(2020) Hua Li et al.   Horticulture Research

Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants

(2020) Alice Lunardon et al.   GENOME RESEARCH

Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism

(2020) Nan Jiang et al.   Nature Communications

BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa

(2020) Bo Zhou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

MiR156 regulates anthocyanin biosynthesis through SPL targets and other microRNAs in poplar

(2020) Yamei Wang et al.   Horticulture Research

PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction

(2020) Yuanlong Liu et al.   PLANT CELL

Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance

(2020) Yajie Li et al.   Nature Communications

Sugar Signaling During Fruit Ripening

(2020) Sara Durán-Soria et al.   Frontiers in Plant Science

Flavonoid biosynthetic and starch and sucrose metabolic pathways are involved in the pigmentation of naturally brown-colored cotton fibers

(2020) Zhen Peng et al.   INDUSTRIAL CROPS AND PRODUCTS

mdm-miR828 Participates in the Feedback Loop to Regulate Anthocyanin Accumulation in Apple Peel

(2020) Bo Zhang et al.   Frontiers in Plant Science

Metabolomic Elucidation of the Effect of Sucrose on the Secondary Metabolite Profiles in Melissa officinalis by Ultraperformance Liquid Chromatography–Mass Spectrometry

(2020) Sooah Kim et al.   ACS Omega

MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis

(2019) Rainer Schwacke et al.   Molecular Plant

­The Role of UV-B Light on Small RNA Activity During Grapevine Berry Development

(2019) Sukumaran Sunitha et al.   G3-Genes Genomes Genetics

Modulation of miRNA expression in natural populations of A. thaliana along a wide altitudinal gradient of Indian Himalayas

(2019) Abhinandan Mani Tripathi et al.   Scientific Reports

MicroRNAs and Their Regulatory Roles in Plant–Environment Interactions

(2019) Xianwei Song et al.   Annual Review of Plant Biology

miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes

(2019) Varsha Tirumalai et al.   JOURNAL OF EXPERIMENTAL BOTANY

Biology and Function of miR159 in Plants

(2019) Anthony A. Millar et al.   Plants-Basel

MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis

(2019) Alexandra Plotnikova et al.   PLANT CELL

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

(2019) Caili Li et al.   PeerJ

The miR396–GRF Regulatory Module Controls the Embryogenic Response in Arabidopsis via an Auxin-Related Pathway

(2019) Szczygieł-Sommer et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A novel approach to carotenoid accumulation in rice callus by mimicking the cauliflower Orange mutation via genome editing

(2019) Akira Endo et al.   Rice

Characterization of Carotenoid Biosynthesis in Newly Isolated Deinococcus sp. AJ005 and Investigation of the Effects of Environmental Conditions on Cell Growth and Carotenoid Biosynthesis

(2019) Jun Young Choi et al.   Marine Drugs

Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato

(2018) Mohammad Yazdani et al.   PLANT BIOTECHNOLOGY JOURNAL

Ambient temperature regulates the expression of a small set of sRNAs influencing plant development through NF-YA2 and YUC2

(2018) Péter Gyula et al.   PLANT CELL AND ENVIRONMENT

miR393 inhibits in vitro shoot regeneration in Arabidopsis thaliana via repressing TIR1

(2018) Long Wang et al.   PLANT SCIENCE

Regulation of microRNA biogenesis and its crosstalk with other cellular pathways

(2018) Thomas Treiber et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Rice peroxisomal ascorbate peroxidase knockdown affects ROS signaling and triggers early leaf senescence

(2017) Carolina W. Ribeiro et al.   PLANT SCIENCE

Small RNAs: Big Impact on Plant Development

(2017) Marco D’Ario et al.   TRENDS IN PLANT SCIENCE

Regulation of miR163 and its targets in defense against Pseudomonas syringae in Arabidopsis thaliana

(2017) Hiu Tung Chow et al.   Scientific Reports

Repression of MYBL2 by Both microRNA858a and HY5 Leads to the Activation of Anthocyanin Biosynthetic Pathway in Arabidopsis

(2016) Yulong Wang et al.   Molecular Plant

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

A high resolution map of theArabidopsis thalianadevelopmental transcriptome based on RNA-seq profiling

(2016) Anna V. Klepikova et al.   PLANT JOURNAL

mRNA decay of most Arabidopsis miRNA targets requires slicer activity of AGO1

(2016) Laura Arribas-Hernández et al.   PLANT PHYSIOLOGY

Role of sugars under abiotic stress

(2016) Fareen Sami et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Improved Placement of Multi-mapping Small RNAs

(2016) Nathan R. Johnson et al.   G3-Genes Genomes Genetics

Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana

(2016) Mingli Xu et al.   PLoS Genetics

Identification of miRNAs associated with dark-induced senescence in Arabidopsis

(2015) Xiaoying Huo et al.   BMC PLANT BIOLOGY

Reactive oxygen species in cell wall metabolism and development in plants

(2015) Anna Kärkönen et al.   PHYTOCHEMISTRY

miR408is involved in abiotic stress responses in Arabidopsis

(2015) Chao Ma et al.   PLANT JOURNAL

A ‘golden’ SNP inCmOrgoverns the fruit flesh color of melon (Cucumis melo)

(2015) Galil Tzuri et al.   PLANT JOURNAL

Enhanced accumulation of carotenoids in sweetpotato plants overexpressing IbOr-Ins gene in purple-fleshed sweetpotato cultivar

(2015) Sung-Chul Park et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Cesium Toxicity Alters MicroRNA Processing and AGO1 Expressions in Arabidopsis thaliana

(2015) Il Lae Jung et al.   PLoS One

ArabidopsisOR proteins are the major posttranscriptional regulators of phytoene synthase in controlling carotenoid biosynthesis

(2015) Xiangjun Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis

(2015) Gang Liang et al.   Scientific Reports

Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality

(2015) Umesh P. Yadav et al.   Frontiers in Plant Science

PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades

(2014) Qingli Guo et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice

(2014) Yujie Fang et al.   JOURNAL OF EXPERIMENTAL BOTANY

A miR169 isoform regulates specific NF-YA targets and root architecture in Arabidopsis

(2014) Céline Sorin et al.   NEW PHYTOLOGIST

ThemiR156-SPL9-DFRpathway coordinates the relationship between development and abiotic stress tolerance in plants

(2014) Long-Gang Cui et al.   PLANT JOURNAL

Expression of Sucrose Transporter cDNAs Specifically in Companion Cells Enhances Phloem Loading and Long-Distance Transport of Sucrose but Leads to an Inhibition of Growth and the Perception of a Phosphate Limitation

(2014) K. Dasgupta et al.   PLANT PHYSIOLOGY

Family-Wide Survey of miR169s and NF-YAs and Their Expression Profiles Response to Abiotic Stress in Maize Roots

(2014) Mingda Luan et al.   PLoS One

Evolutionary history of plant microRNAs

(2014) Richard S. Taylor et al.   TRENDS IN PLANT SCIENCE

miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development

(2014) Xueying Guan et al.   Nature Communications

From dusk till dawn: the Arabidopsis thaliana sugar starving responsive network

(2014) Maria C. Arias et al.   Frontiers in Plant Science

Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana

(2013) Miao Yun Xu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

(2013) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

ABI1 and PP2CA Phosphatases Are Negative Regulators of Snf1-Related Protein Kinase1 Signaling in Arabidopsis

(2013) A. Rodrigues et al.   PLANT CELL

Overexpression of microRNA828 reduces anthocyanin accumulation in Arabidopsis

(2013) Fengxi Yang et al.   PLANT CELL TISSUE AND ORGAN CULTURE

MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis

(2013) Fan Jia et al.   PLANT MOLECULAR BIOLOGY

A Significant Fraction of 21-Nucleotide Small RNA Originates from Phased Degradation of Resistance Genes in Several Perennial Species

(2013) T. Kallman et al.   PLANT PHYSIOLOGY

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

(2013) S. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156A and MIR156C

(2013) Li Yang et al.   eLife

Photosynthetic control of electron transport and the regulation of gene expression

(2012) Christine H. Foyer et al.   JOURNAL OF EXPERIMENTAL BOTANY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification of new microRNA-regulated genes by conserved targeting in plant species

(2012) Uciel Chorostecki et al.   NUCLEIC ACIDS RESEARCH

IAA-Ala Resistant3, an Evolutionarily Conserved Target of miR167, Mediates Arabidopsis Root Architecture Changes during High Osmotic Stress

(2012) N. Kinoshita et al.   PLANT CELL

Identification of sucrose-responsive microRNAs reveals sucrose-regulated copper accumulations in an SPL7-dependent and independent manner in Arabidopsis thaliana

(2012) Ligang Ren et al.   PLANT SCIENCE

Identification of Nitrogen Starvation-Responsive MicroRNAs in Arabidopsis thaliana

(2012) Gang Liang et al.   PLoS One

The role of the miR399-PHO2 module in the regulation of flowering time in response to different ambient temperatures in Arabidopsis thaliana

(2011) Wanhui Kim et al.   MOLECULES AND CELLS

Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis

(2011) Meng Zhao et al.   NEW PHYTOLOGIST

cis- andtrans-Regulation of miR163 and Target Genes Confers Natural Variation of Secondary Metabolites in TwoArabidopsisSpecies and Their Allopolyploids

(2011) Danny W-K. Ng et al.   PLANT CELL

An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis

(2011) Qing-Jun Luo et al.   PLANT MOLECULAR BIOLOGY

Genetic and Genomic Evidence That Sucrose Is a Global Regulator of Plant Responses to Phosphate Starvation in Arabidopsis

(2011) M. Lei et al.   PLANT PHYSIOLOGY

miR393 and Secondary siRNAs Regulate Expression of the TIR1/AFB2 Auxin Receptor Clade and Auxin-Related Development of Arabidopsis Leaves

(2011) A. Si-Ammour et al.   PLANT PHYSIOLOGY

Cross-talk interactions of sucrose and Fusarium oxysporum in the phenylpropanoid pathway and the accumulation and localization of flavonoids in embryo axes of yellow lupine

(2010) Iwona Morkunas et al.   JOURNAL OF PLANT PHYSIOLOGY

siRNAs from miRNA sites mediate DNA methylation of target genes

(2010) Padmanabhan Chellappan et al.   NUCLEIC ACIDS RESEARCH

Complex Regulation of Two Target Genes Encoding SPX-MFS Proteins by Rice miR827 in Response to Phosphate Starvation

(2010) S.-I. Lin et al.   PLANT AND CELL PHYSIOLOGY

TCP Transcription Factors Regulate the Activities of ASYMMETRIC LEAVES1 and miR164, as Well as the Auxin Response, during Differentiation of Leaves in Arabidopsis

(2010) T. Koyama et al.   PLANT CELL

microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis

(2010) Linda Beauclair et al.   PLANT JOURNAL

Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks

(2010) Weixiong Zhang et al.   PLANT MOLECULAR BIOLOGY

Identification of MicroRNAs Involved in Pathogen-Associated Molecular Pattern-Triggered Plant Innate Immunity

(2010) Y. Li et al.   PLANT PHYSIOLOGY

Aquaporin-3 mediates hydrogen peroxide uptake to regulate downstream intracellular signaling

(2010) E. W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs and Their Roles in Plant Development

(2009) Xuemei Chen   Annual Review of Cell and Developmental Biology

miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana

(2009) Jia-Wei Wang et al.   CELL

Control of cell proliferation in Arabidopsis thaliana by microRNA miR396

(2009) R. E. Rodriguez et al.   DEVELOPMENT

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

(2009) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT

Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing

(2009) L.-C. Hsieh et al.   PLANT PHYSIOLOGY

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

Sucrose, sucrosyl oligosaccharides, and oxidative stress: scavenging and salvaging?

(2008) W. Van den Ende et al.   JOURNAL OF EXPERIMENTAL BOTANY

Gibberellins, jasmonate and abscisic acid modulate the sucrose-induced expression of anthocyanin biosynthetic genes inArabidopsis

(2008) Elena Loreti et al.   NEW PHYTOLOGIST

Interplay of miR164,CUP-SHAPED COTYLEDONgenes andLATERAL SUPPRESSORcontrols axillary meristem formation inArabidopsis thaliana

(2008) Smita Raman et al.   PLANT JOURNAL

Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases

(2008) Diana V. Dugas et al.   PLANT MOLECULAR BIOLOGY

Evolution of Arabidopsis thaliana microRNAs from random sequences

(2008) F. Fenselau de Felippes et al.   RNA

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE