Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

Regulatory non-coding RNAs in plants: potential gene resources for the improvement of agricultural traits

(2016) Sang-Yoon Shin et al.   Plant Biotechnology Reports

Identification of novel and salt-responsive miRNAs to explore miRNA-mediated regulatory network of salt stress response in radish (Raphanus sativus L.)

(2015) Xiaochuan Sun et al.   BMC GENOMICS

Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage

(2015) Boon Huat Cheah et al.   BMC GENOMICS

Novel and conserved miRNAs in the halophyte Suaeda maritima identified by deep sequencing and computational predictions using the ESTs of two mangrove plants

(2015) Sachin Ashruba Gharat et al.   BMC PLANT BIOLOGY

Genome-wide identification of chromium stress-responsive micro RNAs and their target genes in tobacco (Nicotiana tabacum) roots

(2015) Syed Asad Hussain Bukhari et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

miR408 overexpression causes increased drought tolerance in chickpea

(2015) Mortaza Hajyzadeh et al.   GENE

Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp.

(2015) Deepti Nigam et al.   GENE

Expression of zma-miR169 miRNAs and their target ZmNF-YA genes in response to abiotic stress in maize leaves

(2015) Mingda Luan et al.   GENE

Identification and Functional Analysis of MicroRNAs and Their Targets in Platanus acerifolia under Lead (Pb) Stress

(2015) Yuanlong Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Overexpression of soybean miR172c confers tolerance to water deficit and salt stress, but increases ABA sensitivity in transgenic Arabidopsis thaliana

(2015) Wenbin Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

MicroRNA: a new target for improving plant tolerance to abiotic stress

(2015) Baohong Zhang   JOURNAL OF EXPERIMENTAL BOTANY

Identification and Characterization of ABA-Responsive MicroRNAs in Rice

(2015) Caijuan Tian et al.   Journal of Genetics and Genomics

MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild-growing species

(2015) Conchita Alonso et al.   Molecular Ecology Resources

sRNAtoolbox: an integrated collection of small RNA research tools

(2015) Antonio Rueda et al.   NUCLEIC ACIDS RESEARCH

The Regulatory Status of Genome-edited Crops

(2015) Jeffrey D. Wolt et al.   PLANT BIOTECHNOLOGY JOURNAL

Small RNA deep sequencing reveals the important role of microRNAs in the halophyteHalostachys caspica

(2015) Ruirui Yang et al.   PLANT BIOTECHNOLOGY JOURNAL

Sp-miR396a-5p acts as a stress-responsive genes regulator by conferring tolerance to abiotic stresses and susceptibility to Phytophthora nicotianae infection in transgenic tobacco

(2015) Lei Chen et al.   PLANT CELL REPORTS

Group II late embryogenesis abundant (LEA) proteins: structural and functional aspects in plant abiotic stress

(2015) Aditya Banerjee et al.   PLANT GROWTH REGULATION

miR408is involved in abiotic stress responses in Arabidopsis

(2015) Chao Ma et al.   PLANT JOURNAL

Genome-wide identification of abiotic stress-regulated and novel microRNAs in mulberry leaf

(2015) Ping Wu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

MicroRNAs in cotton: an open world needs more exploration

(2015) Qinglian Wang et al.   PLANTA

Unique miRNome during anthesis in drought-tolerant indica rice var. Nagina 22

(2015) Shivani Kansal et al.   PLANTA

Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling

(2015) Amita Yadav et al.   PLANTA

Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress

(2015) Aditya Banerjee et al.   PROTOPLASMA

DNA methylation and physio-biochemical analysis of chickpea in response to cold stress

(2015) Aida Rakei et al.   PROTOPLASMA

Metabolic and molecular-genetic regulation of proline signaling and itscross-talk with major effectors mediates abiotic stress tolerance in plants

(2015) Aryadeep ROYCHOUDHURY et al.   TURKISH JOURNAL OF BOTANY

Morphological, physiological and yield responses of durum wheat to pre-anthesis water-deficit stress are genotype-dependent

(2015) Haipei Liu et al.   Crop & Pasture Science

miRTex: A Text Mining System for miRNA-Gene Relation Extraction

(2015) Gang Li et al.   PLoS Computational Biology

miRNA regulation of nutrient homeostasis in plants

(2015) Soumitra Paul et al.   Frontiers in Plant Science

Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

(2015) Maria Barciszewska-Pacak et al.   Frontiers in Plant Science

Targeting Non-Coding RNAs in Plants with the CRISPR-Cas Technology is a Challenge yet Worth Accepting

(2015) Jolly Basak et al.   Frontiers in Plant Science

isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology

(2015) Gaurav Sablok et al.   Frontiers in Plant Science

Profiling the expression domains of a rice-specific microRNA under stress

(2015) Neha Sharma et al.   Frontiers in Plant Science

Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution

(2015) Anita Tripathi et al.   Frontiers in Physiology

Transcripts and MicroRNAs Responding to Salt Stress in Musa acuminata Colla (AAA Group) cv. Berangan Roots

(2015) Wan Sin Lee et al.   PLoS One

Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis)

(2015) Chao Zheng et al.   PLoS One

Genome-Wide Identification of MicroRNAs in Leaves and the Developing Head of Four Durum Genotypes during Water Deficit Stress

(2015) Haipei Liu et al.   PLoS One

miRLocator: Machine Learning-Based Prediction of Mature MicroRNAs within Plant Pre-miRNA Sequences

(2015) Haibo Cui et al.   PLoS One

A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems

(2014) Yifan Peng et al.   BMC BIOINFORMATICS

MicroRNA–target gene responses to lead-induced stress in cotton (Gossypium hirsutum L.)

(2014) Qiuling He et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Conserved miRNAs and Their Response to Salt Stress in Wild Eggplant Solanum linnaeanum Roots

(2014) Yong Zhuang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley

(2014) Katarzyna Kruszka et al.   JOURNAL OF EXPERIMENTAL BOTANY

Global microRNA modification in cotton (Gossypium hirsutumL.)

(2014) Fuliang Xie et al.   PLANT BIOTECHNOLOGY JOURNAL

The key players of the primary root growth and development also function in lateral roots in Arabidopsis

(2014) Huiyu Tian et al.   PLANT CELL REPORTS

Comparison of the physiological effects and transcriptome responses of Populus simonii under different abiotic stresses

(2014) Yuepeng Song et al.   PLANT MOLECULAR BIOLOGY

A Genome-Wide Perspective of miRNAome in Response to High Temperature, Salinity and Drought Stresses in Brassica juncea (Czern) L

(2014) Ankur R. Bhardwaj et al.   PLoS One

Discovery and Analysis of MicroRNAs in Leymus chinensis under Saline-Alkali and Drought Stress Using High-Throughput Sequencing

(2014) Junfeng Zhai et al.   PLoS One

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants

(2014) Deblina Patra et al.   Frontiers in Plant Science

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

isomiRID: a framework to identify microRNA isoforms

(2013) Luiz Felipe Valter de Oliveira et al.   BIOINFORMATICS

Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation

(2013) Feng Xu et al.   BMC GENOMICS

Global transcriptome profiles of Camellia sinensis during cold acclimation

(2013) Xin-Chao Wang et al.   BMC GENOMICS

Characterization of phosphorus-regulated miR399 and miR827 and their isomirs in barley under phosphorus-sufficient and phosphorus-deficient conditions

(2013) Michael Hackenberg et al.   BMC PLANT BIOLOGY

Genome-wide identification of Thellungiella salsuginea microRNAs with putative roles in the salt stress response

(2013) Quan Zhang et al.   BMC PLANT BIOLOGY

PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress

(2013) Shihua Zhang et al.   BMC PLANT BIOLOGY

Introns of plant pri-miRNAs enhance miRNA biogenesis

(2013) Dawid Bielewicz et al.   EMBO REPORTS

isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets

(2013) Gaurav Sablok et al.   FEBS LETTERS

Plant Acyl-CoA:Lysophosphatidylcholine Acyltransferases (LPCATs) Have Different Specificities in Their Forward and Reverse Reactions

(2013) Ida Lager et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

miR172 Regulates Soybean Nodulation

(2013) Zhe Yan et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

Cross-talk between abscisic acid-dependent and abscisic acid-independent pathways during abiotic stress

(2013) Aryadeep Roychoudhury et al.   PLANT CELL REPORTS

Global identification of miRNAs and targets in Populus euphratica under salt stress

(2013) Bosheng Li et al.   PLANT MOLECULAR BIOLOGY

CoLIde

(2013) Irina Mohorianu et al.   RNA Biology

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

C-mii: a tool for plant miRNA and target identification

(2012) Somrak Numnark et al.   BMC GENOMICS

miR395 is a general component of the sulfate assimilation regulatory network in Arabidopsis

(2012) Colette A. Matthewman et al.   FEBS LETTERS

Physiological and molecular analysis of the interaction between aluminium toxicity and drought stress in common bean (Phaseolus vulgaris)

(2012) Zhong-Bao Yang et al.   JOURNAL OF EXPERIMENTAL BOTANY

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

(2012) Jiyuan An et al.   NUCLEIC ACIDS RESEARCH

Regulation of miR399f Transcription by AtMYB2 Affects Phosphate Starvation Responses in Arabidopsis

(2012) D. Baek et al.   PLANT PHYSIOLOGY

A genome-wide survey of microRNA truncation and 3′ nucleotide addition events in larch (Larix leptolepis)

(2012) Junhong Zhang et al.   PLANTA

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Identification of Nitrogen Starvation-Responsive MicroRNAs in Arabidopsis thaliana

(2012) Gang Liang et al.   PLoS One

Interactions of NADP-Reducing Enzymes Across Varying Environmental Conditions: A Model of Biological Complexity

(2012) Teresa Z. Rzezniczak et al.   G3-Genes Genomes Genetics

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

(2011) S. K. Wyman et al.   GENOME RESEARCH

Toward a Digital Gene Response: RNA G-Quadruplexes with Fewer Quartets Fold with Higher Cooperativity

(2011) Melissa A. Mullen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis

(2011) Meng Zhao et al.   NEW PHYTOLOGIST

Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network

(2011) Dortje Golldack et al.   PLANT CELL REPORTS

Interplay of SLIM1 and miR395 in the regulation of sulfate assimilation in Arabidopsis

(2011) Cintia G. Kawashima et al.   PLANT JOURNAL

Phosphate Utilization Efficiency Correlates with Expression of Low-Affinity Phosphate Transporters and Noncoding RNA, IPS1, in Barley

(2011) C. Y. Huang et al.   PLANT PHYSIOLOGY

Genetic Regulation by NLA and MicroRNA827 for Maintaining Nitrate-Dependent Phosphate Homeostasis in Arabidopsis

(2011) Surya Kant et al.   PLoS Genetics

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

(2010) Eric Bonnet et al.   BIOINFORMATICS

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

(2010) Mingming Xin et al.   BMC PLANT BIOLOGY

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

Contribution of the PeroxisomalacoxGene to the Dynamic Balance of Daumone Production inCaenorhabditis elegans

(2010) Hyoe-Jin Joo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica)

(2010) Tian Li et al.   NUCLEIC ACIDS RESEARCH

Global analysis of microRNA in Arabidopsis in response to phosphate starvation as studied by locked nucleic acid-based microarrays

(2010) Maria Lundmark et al.   PHYSIOLOGIA PLANTARUM

A set of miRNAs from Brassica napus in response to sulphate deficiency and cadmium stress

(2010) Si Qi Huang et al.   PLANT BIOTECHNOLOGY JOURNAL

HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models

(2009) Sabah Kadri et al.   BMC BIOINFORMATICS

Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling

(2009) Qing Liu et al.   FEBS LETTERS

Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis

(2009) Dov Moldovan et al.   JOURNAL OF EXPERIMENTAL BOTANY

UV-B-responsive microRNAs in Populus tremula

(2009) Xiaoyun Jia et al.   JOURNAL OF PLANT PHYSIOLOGY

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

Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs

(2009) Bogna Szarzynska et al.   NUCLEIC ACIDS RESEARCH

Expression analysis suggests potential roles of microRNAs for phosphate and arbuscular mycorrhizal signaling inSolanum lycopersicum

(2009) Mian Gu et al.   PHYSIOLOGIA PLANTARUM

Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress

(2009) Catalina Arenas-Huertero et al.   PLANT MOLECULAR BIOLOGY

Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing

(2009) B. D. Pant et al.   PLANT PHYSIOLOGY

Submergence-responsive MicroRNAs are Potentially Involved in the Regulation of Morphological and Metabolic Adaptations in Maize Root Cells

(2008) Zuxin Zhang et al.   ANNALS OF BOTANY

Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula

(2008) Zhao Sheng Zhou et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

(2008) R. D. Morin et al.   GENOME RESEARCH

MicroRNA-mediated Systemic Down-regulation of Copper Protein Expression in Response to Low Copper Availability inArabidopsis

(2008) Salah E. Abdel-Ghany et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis

(2008) Bikram Datt Pant et al.   PLANT JOURNAL

Cell-specific nitrogen responses mediate developmental plasticity

(2008) M. L. Gifford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA