Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance

Role of microRNAs and their target genes in salinity response in plants

(2017) Abolfazl Lotfi et al.   PLANT GROWTH REGULATION

Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

(2017) Philippe Gallusci et al.   TRENDS IN PLANT SCIENCE

Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants

(2017) Ana M. Fortes et al.   Frontiers in Plant Science

Identification of Salt Tolerance-related microRNAs and Their Targets in Maize (Zea mays L.) Using High-throughput Sequencing and Degradome Analysis

(2017) Rong Fu et al.   Frontiers in Plant Science

Differential growth and yield responses of salt-tolerant and susceptible rice cultivars to individual (Na+ and Cl−) and additive stress effects of NaCl

(2016) Vinay Kumar et al.   ACTA PHYSIOLOGIAE PLANTARUM

MicroRNA and target gene responses to salt stress in grafted cucumber seedlings

(2016) Yansu Li et al.   ACTA PHYSIOLOGIAE PLANTARUM

Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses

(2016) Ying Yu et al.   BMC PLANT BIOLOGY

Salt stress alters DNA methylation levels in alfalfa (Medicago spp)

(2016) A. Al-Lawati et al.   GENETICS AND MOLECULAR RESEARCH

Soybean miR172a Improves Salt Tolerance and Can Function as a Long-Distance Signal

(2016) Wen-Jia Pan et al.   Molecular Plant

RNAcentral: a comprehensive database of non-coding RNA sequences

(2016)   NUCLEIC ACIDS RESEARCH

Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels

(2016) Jakub Dolata et al.   PLANT PHYSIOLOGY

Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis

(2016) Cristian Forestan et al.   Scientific Reports

Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants

(2016) Hsiao-Lin V. Wang et al.   Wiley Interdisciplinary Reviews-RNA

Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions

(2016) Rohit Joshi et al.   Frontiers in Plant Science

DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

(2016) Philippe Gallusci et al.   Frontiers in Plant Science

New Insights on Plant Salt Tolerance Mechanisms and Their Potential Use for Breeding

(2016) Moez Hanin et al.   Frontiers in Plant Science

Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis

(2016) Stefanie Dukowic-Schulze et al.   Frontiers in Plant Science

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

(2016) Varsha Shriram et al.   Frontiers in Plant Science

MicroRNA, a new target for engineering new crop cultivars

(2016) Baohong Zhang et al.   Bioengineered

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

(2016) P. A. Crisp et al.   Science Advances

siRNAmod: A database of experimentally validated chemically modified siRNAs

(2016) Showkat Ahmad Dar et al.   Scientific Reports

P-SAMS: a web site for plant artificial microRNA and synthetictrans-acting small interfering RNA design

(2015) Noah Fahlgren et al.   BIOINFORMATICS

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

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

Level and pattern of DNA methylation changes in rice cold tolerance introgression lines derived from Oryza rufipogon Griff.

(2015) Liang-Fang Dai et al.   EUPHYTICA

Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress

(2015) Showkat Ahmad Ganie et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

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

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

(2015) Baohong Zhang   JOURNAL OF EXPERIMENTAL BOTANY

Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel)

(2015) Hana Zandkarimi et al.   MOLECULAR BIOLOGY REPORTS

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

sRNAtoolbox: an integrated collection of small RNA research tools

(2015) Antonio Rueda et al.   NUCLEIC ACIDS RESEARCH

miR408is involved in abiotic stress responses in Arabidopsis

(2015) Chao Ma et al.   PLANT JOURNAL

Constitutive Expression of RiceMicroRNA528Alters Plant Development and Enhances Tolerance to Salinity Stress and Nitrogen Starvation in Creeping Bentgrass

(2015) Shuangrong Yuan et al.   PLANT PHYSIOLOGY

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNAs and drought responses in sugarcane

(2015) Agustina Gentile et al.   Frontiers in Plant Science

Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus

(2015) Reyhaneh Ebrahimi Khaksefidi et al.   Frontiers in Plant Science

Methylation of miRNA genes in the response to temperature stress in Populus simonii

(2015) Dong Ci 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

Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress

(2015) Pingchuan Deng et al.   PLoS One

miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy

(2015) Alexander S. Baras et al.   PLoS One

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

(2015) Rohini Garg et al.   Scientific Reports

Histone acetylation associated up-regulation of the cell wall related genes is involved in salt stress induced maize root swelling

(2014) Hui Li et al.   BMC PLANT BIOLOGY

History and current status of wheat miRNAs using next-generation sequencing and their roles in development and stress

(2014) H. Budak et al.   Briefings in Functional 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

Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton

(2014) Fuliang Xie et al.   JOURNAL OF EXPERIMENTAL BOTANY

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Small RNA deep sequencing identifies novel and salt-stress-regulated microRNAs from roots ofMedicago sativaandMedicago truncatula

(2014) Rui-Cai Long et al.   PHYSIOLOGIA PLANTARUM

Overexpression of a miR393-Resistant Form of Transport Inhibitor Response Protein 1 (mTIR1) Enhances Salt Tolerance by Increased Osmoregulation and Na+ Exclusion in Arabidopsis thaliana

(2014) Zhehao Chen et al.   PLANT AND CELL PHYSIOLOGY

Epigenetic Memory for Stress Response and Adaptation in Plants

(2014) Tetsu Kinoshita et al.   PLANT AND CELL PHYSIOLOGY

Comprehensive genome-wide identification and expression profiling of foxtail millet [Setaria italica (L.)] miRNAs in response to abiotic stress and development of miRNA database

(2014) Yusuf Khan et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Na+ and Cl− ions show additive effects under NaCl stress on induction of oxidative stress and the responsive antioxidative defense in rice

(2014) Tushar Khare et al.   PROTOPLASMA

Import routes and nuclear functions of Argonaute and other small RNA-silencing proteins

(2014) Daniel Schraivogel et al.   TRENDS IN BIOCHEMICAL SCIENCES

Epigenetic Regulation in Plants

(2014) C. S. Pikaard et al.   Cold Spring Harbor Perspectives in Biology

tasiRNA-ARF Pathway Moderates Floral Architecture inArabidopsisPlants Subjected to Drought Stress

(2014) Akihiro Matsui et al.   Biomed Research International

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

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

Individual and additive effects of Na+and Cl−ions on rice under salinity stress

(2014) Vinay Kumar et al.   Archives of Agronomy and Soil Science

Polyamines in response to abiotic stress tolerance through transgenic approaches

(2014) Malabika Roy Pathak et al.   GM Crops & Food-Biotechnology in Agriculture and the Food Chain

tasiRNAdb: a database of ta-siRNA regulatory pathways

(2013) Changqing Zhang et al.   BIOINFORMATICS

PMTED: a plant microRNA target expression database

(2013) Xiuli Sun et al.   BMC BIOINFORMATICS

Compatible Solute Engineering in Plants for Abiotic Stress Tolerance - Role of Glycine Betaine

(2013) Shabir Hussain Wani et al.   CURRENT GENOMICS

ST105 Deep sequencing reveals abundant Pol III retroviral microRNA cluster in Bovine Leukemia Virus-induced leukemia

(2013) Nicolas Rosewick et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

A potential role of microRNAs in plant response to metal toxicity

(2013) Zhi Min Yang et al.   Metallomics

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Epigenetic mechanisms of plant stress responses and adaptation

(2013) Pranav Pankaj Sahu et al.   PLANT CELL REPORTS

MicroRNA-mediated gene regulation: potential applications for plant genetic engineering

(2013) Man Zhou et al.   PLANT MOLECULAR BIOLOGY

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

(2013) Bosheng Li et al.   PLANT MOLECULAR BIOLOGY

Constitutive Expression of a miR319 Gene Alters Plant Development and Enhances Salt and Drought Tolerance in Transgenic Creeping Bentgrass

(2013) M. Zhou et al.   PLANT PHYSIOLOGY

High-Throughput Sequencing of Small RNA Transcriptome Reveals Salt Stress Regulated MicroRNAs in Sugarcane

(2013) Mariana Carnavale Bottino et al.   PLoS One

MicroRNA-mediated regulation of target genes in several brain regions is correlated to both microRNA-targeting-specific promoter methylation and differential microRNA expression

(2013) Y-h Taguchi   BioData Mining

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

(2012) M. B. Stocks et al.   BIOINFORMATICS

High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice

(2012) Blanca E Barrera-Figueroa et al.   BMC PLANT BIOLOGY

microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.)

(2012) Anca Macovei et al.   BMC PLANT BIOLOGY

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

ddm1 plants are sensitive to methyl methane sulfonate and NaCl stresses and are deficient in DNA repair

(2012) Youli Yao et al.   PLANT CELL REPORTS

RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

(2012) Qi Zheng et al.   PLANT JOURNAL

Roles of DICER-LIKE and ARGONAUTE Proteins in TAS-Derived Small Interfering RNA-Triggered DNA Methylation

(2012) L. Wu et al.   PLANT PHYSIOLOGY

MicroRNA Expression Analysis in the Cellulosic Biofuel Crop Switchgrass (Panicum virgatum) under Abiotic Stress

(2012) Guiling Sun et al.   PLoS One

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

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

RNA-directed DNA methylation

(2011) Huiming Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

Salt and Drought Stresses Induce the Aberrant Expression of microRNA Genes in Tobacco

(2011) Taylor P. Frazier et al.   MOLECULAR BIOTECHNOLOGY

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

The Arabidopsis trithorax-like factor ATX1 functions in dehydration stress responses via ABA-dependent and ABA-independent pathways

(2011) Yong Ding et al.   PLANT JOURNAL

Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

(2011) Lei Chen et al.   PLANTA

Plant siRNAs from introns mediate DNA methylation of host genes

(2011) D. Chen et al.   RNA

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

(2010) Eric Bonnet et al.   BIOINFORMATICS

Transcriptional Control of Gene Expression by MicroRNAs

(2010) Basel Khraiwesh et al.   CELL

Non-coding small RNAs responsive to abiotic stress in wheat (Triticum aestivum L.)

(2010) Yingyin Yao et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

(2010) BERNARD ANGERS et al.   MOLECULAR ECOLOGY

MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity

(2010) Oswaldo Valdés-López et al.   NEW PHYTOLOGIST

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

siRNAs from miRNA sites mediate DNA methylation of target genes

(2010) Padmanabhan Chellappan et al.   NUCLEIC ACIDS RESEARCH

Over-expression of osa-MIR396c decreases salt and alkali stress tolerance

(2010) Peng Gao et al.   PLANTA

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

(2008) B. Ben Amor et al.   GENOME RESEARCH

Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana

(2008) H.-H. Liu et al.   RNA