Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies

Small RNA Transcriptome of Hibiscus Syriacus Provides Insights into the Potential Influence of microRNAs in Flower Development and Terpene Synthesis

(2017) Taewook Kim et al.   MOLECULES AND CELLS

Biological functions of natural antisense transcripts

(2016) Wojciech Rosikiewicz et al.   ACTA BIOCHIMICA POLONICA

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)

(2016) Yuanda Lv et al.   BMC GENOMICS

Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum

(2016) Hong Zhang et al.   BMC GENOMICS

Growing Slowly 1locus encodes a PLS-type PPR protein required for RNA editing and plant development in Arabidopsis

(2016) Tingting Xie et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency

(2016) Min Chen et al.   MOLECULAR GENETICS AND GENOMICS

Agronomic nitrogen-use efficiency of rice can be increased by drivingOsNRT2.1expression with theOsNAR2.1promoter

(2016) Jingguang Chen et al.   PLANT BIOTECHNOLOGY JOURNAL

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

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

Transcriptome analysis of nitrogen-starvation-responsive genes in rice

(2015) Wenzhu Yang et al.   BMC PLANT BIOLOGY

Overexpressing of OsAMT1-3, a High Affinity Ammonium Transporter Gene, Modifies Rice Growth and Carbon-Nitrogen Metabolic Status

(2015) Aili Bao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Asparagine Synthetase1, but not Asparagine Synthetase2, is Responsible for the Biosynthesis of Asparagine Following the Supply of Ammonium to Rice Roots

(2015) Miwa Ohashi et al.   PLANT AND CELL PHYSIOLOGY

Application of microRNA gene resources in the improvement of agronomic traits in rice

(2015) Ling-Ling Zheng et al.   PLANT BIOTECHNOLOGY JOURNAL

Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis

(2015) Gang Liang et al.   Scientific Reports

Role of microRNAs involved in plant response to nitrogen and phosphorous limiting conditions

(2015) Giao N. Nguyen et al.   Frontiers in Plant Science

MADS-box Transcription Factor OsMADS25 Regulates Root Development through Affection of Nitrate Accumulation in Rice

(2015) Chunyan Yu et al.   PLoS One

Pentatricopeptide Repeat Proteins in Plants

(2014) Alice Barkan et al.   Annual Review of Plant Biology

MicroRNA-directed cleavage of targets: mechanism and experimental approaches

(2014) June Hyun Park et al.   BMB Reports

Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction

(2014) Yimin Shen et al.   Journal of Chemical Theory and Computation

Rice nitrate transporter OsNPF2.4 functions in low-affinity acquisition and long-distance transport

(2014) Xiudong Xia et al.   JOURNAL OF EXPERIMENTAL BOTANY

AMT1;1 transgenic rice plants with enhanced NH4+ permeability show superior growth and higher yield under optimal and suboptimal NH4+ conditions

(2014) Kosala Ranathunge et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

(2014) Peng Shuai et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evidence supporting distinct functions of three cytosolic glutamine synthetases and two NADH-glutamate synthases in rice

(2014) Tomoyuki Yamaya et al.   JOURNAL OF EXPERIMENTAL BOTANY

A non-canonical plant microRNA target site

(2014) Cécile Brousse et al.   NUCLEIC ACIDS RESEARCH

Biological functions of natural antisense transcripts

(2013) Andreas Werner   BMC BIOLOGY

Physiological analysis of nitrogen-efficient rice overexpressing alanine aminotransferase under different N regimes

(2013) Perrin H. Beatty et al.   Botany

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

The Role of Metallothionein in Oxidative Stress

(2013) Branislav Ruttkay-Nedecky et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching

(2013) Yu-Chan Zhang et al.   NATURE BIOTECHNOLOGY

Nitrogen-Dependent Regulation of De Novo Cytokinin Biosynthesis in Rice: The Role of Glutamine Metabolism as an Additional Signal

(2013) Tomoe Kamada-Nobusada et al.   PLANT AND CELL PHYSIOLOGY

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

(2013) M. Jabnoune et al.   PLANT CELL

NITROGEN LIMITATION ADAPTATION, a Target of MicroRNA827, Mediates Degradation of Plasma Membrane-Localized Phosphate Transporters to Maintain Phosphate Homeostasis in Arabidopsis

(2013) W.-Y. Lin et al.   PLANT CELL

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

(2013) D. Secco et al.   PLANT CELL

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

(2013) Man Zhou et al.   PLANT MOLECULAR BIOLOGY

Manipulation of microRNA expression to improve nitrogen use efficiency

(2013) Jeffrey J. Fischer et al.   PLANT SCIENCE

The Hot Pepper (Capsicum annuum) MicroRNA Transcriptome Reveals Novel and Conserved Targets: A Foundation for Understanding MicroRNA Functional Roles in Hot Pepper

(2013) Dong-Gyu Hwang et al.   PLoS One

Elucidation of miRNAs-Mediated Responses to Low Nitrogen Stress by Deep Sequencing of Two Soybean Genotypes

(2013) Yejian Wang et al.   PLoS One

Pentatricopeptide repeat proteins involved in plant organellar RNA editing

(2013) Yusuke Yagi et al.   RNA Biology

Plant Nitrogen Assimilation and Use Efficiency

(2012) Guohua Xu et al.   Annual Review of Plant Biology

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

(2012) Tingting Lu et al.   BMC GENOMICS

Transcriptome response to nitrogen starvation in rice

(2012) Hongmei Cai et al.   JOURNAL OF BIOSCIENCES

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Expression Patterns of Nine Ammonium Transporters in Rice in Response to N Status

(2012) Su-Mei LI et al.   PEDOSPHERE

Altered expression of thePTR/NRT1homologueOsPTR9affects nitrogen utilization efficiency, growth and grain yield in rice

(2012) Zhongming Fang et al.   PLANT BIOTECHNOLOGY JOURNAL

SLO2, a mitochondrial pentatricopeptide repeat protein affecting several RNA editing sites, is required for energy metabolism

(2012) Qiang Zhu et al.   PLANT JOURNAL

Comparative Analysis of Differentially Expressed Genes in Rice Under Nitrogen and Phosphorus Starvation Stress Conditions

(2012) Hongmei Cai et al.   PLANT MOLECULAR BIOLOGY REPORTER

Nitrogen and phosphorus interaction and cytokinin: Responses of the primary root of Arabidopsis thaliana and the pdr1 mutant

(2012) Taiguer Cerutti et al.   PLANT SCIENCE

Cloning and Characterization of Maize miRNAs Involved in Responses to Nitrogen Deficiency

(2012) Meng Zhao et al.   PLoS One

Genome-Wide Survey and Expression Analysis of Amino Acid Transporter Gene Family in Rice (Oryza sativa L.)

(2012) Heming Zhao et al.   PLoS One

Identification of Nitrogen Starvation-Responsive MicroRNAs in Arabidopsis thaliana

(2012) Gang Liang et al.   PLoS One

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

(2012) J. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hormonal control of nitrogen acquisition: roles of auxin, abscisic acid, and cytokinin

(2011) Takatoshi Kiba et al.   JOURNAL OF EXPERIMENTAL BOTANY

Spatial expression and regulation of rice high-affinity nitrate transporters by nitrogen and carbon status

(2011) Huimin Feng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis

(2011) Meng Zhao et al.   NEW PHYTOLOGIST

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage

(2011) D.-H. Jeong et al.   PLANT CELL

Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.)

(2010) Xiaobo Zhao et al.   BMC PLANT BIOLOGY

Protective effect of metallothionein on oxidative stress-induced DNA damage

(2010) Natalie Chiaverini et al.   FREE RADICAL RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

The SLO1 PPR protein is required for RNA editing at multiple sites with similar upstream sequences in Arabidopsis mitochondria

(2010) Tzu-Ying Sung et al.   PLANT JOURNAL

Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor

(2009) Botao Zhao et al.   BMC MOLECULAR BIOLOGY

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

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rice MicroRNA Effector Complexes and Targets

(2009) L. Wu et al.   PLANT CELL

Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling

(2009) YONG-MEI BI 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

Genetic engineering of improved nitrogen use efficiency in rice by the tissue-specific expression ofalanine aminotransferase

(2008) Ashok K. Shrawat et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)

(2008) C. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA