The long noncoding RNA T5120 regulates nitrate response and assimilation in Arabidopsis

Nitrate Transport, Signaling, and Use Efficiency

(2018) Ya-Yun Wang et al.   Annual Review of Plant Biology

Molecular Regulation of Nitrate Responses in Plants

(2018) Lufei Zhao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis

(2018) Yoshie Maeda et al.   Nature Communications

FIP1 Plays an Important Role in Nitrate Signaling and Regulates CIPK8 and CIPK23 Expression in Arabidopsis

(2018) Chao Wang et al.   Frontiers in Plant Science

The Arabidopsis NLP7 gene regulates nitrate signaling via NRT1.1–dependent pathway in the presence of ammonium

(2018) Lufei Zhao et al.   Scientific Reports

Transcriptional regulation of nitrogen-associated metabolism and growth

(2018) Allison Gaudinier et al.   NATURE

Nitrate signaling and the control of Arabidopsis growth and development

(2018) Isabel Fredes et al.   CURRENT OPINION IN PLANT BIOLOGY

Discovery of nitrate–CPK–NLP signalling in central nutrient–growth networks

(2017) Kun-hsiang Liu et al.   NATURE

The Arabidopsis CPSF30-L gene plays an essential role in nitrate signaling and regulates the nitrate transceptor gene NRT1.1

(2017) Zehui Li et al.   NEW PHYTOLOGIST

A Tripartite Amplification Loop Involving the Transcription Factor WRKY75, Salicylic Acid, and Reactive Oxygen Species Accelerates Leaf Senescence

(2017) Pengru Guo et al.   PLANT CELL

ELF18-INDUCED LONG-NONCODING RNA Associates with Mediator to Enhance Expression of Innate Immune Response Genes in Arabidopsis

(2017) Jun Sung Seo et al.   PLANT CELL

Interacting TCP and NLP transcription factors control plant responses to nitrate availability

(2017) Peizhu Guan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overexpression of the Maize ZmNLP6 and ZmNLP8 Can Complement the Arabidopsis Nitrate Regulatory Mutant nlp7 by Restoring Nitrate Signaling and Assimilation

(2017) Huairong Cao et al.   Frontiers in Plant Science

Functions of plants long non-coding RNAs

(2016) Sarfraz Shafiq et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat

(2016) Siyuan Zhan et al.   BMC GENOMICS

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 characterization of novel lncRNAs in Populus under nitrogen deficiency

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

Nitrate Transport, Sensing, and Responses in Plants

(2016) José A. O'Brien et al.   Molecular Plant

The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators

(2016) Na Xu et al.   PLANT CELL

Overexpression of a pH-sensitive nitrate transporter in rice increases crop yields

(2016) Xiaorong Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transporters Involved in Root Nitrate Uptake and Sensing by Arabidopsis

(2016) Mélanie Noguero et al.   Frontiers in Plant Science

Overexpression of Arabidopsis NLP7 improves plant growth under both nitrogen-limiting and -sufficient conditions by enhancing nitrogen and carbon assimilation

(2016) Lin-Hui Yu et al.   Scientific Reports

Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development

(2015) Chunying Kang et al.   BMC GENOMICS

Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing

(2015) Tian-Zuo Wang et al.   BMC PLANT BIOLOGY

Plant nitrogen assimilation and its regulation: a complex puzzle with missing pieces

(2015) Anne Krapp   CURRENT OPINION IN PLANT BIOLOGY

Molecular functions of long noncoding transcripts in plants

(2015) Jae Bok Heo et al.   JOURNAL OF PLANT BIOLOGY

Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies

(2015) Bin Hu et al.   NATURE GENETICS

Multiple mechanisms of nitrate sensing by Arabidopsis nitrate transceptor NRT1.1

(2015) E. Bouguyon et al.   Nature Plants

Nitrogen signalling pathways shaping root system architecture: an update

(2014) Brian G Forde   CURRENT OPINION IN PLANT BIOLOGY

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

The Primary Nitrate Response: a multifaceted signalling pathway

(2014) Anna Medici et al.   JOURNAL OF EXPERIMENTAL BOTANY

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis

(2014) Yuqiu Wang et al.   Molecular Plant

Characterization of stress-responsive lncRNAs inArabidopsis thalianaby integrating expression, epigenetic and structural features

(2014) Chao Di et al.   PLANT JOURNAL

Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response ofArabidopsis thalianaroots

(2014) José M. Alvarez et al.   PLANT JOURNAL

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light

(2014) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrate foraging byArabidopsisroots is mediated by the transcription factor TCP20 through the systemic signaling pathway

(2014) Peizhu Guan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nutrient computation for root architecture

(2014) T. Bisseling et al.   SCIENCE

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots

(2013) Elena A Vidal et al.   BMC GENOMICS

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

ETHYLENE-INSENSITIVE3 Is a Senescence-Associated Gene That Accelerates Age-Dependent Leaf Senescence by Directly Repressing miR164 Transcription in Arabidopsis

(2013) Z. Li et al.   PLANT CELL

Arabidopsis NIN-like transcription factors have a central role in nitrate signalling

(2013) Mineko Konishi et al.   Nature Communications

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

(2013) Chloé Marchive et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Plant Nitrogen Assimilation and Use Efficiency

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

Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants

(2012) Yijun Meng et al.   BMC GENOMICS

The role of long non-coding RNA in transcriptional gene silencing

(2012) Andrzej T Wierzbicki   CURRENT OPINION IN PLANT BIOLOGY

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa

(2012) Ting-Ting Liu et al.   Molecular Plant

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

(2011) Mingming Xin et al.   BMC PLANT BIOLOGY

Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis

(2011) Gang Li et al.   NATURE CELL BIOLOGY

ArabidopsisNitrate Transporter NRT1.9 Is Important in Phloem Nitrate Transport

(2011) Ya-Yun Wang et al.   PLANT CELL

Nitrate signaling: adaptation to fluctuating environments

(2010) Gabriel Krouk et al.   CURRENT OPINION IN PLANT BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

miR390,Arabidopsis TAS3tasiRNAs, and TheirAUXIN RESPONSE FACTORTargets Define an Autoregulatory Network Quantitatively Regulating Lateral Root Growth

(2010) Elena Marin et al.   PLANT CELL

Identification of a nitrate-responsive cis-element in the Arabidopsis NIR1 promoter defines the presence of multiple cis-regulatory elements for nitrogen response

(2010) Mineko Konishi et al.   PLANT JOURNAL

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana

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

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

CHL1 Functions as a Nitrate Sensor in Plants

(2009) Cheng-Hsun Ho et al.   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

(2009) Szymon Swiezewski et al.   NATURE

A Genetic Screen for Nitrate Regulatory Mutants Captures the Nitrate Transporter Gene NRT1.1

(2009) R. Wang et al.   PLANT PHYSIOLOGY

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL

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

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

An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants

(2008) Abdelaty Saleh et al.   Nature Protocols

Nitrate signalling mediated by the NRT1.1 nitrate transporter antagonises l-glutamate-induced changes in root architecture

(2008) Pia Walch-Liu et al.   PLANT JOURNAL

The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis

(2008) Loren Castaings et al.   PLANT JOURNAL

AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response

(2008) Heng-Cheng Hu et al.   PLANT JOURNAL

Diamonds in the rough: mRNA-like non-coding RNAs

(2008) Linda A. Rymarquis et al.   TRENDS IN PLANT SCIENCE