Interactions and links among the noncoding RNAs in plants under stresses

PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA interaction prediction

(2020) Qiang Kang et al.   BIOINFORMATICS

Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress

(2020) Lingling Lv et al.   PLoS One

Identification of lncRNAs and their regulatory relationships with target genes and corresponding miRNAs in melon response to powdery mildew fungi

(2020) Xiaoxu Zhou et al.   GENE

Identification of miR390-TAS3-ARF pathway in response to salt stress in Helianthus tuberosus L.

(2020) Fen Liang Wen et al.   GENE

Sly‐lncRNA15492 interacts with Sly‐miR482a and affects Solanum lycopersicum immunity against Phytophthora infestans

(2020) Ning Jiang et al.   PLANT JOURNAL

Noncoding RNAs: functional regulatory factors in tomato fruit ripening

(2020) Lili Ma et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide identification of Arabidopsis long noncoding RNAs in response to the blue light

(2020) Zhenfei Sun et al.   Scientific Reports

Identification of tomato circular RNAs responsive to Phytophthora infestans

(2020) Yu-Hui Hong et al.   GENE

Identification and functional prediction of soybean CircRNAs involved in low-temperature responses

(2020) Xuesong Wang et al.   JOURNAL OF PLANT PHYSIOLOGY

Rcirc: An R Package for circRNA Analyses and Visualization

(2020) Peisen Sun et al.   Frontiers in Genetics

Differential co-expression networks of long non-coding RNAs and mRNAs in Cleistogenes songorica under water stress and during recovery

(2019) Qi Yan et al.   BMC PLANT BIOLOGY

Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms

(2019) Yuwen Yang et al.   PLoS Pathogens

Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction

(2019) Ning Jiang et al.   Horticulture Research

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs

(2019) Cristiane P. G. Calixto et al.   Frontiers in Plant Science

Advances in understanding salt tolerance in rice

(2019) Showkat Ahmad Ganie et al.   THEORETICAL AND APPLIED GENETICS

Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato

(2019) Alex Canto-Pastor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A large‐scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis

(2019) Pei Zhang et al.   PLANT JOURNAL

PLIT: An alignment-free computational tool for identification of long non-coding RNAs in plant transcriptomic datasets

(2019) Sumukh Deshpande et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Identification of cucumber circular RNAs responsive to salt stress

(2019) Yong-Xing Zhu et al.   BMC PLANT BIOLOGY

Recent advances in small RNA mediated plant-virus interactions

(2019) Ashish Prasad et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Identification of lncRNAs responsive to infection by Plasmodiophora brassicae in clubroot-susceptible and -resistant Brassica napus lines carrying resistance introgressed from rutabaga

(2019) Aarohi Summanwar et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Characterization and cloning of grape circular RNAs identified the cold resistance-related Vv-circATS1

(2019) Zhen Gao et al.   PLANT PHYSIOLOGY

Systematic identification of long non‐coding RNA s expressed during light‐induced anthocyanin accumulation in apple fruit

(2019) Tuo Yang et al.   PLANT JOURNAL

Small RNAs – Big Players in Plant-Microbe Interactions

(2019) Chien-Yu Huang et al.   Cell Host & Microbe

Micro RNA 528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper‐containing proteins in monocots

(2019) Hong Zhu et al.   NEW PHYTOLOGIST

Genome-wide Identification of LncRNAs and Analysis of CeRNA Networks during Tomato Resistance to Phytophthora infestans

(2019) Jun Cui et al.   PHYTOPATHOLOGY

Plant Noncoding RNAs: Hidden Players in Development and Stress Responses

(2019) Yu Yu et al.   Annual Review of Cell and Developmental Biology

Function of miR825 and miR825* as Negative Regulators in Bacillus cereus AR156-elicited Systemic Resistance to Botrytis cinerea in Arabidopsis thaliana

(2019) Pingping Nie et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Brassica miRNA Regulates Plant Growth and Immunity through Distinct Modes of Action

(2019) Chen Cui et al.   Molecular Plant

Super-precise new CRISPR tool could tackle a plethora of genetic diseases

(2019) Heidi Ledford   NATURE

Chinese wheat mosaic virus ‐derived vsiRNA‐20 can regulate virus infection in wheat through inhibition of vacuolar‐ (H + )‐PPase induced cell death

(2019) Jian Yang et al.   NEW PHYTOLOGIST

Re-analysis of long non-coding RNAs and prediction of circRNAs reveal their novel roles in susceptible tomato following TYLCV infection

(2018) Jinyan Wang et al.   BMC PLANT BIOLOGY

Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress

(2018) Fenni Deng et al.   BMC PLANT BIOLOGY

Integrative analysis of long non-coding RNA acting as ceRNAs involved in chilling injury in tomato fruit

(2018) Yunxiang Wang et al.   GENE

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

(2018) Michael J. Axtell et al.   PLANT CELL

The PILNCR1-miR399 regulatory module is important for low-phosphate tolerance in maize

(2018) Qingguo Du et al.   PLANT PHYSIOLOGY

DAWDLE Interacts with DICER-LIKE Proteins to Mediate Small RNA Biogenesis

(2018) Shuxin Zhang et al.   PLANT PHYSIOLOGY

Transcriptome and miRNA analyses of the response to Corynespora cassiicola in cucumber

(2018) Xiangyu Wang et al.   Scientific Reports

A role for small RNA in regulating innate immunity during plant growth

(2018) Yingtian Deng et al.   PLoS Pathogens

A Novel LncRNA, MuLnc1, Associated With Environmental Stress in Mulberry (Morus multicaulis)

(2018) Ying-Ping Gai et al.   Frontiers in Plant Science

Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq

(2018) Liuxin Xiang et al.   PeerJ

Identification and characterization of long noncoding RNA in Paulownia tomentosa treated with methyl methane sulfonate

(2018) Zhe Wang et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Function identification of miR482b, a negative regulator during tomato resistance to Phytophthora infestans

(2018) Ning Jiang et al.   Horticulture Research

Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency

(2018) Zhaoliang Zhang et al.   Journal of Integrative Plant Biology

LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato- Phytophthora infestans interactions

(2018) Jun Cui et al.   PLANT JOURNAL

Unveiling gibberellin-responsive coding and long noncoding RNAs in maize

(2018) Yijun Wang et al.   PLANT MOLECULAR BIOLOGY

Exploring miRNAs for developing climate-resilient crops: A perspective review

(2018) Jin Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

PlantcircBase: A Database for Plant Circular RNAs

(2017) Qinjie Chu et al.   Molecular Plant

Elucidating the molecular mechanisms mediating plant salt-stress responses

(2017) Yongqing Yang et al.   NEW PHYTOLOGIST

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

The functions of plant small RNAs in development and in stress responses

(2017) Shengjun Li et al.   PLANT JOURNAL

Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance toPhytophthora infestansby co-expressing glutaredoxin

(2017) Jun Cui et al.   PLANT JOURNAL

Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis

(2017) Ting Pan et al.   PLANT MOLECULAR BIOLOGY

MicroRNA396a-5p and -3p induce tomato disease susceptibility by suppressing target genes and upregulating salicylic acid

(2017) Lei Chen et al.   PLANT SCIENCE

Effective enhancement of resistance to Phytophthora infestans by overexpression of miR172a and b in Solanum lycopersicum

(2017) Yushi Luan et al.   PLANTA

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

(2017) Monika Piwecka et al.   SCIENCE

Transcriptome-wide identification of host genes targeted by tomato spotted wilt virus-derived small interfering RNAs

(2017) Shunmugiah V. Ramesh et al.   VIRUS RESEARCH

Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana

(2017) Gang Chen et al.   Frontiers in Plant Science

Characterization and Function of MicroRNA∗s in Plants

(2017) Wei-wei Liu et al.   Frontiers in Plant Science

A long noncoding RNA involved in rice reproductive development by negatively regulating osa-miR160

(2017) Meng Wang et al.   Science Bulletin

Combining Results from Distinct MicroRNA Target Prediction Tools Enhances the Performance of Analyses

(2017) Arthur C. Oliveira et al.   Frontiers in Genetics

Non-coding RNAs and Their Roles in Stress Response in Plants

(2017) Jingjing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Conservation and Function of RNA Secondary Structure in Plants

(2016) Lee E. Vandivier et al.   Annual Review of Plant Biology

Deciphering the roles of circRNAs on chilling injury in tomato

(2016) Jinhua Zuo et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Long noncoding RNAs: Re-writing dogmas of RNA processing and stability

(2016) Jeremy E. Wilusz   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2016) Hong Zhang et al.   BMC GENOMICS

Bacillus cereusAR156 primes induced systemic resistance by suppressing miR825/825* and activating defense-related genes inArabidopsis

(2016) Dongdong Niu et al.   Journal of Integrative Plant Biology

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

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

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice

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

Transcription factors involved in drought tolerance and their possible role in developing drought tolerant cultivars with emphasis on wheat (Triticum aestivum L.)

(2016) Vijay Gahlaut et al.   THEORETICAL AND APPLIED GENETICS

Characterization of long non-coding RNAs involved in cadmium toxic response in Brassica napus

(2016) Sheng Jun Feng et al.   RSC Advances

PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)

(2016) Gökhan Karakülah et al.   PLoS One

Long non-coding RNAs and their functions in plants

(2015) Julia A Chekanova   CURRENT OPINION IN PLANT BIOLOGY

Primary transcripts of microRNAs encode regulatory peptides

(2015) Dominique Lauressergues et al.   NATURE

The noncoding RNAs SNORD50A and SNORD50B bind K-Ras and are recurrently deleted in human cancer

(2015) Zurab Siprashvili et al.   NATURE GENETICS

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypiumspp.)

(2015) Maojun Wang et al.   NEW PHYTOLOGIST

Widespread noncoding circular RNAs in plants

(2015) Chu-Yu Ye et al.   NEW PHYTOLOGIST

An Lnc RNA (GAS5)/SnoRNA-derived piRNA induces activation of TRAIL gene by site-specifically recruiting MLL/COMPASS-like complexes

(2015) Xin He et al.   NUCLEIC ACIDS RESEARCH

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

Inhibiting plant microRNA activity: molecularSPONGEs, targetMIMICsand STTMs all display variable efficacies against target microRNAs

(2015) Marlene Reichel et al.   PLANT BIOTECHNOLOGY JOURNAL

Transcriptome-wide investigation of circular RNAs in rice

(2015) Tingting Lu et al.   RNA

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

(2015) Yuan Gao et al.   GENOME BIOLOGY

Drought tolerance evaluation of tobacco plants transformed with different set of genes under laboratory and field conditions

(2015) Yuanhua Wang et al.   Science Bulletin

Engineering thermotolerant plants: a solution to protecting crop production threatened by global warming

(2015) Jianmin Wan   Science Bulletin

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

(2015) Jinyan Wang et al.   Scientific Reports

A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction

(2014) Prashant K Srivastava et al.   BMC GENOMICS

microRNA biogenesis, degradation and activity in plants

(2014) Meng Xie et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Different roles for RNA silencing and RNA processing components in virus recovery and virus-induced gene silencing in plants

(2014) Xiaofang Ma 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

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

PNRD: a plant non-coding RNA database

(2014) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Evolutionary history of plant microRNAs

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

The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling

(2014) Jie Liu et al.   PLoS Genetics

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.)

(2013) CHUNHUA YANG et al.   PLANT CELL AND ENVIRONMENT

miRNA*: A Passenger Stranded in RNA-Induced Silencing Complex?

(2012) S. M. Mah et al.   CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION

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

(2012) Andrzej T Wierzbicki   CURRENT OPINION IN PLANT BIOLOGY

RNA Silencing and Plant Viral Diseases

(2012) Ming-Bo Wang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Effective Small RNA Destruction by the Expression of a Short Tandem Target Mimic in Arabidopsis

(2012) J. Yan et al.   PLANT CELL

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393∗-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12

(2011) Xiaoming Zhang et al.   MOLECULAR CELL

Top 10 plant viruses in molecular plant pathology

(2011) KAREN-BETH G. SCHOLTHOF et al.   MOLECULAR PLANT PATHOLOGY

Identification of human miRNA precursors that resemble box C/D snoRNAs

(2011) Motoharu Ono et al.   NUCLEIC ACIDS RESEARCH

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis

(2011) E. A. Devers et al.   PLANT PHYSIOLOGY

Viral Small Interfering RNAs Target Host Genes to Mediate Disease Symptoms in Plants

(2011) Neil A. Smith et al.   PLoS Pathogens

A Viral Satellite RNA Induces Yellow Symptoms on Tobacco by Targeting a Gene Involved in Chlorophyll Biosynthesis using the RNA Silencing Machinery

(2011) Hanako Shimura et al.   PLoS Pathogens

Efficient Silencing of Endogenous MicroRNAs Using Artificial MicroRNAs in Arabidopsis thaliana

(2010) Andrew L. Eamens et al.   Molecular Plant

PmiRKB: a plant microRNA knowledge base

(2010) Y. Meng et al.   NUCLEIC ACIDS RESEARCH

LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems

(2010) Silke Schulze et al.   PLANT JOURNAL

A Collection of Target Mimics for Comprehensive Analysis of MicroRNA Function in Arabidopsis thaliana

(2010) Marco Todesco et al.   PLoS Genetics

Predicting microRNA targets and functions: traps for the unwary

(2009) William Ritchie et al.   NATURE METHODS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

PMRD: plant microRNA database

(2009) Zhenhai Zhang et al.   NUCLEIC ACIDS RESEARCH

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

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

RNA Silencing in Plants: Yesterday, Today, and Tomorrow

(2008) A. Eamens et al.   PLANT PHYSIOLOGY