From “Dark Matter” to “Star”: Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

lncRNA–DNA hybrids regulate distant genes

(2020) Aina Maria Mas et al.   EMBO REPORTS

Human Long Noncoding RNA Interactome: Detection, Characterization and Function

(2020) Kazimierczyk et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA

(2020) Federico Ariel et al.   MOLECULAR CELL

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

The Arabidopsis lnc RNA ASCO modulates the transcriptome through interaction with splicing factors

(2020) Richard Rigo et al.   EMBO REPORTS

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

(2020) Ning Jiang et al.   PLANT JOURNAL

An miRNA-encoded small peptide, vvi-miPEP171d1, regulates adventitious root formation

(2020) Qiu-ju Chen et al.   PLANT PHYSIOLOGY

Research Progress on Plant Long Non-Coding RNA

(2020) Ling Wu et al.   Plants-Basel

Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

(2020) Uday Chand Jha et al.   BMC PLANT BIOLOGY

Functional Long Non-coding RNAs Evolve from Junk Transcripts

(2020) Alexander F. Palazzo et al.   CELL

PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs

(2020) Jingjing Jin et al.   NUCLEIC ACIDS RESEARCH

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

(2020) Muhammad Waseem et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants

(2020) Lianhe Zhao et al.   NUCLEIC ACIDS RESEARCH

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

(2020) Bailing Zhou et al.   NUCLEIC ACIDS RESEARCH

Noncoding but Coding: Pri-miRNA into the Action

(2020) Ashish Prasad et al.   TRENDS IN PLANT SCIENCE

Reproductive phasiRNAs regulate reprogramming of gene expression and meiotic progression in rice

(2020) Yu-Chan Zhang et al.   Nature Communications

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

Evolutionary dynamics of linc RNA transcription in nine citrus species

(2019) Lili Ke et al.   PLANT JOURNAL

MicroRNAs and Their Regulatory Roles in Plant–Environment Interactions

(2019) Xianwei Song et al.   Annual Review of Plant Biology

PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR

(2019) Yongke Tian et al.   Science Advances

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

(2019) Tuo Yang et al.   PLANT JOURNAL

Predicting functional long non-coding RNAs validated by low throughput experiments

(2019) Bailing Zhou et al.   RNA Biology

Plant Noncoding RNAs: Hidden Players in Development and Stress Responses

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

Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction

(2019) Jianying Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

(2019) Jaswinder Singh et al.   Nature Communications

LncRNA39026 Enhances Tomato Resistance to Phytophthora infestans by Decoying miR168a and Inducing PR Gene Expression

(2019) Xinxin Hou et al.   PHYTOPATHOLOGY

Expressivity of the key genes associated with seed and pod development is highly regulated via lncRNAs and miRNAs in Pigeonpea

(2019) Antara Das et al.   Scientific Reports

Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering

(2019) Chen Zhu et al.   Frontiers in Plant Science

Transcriptomic and functional analyses unveil the role of long non-coding RNAs in anthocyanin biosynthesis during sea buckthorn fruit ripening

(2018) Guoyun Zhang et al.   DNA RESEARCH

Analysis of long-non-coding RNAs associated with ethylene in tomato

(2018) Yunxiang Wang et al.   GENE

Classification and experimental identification of plant long non-coding RNAs

(2018) Muneeza I. Rai et al.   GENOMICS

A novel antisense long noncoding RNA,TWISTED LEAF , maintains leaf blade flattening by regulating its associated sense R2R3-MYB gene in rice

(2018) Xue Liu et al.   NEW PHYTOLOGIST

Osmotic stress-responsive promoter upstream transcripts (PROMPTs) act as carriers of MYB transcription factors to induce the expression of target genes in Populus simonii

(2018) Yuepeng Song et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2018) Qingguo Du et al.   PLANT PHYSIOLOGY

lncRNAs in Plant and Animal Sexual Reproduction

(2018) Agnieszka A. Golicz et al.   TRENDS IN PLANT SCIENCE

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

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

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

Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice

(2018) Ying Wang et al.   Nature Communications

Genome-wide identification of long non-coding RNA targets of the tomato MADS box transcription factor RIN and function analysis

(2018) Tongtong Yu et al.   ANNALS OF BOTANY

ELF18-INDUCED LONG NONCODING RNA 1 evicts fibrillarin from mediator subunit to enhance PATHOGENESIS-RELATED GENE 1 (PR1 ) expression

(2018) Jun Sung Seo et al.   NEW PHYTOLOGIST

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

(2018) Peter Kindgren et al.   Nature Communications

Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA

(2018) Xinyue Zhao et al.   Nature Communications

Genome-Wide Analysis of Long Non-Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process

(2017) et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatula

(2017) Tianzuo Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

miR3954 is a trigger of phasiRNAs that affects flowering time in citrus

(2017) Yuanlong Liu 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

A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

(2017) Tao Qin et al.   PLANT PHYSIOLOGY

Modular function of long noncoding RNA, COLDAIR, in the vernalization response

(2017) Dong-Hwan Kim et al.   PLoS Genetics

Regulation of rice root development by a retrotransposon acting as a microRNA sponge

(2017) Jungnam Cho et al.   eLife

How do lncRNAs regulate transcription?

(2017) Yicheng Long et al.   Science Advances

Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing

(2016) Reina Komiya   JOURNAL OF PLANT RESEARCH

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

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

Epigenetic Modifications and Plant Hormone Action

(2016) Chizuko Yamamuro et al.   Molecular Plant

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

Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization

(2016) Julia I. Qüesta et al.   SCIENCE

Mechanisms of microRNA turnover

(2015) Maryam Sanei et al.   CURRENT OPINION IN PLANT BIOLOGY

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

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long noncoding RNA transcriptome of plants

(2015) Jun Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

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

(2014) Federico Ariel et al.   MOLECULAR CELL

Heat shock factor HSFB2a involved in gametophyte development of Arabidopsis thaliana and its expression is controlled by a heat-inducible long non-coding antisense RNA

(2014) Markus Wunderlich et al.   PLANT MOLECULAR BIOLOGY

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

Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor

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

Arabidopsis RRP6L1 and RRP6L2 Function in FLOWERING LOCUS C Silencing via Regulation of Antisense RNA Synthesis

(2014) Jun-Hye Shin et al.   PLoS Genetics

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156A and MIR156C

(2013) Li Yang et al.   eLife

Complexity of miRNA-dependent regulation in root symbiosis

(2012) J. Bazin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide views of long non-coding RNAs

(2011) Mary Muers   NATURE REVIEWS GENETICS

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

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

A novel RNA-binding peptide regulates the establishment of theMedicago truncatula-Sinorhizobium melilotinitrogen-fixing symbiosis

(2009) Philippe Laporte et al.   PLANT JOURNAL

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

Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p

(2008) Kevin P. Callahan et al.   NUCLEIC ACIDS RESEARCH