Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions

Control of cognate sense mRNA translation by cis-natural antisense RNAs

(2019) Jules Deforges et al.   PLANT PHYSIOLOGY

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

(2018) Yoshie Maeda et al.   Nature Communications

Transposon-Derived Non-coding RNAs and Their Function in Plants

(2018) Jungnam Cho   Frontiers in Plant Science

Emerging Roles of Sphingolipid Signaling in Plant Response to Biotic and Abiotic Stresses

(2018) Usman Ali et al.   Molecular Plant

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

Over-expression of GmKR3, a TIR–NBS–LRR type R gene, confers resistance to multiple viruses in soybean

(2018) Hongwei Xun et al.   PLANT MOLECULAR BIOLOGY

Divergent lncRNA GATA3-AS1 Regulates GATA3 Transcription in T-Helper 2 Cells

(2018) Hunter R. Gibbons et al.   Frontiers in Immunology

The functions and unique features of long intergenic non-coding RNA

(2017) Julia D. Ransohoff et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Long-Noncoding RNA ELENA1 Functions in Plant Immunity

(2017) Jennifer Mach   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

Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants

(2017) Dong Wang et al.   PLANT JOURNAL

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation

(2017) Jérémie Bazin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNAs in the model species Brachypodium distachyon

(2017) Concetta De Quattro et al.   Scientific Reports

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

(2017) Jungnam Cho et al.   eLife

The Solanum lycopersicum WRKY3 Transcription Factor SlWRKY3 Is Involved in Salt Stress Tolerance in Tomato

(2017) Imène Hichri et al.   Frontiers in Plant Science

Abscisic Acid as Pathogen Effector and Immune Regulator

(2017) Laurens Lievens et al.   Frontiers in Plant Science

Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana

(2016) Jiapei Yuan et al.   BMC GENOMICS

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation

(2016) Sara C. Cloutier et al.   MOLECULAR CELL

The role of DNA (de)methylation in immune responsiveness of Arabidopsis

(2016) Ana López Sánchez et al.   PLANT JOURNAL

Genome-wide assessment of differential translations with ribosome profiling data

(2016) Zhengtao Xiao et al.   Nature Communications

Controlled activation of retrotransposition for plant breeding

(2015) Jerzy Paszkowski   CURRENT OPINION IN BIOTECHNOLOGY

Long non-coding RNAs and their functions in plants

(2015) Julia A Chekanova   CURRENT OPINION IN PLANT BIOLOGY

Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

(2015) C. Yuan et al.   DNA RESEARCH

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato

(2015) Xin Wang et al.   NEW PHYTOLOGIST

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline

(2014) Toshiaki Watanabe et al.   GENOME RESEARCH

Roles of plant hormones in the regulation of host-virus interactions

(2014) Mazen Alazem et al.   MOLECULAR PLANT PATHOLOGY

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

(2014) Chao Di et al.   PLANT JOURNAL

Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering inArabidopsis thaliana

(2014) Friedrich Fauser et al.   PLANT JOURNAL

The Long Non-Coding RNA GAS5 Cooperates with the Eukaryotic Translation Initiation Factor 4E to Regulate c-Myc Translation

(2014) Guangzhen Hu et al.   PLoS One

Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)

(2013) Hu Zheng et al.   BMC GENOMICS

Conservation and Functional Element Discovery in 20 Angiosperm Plant Genomes

(2013) D. Hupalo et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

(2013) Q. Sun et al.   SCIENCE

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon et al.   MOLECULAR CELL

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

The DNA dioxygenase ALKBH2 protects Arabidopsis thaliana against methylation damage

(2012) Trine J. Meza et al.   NUCLEIC ACIDS RESEARCH

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

(2012) J. Liu et al.   PLANT CELL

Knockdown of FIBRILLIN4 Gene Expression in Apple Decreases Plastoglobule Plastoquinone Content

(2012) Dharmendra K. Singh et al.   PLoS One

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sphingolipids and Plant Defense/Disease: The “Death” Connection and Beyond

(2012) Robert Berkey et al.   Frontiers in Plant Science

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

FIBRILLIN4 Is Required for Plastoglobule Development and Stress Resistance in Apple and Arabidopsis

(2010) D. K. Singh et al.   PLANT PHYSIOLOGY

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173

(2009) Felipe F Felippes et al.   EMBO REPORTS

Targeted 3' Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing

(2009) F. Liu et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Roles of Arabidopsis WRKY3 and WRKY4 Transcription Factors in Plant Responses to Pathogens

(2008) Zhibing Lai et al.   BMC PLANT BIOLOGY

Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa

(2008) X. Zhou et al.   GENOME RESEARCH

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

(2008) Jiong-Tang Li et al.   NUCLEIC ACIDS RESEARCH

Induced Plant Defenses in the Natural Environment: Nicotiana attenuata WRKY3 and WRKY6 Coordinate Responses to Herbivory

(2008) M. Skibbe et al.   PLANT CELL

Functional Characterization of a Higher Plant Sphingolipid  4-Desaturase: Defining the Role of Sphingosine and Sphingosine-1-Phosphate in Arabidopsis

(2008) L. V. Michaelson et al.   PLANT PHYSIOLOGY

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley

(2008) M. A. Held et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual coding of siRNAs and miRNAs by plant transposable elements

(2008) J. Piriyapongsa et al.   RNA