RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

The expanded tomato fruit volatile landscape

(2014) José L. Rambla 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

Identification of microRNAs in six solanaceous plants and their potential link with phosphate and mycorrhizal signaling

(2014) Mian Gu et al.   Journal of Integrative Plant Biology

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

(2014) Chao Di et al.   PLANT JOURNAL

Functional interactions among microRNAs and long noncoding RNAs

(2014) Je-Hyun Yoon et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2014) Lin Li et al.   GENOME BIOLOGY

Long noncoding RNAs: New regulators in plant development

(2013) Yu-Chan Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The history of tomato: From domestication to biopharming

(2013) Véronique Bergougnoux   BIOTECHNOLOGY ADVANCES

Functional genomics of tomato in a post-genome-sequencing phase

(2013) Koh Aoki et al.   BREEDING SCIENCE

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Epigenetic regulation by long noncoding RNAs in plants

(2013) Jae Bok Heo et al.   CHROMOSOME RESEARCH

Global and local perturbation of the tomato microRNA pathway by atrans-activatedDICER-LIKE 1mutant

(2013) Michael Kravchik et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

(2013) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

Predicting long non-coding RNAs using RNA sequencing

(2013) Nicholas E. Ilott et al.   METHODS

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Long noncoding RNAs responsive toFusarium oxysporuminfection inArabidopsis thaliana

(2013) Qian-Hao Zhu et al.   NEW PHYTOLOGIST

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

A Large-Scale Identification of Direct Targets of the Tomato MADS Box Transcription Factor RIPENING INHIBITOR Reveals the Regulation of Fruit Ripening

(2013) M. Fujisawa et al.   PLANT CELL

Molecular and genetic regulation of fruit ripening

(2013) Nigel E. Gapper et al.   PLANT MOLECULAR BIOLOGY

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

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

Dissection of Tomato Lycopene Biosynthesis through Virus-Induced Gene Silencing

(2013) E. Fantini et al.   PLANT PHYSIOLOGY

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

(2013) Q. Sun et al.   SCIENCE

Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

(2013) Vinod Kumar et al.   PLoS Genetics

Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits

(2012) Jinhua Zuo et al.   BMC GENOMICS

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

(2012) Andrzej T Wierzbicki   CURRENT OPINION IN PLANT BIOLOGY

Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing

(2012) Tingting Li et al.   GENOMICS

Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato

(2012) Rahul Kumar et al.   MOLECULAR GENETICS AND GENOMICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

PsRobot: a web-based plant small RNA meta-analysis toolbox

(2012) Hua-Jun Wu et al.   NUCLEIC ACIDS RESEARCH

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

(2012) J. Liu et al.   PLANT CELL

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

(2012) Susan Boerner 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

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

A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis

(2012) Juan Wu et al.   RNA Biology

Molecular Functions of Long Non-Coding RNAs in Plants

(2012) Qian-Hao Zhu et al.   Genes

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

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening

(2011) R. Karlova et al.   PLANT CELL

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Unraveling the regulatory network of the MADS box transcription factor RIN in fruit ripening

(2011) Guozheng Qin et al.   PLANT JOURNAL

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

(2011) Irina Mohorianu et al.   PLANT JOURNAL

The Tomato MADS-Box Transcription Factor RIPENING INHIBITOR Interacts with Promoters Involved in Numerous Ripening Processes in a COLORLESS NONRIPENING-Dependent Manner

(2011) C. Martel et al.   PLANT PHYSIOLOGY

Coupling Virus-Induced Gene Silencing to Exogenous Green Fluorescence Protein Expression Provides a Highly Efficient System for Functional Genomics in Arabidopsis and across All Stages of Tomato Fruit Development

(2011) L. Quadrana et al.   PLANT PHYSIOLOGY

The Role of MicroRNAs in Phosphorus Deficiency Signaling

(2011) H.-F. Kuo et al.   PLANT PHYSIOLOGY

New dimensions for VIGS in plant functional genomics

(2011) Muthappa Senthil-Kumar et al.   TRENDS IN PLANT SCIENCE

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

(2011) Eun-Deok Kim et al.   TRENDS IN PLANT SCIENCE

Over-expression of microRNA169 confers enhanced drought tolerance to tomato

(2010) Xiaohui Zhang et al.   BIOTECHNOLOGY LETTERS

Small RNA-mediated epigenetic modifications in plants

(2010) Stacey A Simon et al.   CURRENT OPINION IN PLANT BIOLOGY

A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening

(2010) Mi-Young Chung et al.   PLANT JOURNAL

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Cap and cap-binding proteins in the control of gene expression

(2010) Ivan Topisirovic et al.   Wiley Interdisciplinary Reviews-RNA

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Szymon Swiezewski et al.   NATURE

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation

(2009) D. Orzaez et al.   PLANT PHYSIOLOGY

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

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

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

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

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

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