RNA regulatory networks in animals and plants: a long noncoding RNA perspective

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

(2014) H. Wang et al.   GENOME RESEARCH

A Feedforward Regulatory Loop between HuR and the Long Noncoding RNA linc-MD1 Controls Early Phases of Myogenesis

(2014) Ivano Legnini et al.   MOLECULAR CELL

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

(2014) Lin Li et al.   GENOME BIOLOGY

PLncDB: plant long non-coding RNA database

(2013) J. Jin et al.   BIOINFORMATICS

Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

(2013) Xiang Yu et al.   BMC PLANT BIOLOGY

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

(2013) S. Li et al.   GENOME RESEARCH

Analysis of long non-coding RNAs produced by a specialized RNA polymerase in Arabidopsis thaliana

(2013) M. Jordan Rowley et al.   METHODS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

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

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

(2013) D. Secco et al.   PLANT CELL

Deep RNA-Seq uncovers the peach transcriptome landscape

(2013) Lu Wang et al.   PLANT MOLECULAR BIOLOGY

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

(2013) Xin Qi 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

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing

(2013) A. E. Loraine et al.   PLANT PHYSIOLOGY

The Differential Transcription Network between Embryo and Endosperm in the Early Developing Maize Seed

(2013) X. Lu et al.   PLANT PHYSIOLOGY

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome

(2012) Ashwini Jeggari et al.   BIOINFORMATICS

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

(2012) Tingting Lu et al.   BMC GENOMICS

A non-coding RNA locus mediates environment-conditioned male sterility in rice

(2012) Danmeng Zhu et al.   CELL RESEARCH

Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA

(2012) Hai Zhou et al.   CELL RESEARCH

Functional Interplay between RNA-Binding Protein HuR and microRNAs

(2012) Subramanya Srikantan et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

An alternative telomerase RNA in Arabidopsis modulates enzyme activity in response to DNA damage

(2012) C. Cifuentes-Rojas et al.   GENES & DEVELOPMENT

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

(2012) J. E. Wilusz et al.   GENES & DEVELOPMENT

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

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

(2012) T. Derrien et al.   GENOME RESEARCH

Regulatory long non-coding RNA and its functions

(2012) Yong Huang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

LincRNA-p21 Suppresses Target mRNA Translation

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

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

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

(2012) Claudia Carrieri et al.   NATURE

Combined RNAi and localization for functionally dissecting long noncoding RNAs

(2012) Debojyoti Chakraborty et al.   NATURE METHODS

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

(2012) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

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

(2012) J. Liu et al.   PLANT CELL

RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

(2012) Qi Zheng et al.   PLANT JOURNAL

Characteristics and Significance of Intergenic Polyadenylated RNA Transcription in Arabidopsis

(2012) G. D. Moghe et al.   PLANT PHYSIOLOGY

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

Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MEN  noncoding RNAs

(2012) J. A. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AS1DHRS4, a head-to-head natural antisense transcript, silences the DHRS4 gene cluster in cis and trans

(2012) Q. 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

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs

(2012) F. Niazi et al.   RNA

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Emerging roles of RNA and RNA-binding protein network in cancer cells

(2011) Mee-Young Kim et al.   BMB Reports

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

Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk

(2011) Guangfu Jin et al.   CARCINOGENESIS

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

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

(2011) Leonardo Salmena et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

HuR function in disease

(2011) Subramanya Srikantan   Frontiers in Bioscience-Landmark

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

(2011) David Managadze et al.   Genome Biology and Evolution

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

PlantNATsDB: a comprehensive database of plant natural antisense transcripts

(2011) D. Chen et al.   NUCLEIC ACIDS RESEARCH

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

(2011) M. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Rice PHO1 Gene Family Reveals a Key Role for OsPHO1;2 in Phosphate Homeostasis and the Evolution of a Distinct Clade in Dicotyledons

(2010) D. Secco et al.   PLANT PHYSIOLOGY

Two RNA subunits and POT1a are components of Arabidopsis telomerase

(2010) C. Cifuentes-Rojas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide computational identification and manual annotation of human long noncoding RNA genes

(2010) H. Jia et al.   RNA

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana

(2009) Dandan Song et al.   BMC BIOINFORMATICS

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

(2009) Szymon Swiezewski et al.   NATURE

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

NRED: a database of long noncoding RNA expression

(2008) Marcel E. Dinger et al.   NUCLEIC ACIDS RESEARCH

The evolution of courtship behaviors through the origination of a new gene in Drosophila

(2008) H. Dai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA