Molecular Functions of Long Non-Coding RNAs in Plants

Coding vs non-coding: Translatability of short ORFs found in putative non-coding transcripts

(2011) Yuji Kageyama et al.   BIOCHIMIE

An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

(2011) Pavel Sumazin 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

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

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

(2011) Leonardo Salmena et al.   CELL

Environmentally coordinated epigenetic silencing of FLC by protein and long noncoding RNA components

(2011) Dong-Hwan Kim et al.   CURRENT OPINION IN PLANT BIOLOGY

Encoding memory of winter by noncoding RNAs

(2011) Jae Bok Heo et al.   Epigenetics

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

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

(2011) Ci Chu et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts

(2011) Chris A. Helliwell et al.   PLoS One

Long non-coding RNA-mediated mechanisms independent of the RNAi pathway in animals and plants

(2011) Phil Chi Khang Au et al.   RNA Biology

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

(2011) S. Washietl et al.   RNA

Coding RNAs with a non-coding function: Maintenance of open chromatin structure

(2011) Maïwen Caudron-Herger et al.   Nucleus

RNA traffic control of chromatin complexes

(2010) Magdalena J Koziol et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

An endogenous, systemic RNAi pathway in plants

(2010) Patrice Dunoyer et al.   EMBO JOURNAL

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

(2010) Z. J. Lu et al.   GENOME RESEARCH

Characterization of the RNA content of chromatin

(2010) T. Mondal et al.   GENOME RESEARCH

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

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

(2010) Jing Zhao et al.   MOLECULAR CELL

Small RNAs are on the move

(2010) Daniel H. Chitwood et al.   NATURE

Chromatin remodelling during development

(2010) Lena Ho et al.   NATURE

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Mining Mammalian Transcript Data for Functional Long Non-Coding RNAs

(2010) Amit N. Khachane et al.   PLoS One

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

miRNAs in the biogenesis of trans-acting siRNAs in higher plants

(2010) Edwards Allen et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2010) Marco Todesco et al.   PLoS Genetics

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes

(2009) G. Solda et al.   BRIEFINGS IN BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Emerging similarities in epigenetic gene silencing by long noncoding RNAs

(2009) Takashi Nagano et al.   MAMMALIAN GENOME

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

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: insights into functions

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

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

Regulatory roles of natural antisense transcripts

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

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

(2009) Philippe Laporte et al.   PLANT JOURNAL

AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling

(2009) H. Rehrauer et al.   PLANT PHYSIOLOGY

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

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

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

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

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

(2008) Brian T. Wilhelm et al.   NATURE

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Stable knockdown of microRNA in vivo by lentiviral vectors

(2008) Bernhard Gentner et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis

(2008) Bikram Datt Pant et al.   PLANT JOURNAL

A PHD-Polycomb Repressive Complex 2 triggers the epigenetic silencing of FLC during vernalization

(2008) F. De Lucia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

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

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