Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis

No-Nonsense Functions for Long Noncoding RNAs

(2011) Takashi Nagano et al.   CELL

RNA templating the epigenome

(2011) Robert C. Spitale et al.   Epigenetics

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

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

Xist regulation and function eXplored

(2011) Daphne B. Pontier et al.   HUMAN GENETICS

Molecular Mechanisms of Long Noncoding RNAs

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

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

Long noncoding RNAs: the search for function

(2011) Monya Baker   NATURE METHODS

ncFANs: a web server for functional annotation of long non-coding RNAs

(2011) Q. Liao et al.   NUCLEIC ACIDS RESEARCH

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

A Global Clustering Algorithm to Identify Long Intergenic Non-Coding RNA - with Applications in Mouse Macrophages

(2011) Lana X. Garmire et al.   PLoS One

RNA splicing control

(2011) Xinying Zong et al.   RNA Biology

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

(2010) Alberto Risueño et al.   BMC BIOINFORMATICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

Epigenetics of imprinted long non-coding RNAs

(2010) Faizaan Mohammad et al.   Epigenetics

Large non-coding RNAs: missing links in cancer?

(2010) M. Huarte et al.   HUMAN MOLECULAR GENETICS

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

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

(2010) Jing Zhao et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

The non-coding RNA TERRA is a natural ligand and direct inhibitor of human telomerase

(2010) Sophie Redon et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

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

ncRNAimprint: A comprehensive database of mammalian imprinted noncoding RNAs

(2010) Y. Zhang et al.   RNA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

The function of non-coding RNAs in genomic imprinting

(2009) M. V. Koerner et al.   DEVELOPMENT

A ‘higher order’ of telomere regulation: telomere heterochromatin and telomeric RNAs

(2009) Stefan Schoeftner et al.   EMBO JOURNAL

The long and the short of it: RNA-directed chromatin asymmetry in mammalian X-chromosome inactivation

(2009) Chandrasekhar Kanduri et al.   FEBS LETTERS

Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome

(2009) J. T. Lee   GENES & DEVELOPMENT

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

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

(2009) Mitchell Guttman et al.   NATURE

Long non-coding RNAs: insights into functions

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

Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase

(2009) Federica Ferri et al.   NUCLEIC ACIDS RESEARCH

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

Non-coding RNAs in imprinted gene clusters

(2008) Hélène Royo et al.   BIOLOGY OF THE CELL

MicroRNA-encoding long non-coding RNAs

(2008) Shunmin He et al.   BMC GENOMICS

Noncoding RNA in development

(2008) Paulo P. Amaral et al.   MAMMALIAN GENOME

Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster

(2008) Trilochan Sahoo et al.   NATURE GENETICS

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

NRED: a database of long noncoding RNA expression

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

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

(2008) T. Mituyama et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Poly A- Transcripts Expressed in HeLa Cells

(2008) Qingfa Wu et al.   PLoS One

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

(2008) T. Nagano et al.   SCIENCE

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

(2008) J. Zhao et al.   SCIENCE

Physiological assembly and activity of human telomerase complexes

(2007) Kathleen Collins   MECHANISMS OF AGEING AND DEVELOPMENT