Cis-acting noncoding RNAs: friends and foes

A Long ncRNA Links Copy Number Variation to a Polycomb/Trithorax Epigenetic Switch in FSHD Muscular Dystrophy

(2012) Daphne S. Cabianca et al.   CELL

Non-coding RNAs with essential roles in neurodegenerative disorders

(2012) Evgenia Salta et al.   LANCET NEUROLOGY

LincRNA-p21 Suppresses Target mRNA Translation

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

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation

(2012) Farzaneh Modarresi et al.   NATURE BIOTECHNOLOGY

Intronic RNAs mediate EZH2 regulation of epigenetic targets

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts

(2012) Marco Magistri et al.   TRENDS IN GENETICS

Genomic Imprinting: A Mammalian Epigenetic Discovery Model

(2011) Denise P. Barlow   Annual Review of Genetics

ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs

(2011) Liuqing Yang et al.   CELL

Shaping the Genome with Non-Coding RNAs

(2011) Xue Q.D. Wang et al.   CURRENT GENOMICS

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

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

Extensive relationship between antisense transcription and alternative splicing in the human genome

(2011) A. Sorana Morrissy et al.   GENOME RESEARCH

Role of Noncoding RNA ANRIL in Genesis of Plexiform Neurofibromas in Neurofibromatosis Type 1

(2011) Eric Pasmant et al.   JNCI-Journal of the National Cancer Institute

RETRACTED: The Noncoding RNA Mistral Activates Hoxa6 and Hoxa7 Expression and Stem Cell Differentiation by Recruiting MLL1 to Chromatin

(2011) Stéphane Bertani et al.   MOLECULAR CELL

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Genomic imprinting: the emergence of an epigenetic paradigm

(2011) Anne C. Ferguson-Smith   NATURE REVIEWS GENETICS

Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control

(2011) Jeannie T. Lee   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

(2011) Eivind Valen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CTCF Regulates Ataxin-7 Expression through Promotion of a Convergently Transcribed, Antisense Noncoding RNA

(2011) Bryce L. Sopher et al.   NEURON

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

(2011) R. A. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The emerging role of RNA in the regulation of gene transcription in human cells

(2011) Kevin V. Morris   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

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

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

Characterization of the RNA content of chromatin

(2010) T. Mondal et al.   GENOME RESEARCH

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

Molecular Interplay of the Noncoding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a

(2010) Kyoko L. Yap et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 INK4B tumor suppressor gene

(2010) Y Kotake et al.   ONCOGENE

Noncoding RNA Gas5 Is a Growth Arrest- and Starvation-Associated Repressor of the Glucocorticoid Receptor

(2010) T. Kino et al.   Science Signaling

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression

(2010) Michael S. Cunnington et al.   PLoS Genetics

Evidence for natural antisense transcript-mediated inhibition of microRNA function

(2010) Mohammad Ali Faghihi et al.   GENOME BIOLOGY

Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression

(2009) Tarmo Annilo et al.   BMC MOLECULAR BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

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

(2009) Mitchell Guttman et al.   NATURE

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Genome-wide association study identifies three loci associated with melanoma risk

(2009) D Timothy Bishop et al.   NATURE GENETICS

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló et al.   NATURE STRUCTURAL & MOLECULAR 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

Role of human noncoding RNAs in the control of tumorigenesis

(2009) L. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus

(2009) Raffaella Nativio et al.   PLoS Genetics

A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition

(2008) M. Beltran et al.   GENES & DEVELOPMENT

Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci

(2008) Rodrigo Louro et al.   GENOMICS

Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA

(2008) Wenqiang Yu et al.   NATURE

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase

(2008) Mohammad Ali Faghihi et al.   NATURE MEDICINE

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

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

(2008) T. Nagano et al.   SCIENCE

Gene Regulation in the Third Dimension

(2008) J. Dekker   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Bidirectional Transcription Directs Both Transcriptional Gene Activation and Suppression in Human Cells

(2008) Kevin V. Morris et al.   PLoS Genetics