Modular regulatory principles of large non-coding RNAs

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

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

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

(2011) Liuqing Yang et al.   CELL

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon 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

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

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

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

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

(2011) Ci Chu et al.   MOLECULAR CELL

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

(2011) Kevin C. Wang et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

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

(2011) Tiffany Hung et al.   NATURE GENETICS

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

The Long Noncoding RNA, Jpx, Is a Molecular Switch for X Chromosome Inactivation

(2010) Di Tian et al.   CELL

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

RNA traffic control of chromatin complexes

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

The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA

(2010) S. Kaneko et al.   GENES & DEVELOPMENT

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

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

(2010) Jing Zhao et al.   MOLECULAR CELL

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

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

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

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

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

(2010) T. Kino et al.   Science Signaling

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

The function of non-coding RNAs in genomic imprinting

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

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

(2009) J. T. Lee   GENES & DEVELOPMENT

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

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

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

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

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

(2008) Xiangting Wang et al.   NATURE

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2008) J. Zhao et al.   SCIENCE

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

(2008) Michael F. Lin et al.   PLoS Computational Biology

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology