Structure and function of long noncoding RNAs in epigenetic regulation

A Comparison of Genotype-Phenotype Maps for RNA and Proteins

(2012) Evandro Ferrada et al.   BIOPHYSICAL JOURNAL

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

(2012) S. F. Pinter et al.   GENOME RESEARCH

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

(2012) T. Derrien et al.   GENOME RESEARCH

Long Noncoding RNAs with snoRNA Ends

(2012) Qing-Fei Yin et al.   MOLECULAR CELL

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation

(2012) Jennifer Grant et al.   NATURE

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

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

(2012) Claudia Carrieri et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

A rule of seven in Watson-Crick base-pairing of mismatched sequences

(2012) Ibrahim I Cisse et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

The role of robustness in phenotypic adaptation and innovation

(2012) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

(2012) Bin Zhang et al.   Cell Reports

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

The evolution of RNAs with multiple functions

(2011) Marcel E. Dinger et al.   BIOCHIMIE

Ribozymes: Flexible molecular devices at work

(2011) Giulia Talini et al.   BIOCHIMIE

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

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies 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

Emerging structural themes in large RNA molecules

(2011) Nicholas J Reiter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

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

(2011) Ci Chu et al.   MOLECULAR CELL

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

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

(2011) Kevin C. Wang et al.   NATURE

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

(2011) Eric J. Hayden et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Nucleation of nuclear bodies by RNA

(2011) Sergey P. Shevtsov et al.   NATURE CELL BIOLOGY

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin

(2011) Christèle Maison et al.   NATURE GENETICS

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

Potential in vivo roles of nucleic acid triple-helices

(2011) Fabian A. Buske et al.   RNA Biology

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

(2011) C. J. Delebecque et al.   SCIENCE

Structural and Functional Differences in the Long Non-Coding RNA Hotair in Mouse and Human

(2011) Patrick Schorderet et al.   PLoS Genetics

Heterochromatin maintenance and establishment: Lessons from the mouse pericentromere

(2011) Geneviève Almouzni et al.   Nucleus

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

Epigenetics of imprinted long non-coding RNAs

(2010) Faizaan Mohammad et al.   Epigenetics

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

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

(2010) Vidisha Tripathi 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

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

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

(2010) Laura Poliseno et al.   NATURE

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

Grand Challenge Commentary: RNA epigenetics?

(2010) Chuan He   Nature Chemical Biology

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

Expression of distinct RNAs from 3′ untranslated regions

(2010) Tim R. Mercer et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

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

Detection of RNA modifications

(2010) Stefanie Kellner et al.   RNA Biology

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

The X as Model for RNA's Niche in Epigenomic Regulation

(2010) J. T. Lee   Cold Spring Harbor Perspectives in Biology

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Epigenetics: heterochromatin meets RNAi

(2009) Ingela Djupedal et al.   CELL RESEARCH

Maternally Expressed Gene 3 (MEG3) Noncoding Ribonucleic Acid: Isoform Structure, Expression, and Functions

(2009) Xun Zhang et al.   ENDOCRINOLOGY

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

(2009) Mitchell Guttman et al.   NATURE

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

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

Complex architecture and regulated expression of the Sox2ot locus during vertebrate development

(2009) P. P. Amaral et al.   RNA

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

Neutral network sizes of biological RNA molecules can be computed and are not atypically small

(2008) Thomas Jörg et al.   BMC BIOINFORMATICS

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

(2008) Jeremy E. Wilusz et al.   CELL

Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock

(2008) Peter D. Mariner et al.   MOLECULAR CELL

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

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

A stress-responsive RNA switch regulates VEGFA expression

(2008) Partho Sarothi Ray et al.   NATURE

A structural understanding of the dynamic ribosome machine

(2008) Thomas A. Steitz   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Intersection of the RNA Interference and X-Inactivation Pathways

(2008) Y. Ogawa 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

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

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

Is evolvability evolvable?

(2007) Massimo Pigliucci   NATURE REVIEWS GENETICS