Regulation of mammalian cell differentiation by long non-coding RNAs

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Suppression of progenitor differentiation requires the long noncoding RNA ANCR

(2012) M. Kretz et al.   GENES & DEVELOPMENT

LincRNA-p21 Suppresses Target mRNA Translation

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

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Combined RNAi and localization for functionally dissecting long noncoding RNAs

(2012) Debojyoti Chakraborty et al.   NATURE METHODS

Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

(2012) V. A. Moran et al.   NUCLEIC ACIDS RESEARCH

The hallmarks of cancer

(2012) Tony Gutschner et al.   RNA Biology

Loss of the abundant nuclear non-coding RNAMALAT1is compatible with life and development

(2012) Moritz Eißmann et al.   RNA Biology

Malat1 is not an essential component of nuclear speckles in mice

(2012) S. Nakagawa et al.   RNA

Use and Abuse of RNAi to Study Mammalian Gene Function

(2012) W. G. Kaelin   SCIENCE

Flowering time control: another window to the connection between antisense RNA and chromatin

(2012) Robert Ietswaart et al.   TRENDS IN GENETICS

Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains

(2012) Le Cong et al.   Nature Communications

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

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

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

The sequence, structure and evolutionary features of HOTAIR in mammals

(2011) Sha He et al.   BMC EVOLUTIONARY BIOLOGY

Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers

(2011) R. Kogo et al.   CANCER RESEARCH

ceRNAs: miRNA Target Mimic Mimics

(2011) Ignacio Rubio-Somoza et al.   CELL

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   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

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation

(2011) W. Hu et al.   GENES & DEVELOPMENT

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

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

Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

(2011) Shinichi Nakagawa et al.   JOURNAL OF CELL BIOLOGY

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

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang 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

Nuclear export dynamics of RNA–protein complexes

(2011) David Grünwald et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Transcription by RNA polymerase III: more complex than we thought

(2011) Robert J. White   NATURE REVIEWS GENETICS

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

(2011) Anton Wutz   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

Transcriptional mechanisms regulating skeletal muscle differentiation, growth and homeostasis

(2011) Thomas Braun et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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 Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina

(2011) N. Meola et al.   RNA

Long noncoding RNAs and human disease

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

Tsx Produces a Long Noncoding RNA and Has General Functions in the Germline, Stem Cells, and Brain

(2011) Montserrat C. Anguera et al.   PLoS Genetics

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

(2011) Patrick Schorderet et al.   PLoS Genetics

The long noncoding RNA RNCR2 directs mouse retinal cell specification.

(2010) Nicole A Rapicavoli et al.   BMC DEVELOPMENTAL BIOLOGY

Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse

(2010) Björn Reinius et al.   BMC GENOMICS

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

(2010) Tim R Mercer et al.   BMC NEUROSCIENCE

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

(2010) Maite Huarte et al.   CELL

Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

(2010) Jacob H. Hanna et al.   CELL

Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1

(2010) F. Mohammad et al.   DEVELOPMENT

Increased Expression of Angiogenic Genes in the Brains of MouseMeg3-Null Embryos

(2010) Francesca E. Gordon et al.   ENDOCRINOLOGY

Induced pluripotency: history, mechanisms, and applications

(2010) M. Stadtfeld 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

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

(2010) Jing Zhao et al.   MOLECULAR CELL

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

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

A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo

(2009) K. Li et al.   BLOOD

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

(2009) X. Zhang et al.   BLOOD

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing

(2009) L. Redrup et al.   DEVELOPMENT

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

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

Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry

(2009) Allison M Bond et al.   NATURE NEUROSCIENCE

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

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

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

Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells

(2009) J. Sheik Mohamed et al.   RNA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

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

Nkx2.2 antisense RNA overexpression enhanced oligodendrocytic differentiation

(2008) Shiro Tochitani et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

SMD and NMD are competitive pathways that contribute to myogenesis: effects on PAX3 and myogenin mRNAs

(2008) C. Gong et al.   GENES & DEVELOPMENT

MEN  /  nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

(2008) H. Sunwoo et al.   GENOME RESEARCH

Noncoding RNA in development

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

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

MicroRNAs in the Hox network: an apparent link to posterior prevalence

(2008) Soraya Yekta et al.   NATURE REVIEWS GENETICS

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

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