Long Noncoding RNAs: New Players in the Molecular Mechanism for Maintenance and Differentiation of Pluripotent Stem Cells

Genome Regulation by Long Noncoding RNAs

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

Variations in the epigenetic regulation of lineage-specific genes among human pluripotent stem cell lines

(2012) Hyemin Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Pivots of pluripotency: The roles of non-coding RNA in regulating embryonic and induced pluripotent stem cells

(2012) Jeffrey S. Huo et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Progress made in the reprogramming field: new factors, new strategies and a new outlook

(2012) Samer MI Hussein et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Whole-genome microRNA screening identifies let-7 and mir-18 as regulators of germ layer formation during early embryogenesis

(2012) A. R. Colas et al.   GENES & DEVELOPMENT

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

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Uncovering the role of genomic “dark matter” in human disease

(2012) Lance Martin et al.   JOURNAL OF CLINICAL INVESTIGATION

Regulatory long non-coding RNA and its functions

(2012) Yong Huang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Learning the molecular mechanisms of the reprogramming factors: let's start from microRNAs

(2012) Chao-Shun Yang et al.   Molecular BioSystems

ENCODE: The human encyclopaedia

(2012) Brendan Maher   NATURE

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Combined RNAi and localization for functionally dissecting long noncoding RNAs

(2012) Debojyoti Chakraborty et al.   NATURE METHODS

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

(2012) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

(2012) Satish Sati et al.   NUCLEIC ACIDS RESEARCH

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

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

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

(2012) S. Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long non-coding RNAs in stem cell pluripotency

(2012) Shi-Yan Ng et al.   Wiley Interdisciplinary Reviews-RNA

The evolution of RNAs with multiple functions

(2011) Marcel E. Dinger et al.   BIOCHIMIE

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

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

(2011) Marcella Cesana et al.   CELL

Active chromatin and noncoding RNAs: an intimate relationship

(2011) Ryan A Flynn et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

A new 'Linc' between noncoding RNAs and blood development

(2011) V. R. Paralkar 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

Molecular Mechanisms of Long Noncoding RNAs

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

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

Non-coding RNAs as regulators of embryogenesis

(2011) Andrea Pauli et al.   NATURE REVIEWS GENETICS

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

(2011) Mingyan Lin et al.   PLoS One

MicroRNA reins in embryonic and cancer stem cells

(2011) Bibekanand Mallick et al.   RNA Biology

The long noncoding RNA Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina

(2011) N. Meola et al.   RNA

X-chromosome epigenetic reprogramming in pluripotent stem cells via noncoding genes

(2011) Daniel H. Kim et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart?

(2011) Josipa Bilic et al.   STEM CELLS

Stem Cell Standardization

(2011) Paolo Di Nardo et al.   STEM CELLS AND DEVELOPMENT

Long Noncoding RNAs, Chromatin, and Development

(2011) Daniel P. Caley et al.   TheScientificWorldJOURNAL

Prospects of Induced Pluripotent Stem Cell Technology in Regenerative Medicine

(2011) Feng Zhang et al.   TISSUE ENGINEERING PART B-REVIEWS

MacroRNA underdogs in a microRNA world: Evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA

(2010) Leonard Lipovich et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

Role of H3K27 methylation in the regulation of lncRNA expression

(2010) Susan C Wu et al.   CELL RESEARCH

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

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

(2010) Matthias Stadtfeld 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

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

A Fresh Look at iPS Cells

(2009) Shinya Yamanaka   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Long noncoding RNAs: functional surprises from the RNA world

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

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen et al.   MOLECULAR CELL

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

(2009) Mitchell Guttman et al.   NATURE

The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting

(2009) Mary E. Donohoe et al.   NATURE

Long non-coding RNAs: insights into functions

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

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

(2009) J. Sheik Mohamed et al.   RNA

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

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

Defining Molecular Cornerstones during Fibroblast to iPS Cell Reprogramming in Mouse

(2008) Matthias Stadtfeld et al.   Cell Stem Cell

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

Noncoding RNA in development

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

Molecular Coupling of Xist Regulation and Pluripotency

(2008) P. Navarro et al.   SCIENCE

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

(2008) J. Zhao et al.   SCIENCE

Engaging the Media

(2008) Graham C. Parker   STEM CELLS AND DEVELOPMENT

Dicer regulates Xist promoter methylation in ES cells indirectly through transcriptional control of Dnmt3a

(2008) Tatyana B Nesterova et al.   Epigenetics & Chromatin

Stem cell myths

(2007) T. Magnus et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES