Non-coding RNA: a new frontier in regulatory biology

Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes

(2014) Lisa L. Hall et al.   CELL

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

(2014) Katsutoshi Imamura et al.   MOLECULAR CELL

Control of Cdc28 CDK1 by a Stress-Induced lncRNA

(2014) Mariona Nadal-Ribelles et al.   MOLECULAR CELL

The Dharma of Nonsense-Mediated mRNA Decay in Mammalian Cells

(2014) Maximilian Wei-Lin Popp et al.   MOLECULES AND CELLS

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Regulation of the Apolipoprotein Gene Cluster by a Long Noncoding RNA

(2014) Paul Halley et al.   Cell Reports

Circulating MicroRNAs as biomarkers for disease staging in multiple sclerosis

(2013) Roopali Gandhi et al.   ANNALS OF NEUROLOGY

Organizing Principles of Mammalian Nonsense-Mediated mRNA Decay

(2013) Maximilian Wei-Lin Popp et al.   Annual Review of Genetics

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release

(2013) Wen Liu et al.   CELL

Xist RNA Is a Potent Suppressor of Hematologic Cancer in Mice

(2013) Eda Yildirim et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism

(2013) Jamy C Peng et al.   CURRENT OPINION IN CELL BIOLOGY

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

piRNA-Triggered MIWI Ubiquitination and Removal by APC/C in Late Spermatogenesis

(2013) Shuang Zhao et al.   DEVELOPMENTAL CELL

The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

(2013) Phillip Grote et al.   DEVELOPMENTAL CELL

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

(2013) H. Maamar et al.   GENES & DEVELOPMENT

TALEN or Cas9 – Rapid, Efficient and Specific Choices for Genome Modifications

(2013) Chuanxian Wei et al.   Journal of Genetics and Genomics

The Imprinted H19 LncRNA Antagonizes Let-7 MicroRNAs

(2013) Amanda N. Kallen et al.   MOLECULAR CELL

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

(2013) Matthew D. Simon et al.   NATURE

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

(2013) Liuqing Yang et al.   NATURE

Crystal structure of Prp8 reveals active site cavity of the spliceosome

(2013) Wojciech P. Galej et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Lack of detectable oral bioavailability of plant microRNAs after feeding in mice

(2013) Brent Dickinson et al.   NATURE BIOTECHNOLOGY

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Finding the end: recruitment of telomerase to telomeres

(2013) Jayakrishnan Nandakumar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3′ UTRs

(2013) David Zünd et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells

(2013) Syuzo Kaneko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

RNA-protein analysis using a conditional CRISPR nuclease

(2013) H. Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response

(2013) M. T. Paulsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Long noncoding RNAs: fresh perspectives into the RNA world

(2013) Lin Yang et al.   TRENDS IN BIOCHEMICAL SCIENCES

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

Trash or Treasure: extracellular microRNAs and cell-to-cell communication

(2013) Nobuyoshi Kosaka et al.   Frontiers in Genetics

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

Genome Regulation by Long Noncoding RNAs

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

The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells

(2012) T. Gutschner et al.   CANCER RESEARCH

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

(2012) Alfredo Castello et al.   CELL

Structure and assembly of the SF3a splicing factor complex of U2 snRNP

(2012) Pei-Chun Lin et al.   EMBO JOURNAL

Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles

(2012) Takao Naganuma et al.   EMBO JOURNAL

Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis

(2012) E. J. Gardner et al.   GENES & DEVELOPMENT

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

(2012) J. E. Wilusz et al.   GENES & DEVELOPMENT

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai 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

MS2-TRAP (MS2-tagged RNA affinity purification): Tagging RNA to identify associated miRNAs

(2012) Je-Hyun Yoon et al.   METHODS

Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation

(2012) Rui Xiao et al.   MOLECULAR CELL

Long Noncoding RNAs with snoRNA Ends

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

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

An unconventional role for miRNA: let-7 activates Toll-like receptor 7 and causes neurodegeneration

(2012) Sabrina M Lehmann et al.   NATURE NEUROSCIENCE

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MEN  noncoding RNAs

(2012) J. A. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bedrock displacements in Greenland manifest ice mass variations, climate cycles and climate change

(2012) Michael Bevis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNAs bind to Toll-like receptors to induce prometastatic inflammatory response

(2012) M. Fabbri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity

(2012) Zachary T. Campbell et al.   Cell Reports

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

(2011) Liuqing Yang et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

(2011) Lin Zhang et al.   CELL RESEARCH

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

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

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

(2011) Ci Chu et al.   MOLECULAR CELL

A microRNA regulon that mediates endothelial recruitment and metastasis by cancer cells

(2011) Kim J. Png et al.   NATURE

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

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins

(2011) Kasey C. Vickers et al.   NATURE CELL BIOLOGY

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

(2011) Tiffany Hung et al.   NATURE GENETICS

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

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

DUFs: families in search of function

(2010) Alex Bateman et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

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

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

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Secreted Monocytic miR-150 Enhances Targeted Endothelial Cell Migration

(2010) Yujing Zhang et al.   MOLECULAR CELL

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

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

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

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

(2010) Sabine Loewer et al.   NATURE GENETICS

Small RNA sorting: matchmaking for Argonautes

(2010) Benjamin Czech et al.   NATURE REVIEWS GENETICS

Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

(2010) R. M. Mitton-Fry 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

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

The Long Arm of Long Noncoding RNAs: Roles as Sensors Regulating Gene Transcriptional Programs

(2010) X. Wang et al.   Cold Spring Harbor Perspectives in Biology

Biogenesis of Nuclear Bodies

(2010) M. Dundr et al.   Cold Spring Harbor Perspectives in Biology

The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect

(2009) Travis Thomson et al.   Annual Review of Cell and Developmental Biology

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

Nuclear organization in the 3D space of the nucleus—cause or consequence?

(2009) Esperanza Nunez et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Paraspeckles: nuclear bodies built on long noncoding RNA

(2009) Charles S. Bond et al.   JOURNAL OF CELL BIOLOGY

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

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

SR Proteins in Vertical Integration of Gene Expression from Transcription to RNA Processing to Translation

(2009) Xiang-Yang Zhong et al.   MOLECULAR CELL

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

(2009) Mitchell Guttman et al.   NATURE

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

(2009) Yanli Wang et al.   NATURE

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

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

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

(2008) Jeremy E. Wilusz et al.   CELL

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

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

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

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

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

(2008) Yanli Wang et al.   NATURE

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

(2008) Xiangting Wang et al.   NATURE

Structure of the guide-strand-containing argonaute silencing complex

(2008) Yanli 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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules

(2008) Q. Hu 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

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE