Long ncRNA A-ROD activates its target gene DKK1 at its release from chromatin

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription

(2017) Michael S Werner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription

(2017) Michael S Werner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Antisense targeting of 3′ end elements involved inDUX4mRNA processing is an efficient therapeutic strategy for facioscapulohumeral dystrophy: a new gene-silencing approach

(2016) Anne-Charlotte Marsollier et al.   HUMAN MOLECULAR GENETICS

A Long Noncoding RNA Regulates Sister Chromatid Cohesion

(2016) Francesco P. Marchese et al.   MOLECULAR CELL

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Serial interactome capture of the human cell nucleus

(2016) Thomas Conrad et al.   Nature Communications

Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

(2016) Lovorka Stojic et al.   Nature Communications

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Long ncRNA expression associates with tissue-specific enhancers

(2015) Dubravka Vučićević et al.   CELL CYCLE

EBP1 protein modulates the expression of human MHC class II molecules in non-hematopoietic cancer cells

(2015) LAURA PISAPIA et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes

(2015) Michael S. Werner et al.   Cell Reports

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

(2014) Thomas Trimarchi et al.   CELL

Enhancer RNAs

(2014) Wenbo Li et al.   CELL CYCLE

The long non-coding RNA Paupar regulates the expression of both local and distal genes

(2014) K. W. Vance et al.   EMBO JOURNAL

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Genome-Wide Binding of MBD2 Reveals Strong Preference for Highly Methylated Loci

(2014) Roberta Menafra et al.   PLoS One

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

(2014) C.-L. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

Microprocessor Activity Controls Differential miRNA Biogenesis In Vivo

(2014) Thomas Conrad et al.   Cell Reports

RNAi Factors Are Present and Active in Human Cell Nuclei

(2014) Keith T. Gagnon et al.   Cell Reports

Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers

(2013) Ulf Andersson Ørom et al.   CELL

The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-γ Locus

(2013) J. Antonio Gomez et al.   CELL

Identification of a long non-coding RNA-associated RNP complex regulating metastasis at the translational step

(2013) Kiranmai Gumireddy et al.   EMBO JOURNAL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

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

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

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression

(2013) A. Pandya-Jones et al.   RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

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

(2012) T. Derrien et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

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

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

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

(2011) Kevin C. Wang et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

(2010) Roy Joseph et al.   Molecular Systems Biology

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions

(2009) Roberto Perales et al.   MOLECULAR CELL

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

Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing

(2009) F. Rigo et al.   RNA

Dkk-1 secreted by mesenchymal stem cells inhibits growth of breast cancer cells via depression of Wnt signalling

(2008) Ling Qiao et al.   CANCER LETTERS

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

(2008) Leighton J. Core et al.   SCIENCE