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

Unlinking an lncRNA from Its Associated cis Element

(2016) Vikram R. Paralkar et al.   MOLECULAR CELL

“Cat’s Cradling” the 3D Genome by the Act of LncRNA Transcription

(2016) Marta Melé et al.   MOLECULAR CELL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

(2016) Takamitsu Hattori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Pitx2 modulates a Tbx5 -dependent gene regulatory network to maintain atrial rhythm

(2016) Rangarajan D. Nadadur et al.   Science Translational Medicine

Toward a Consensus on the Binding Specificity and Promiscuity of PRC2 for RNA

(2015) Chen Davidovich et al.   MOLECULAR CELL

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide

(2015) Adrian T. Grzybowski et al.   MOLECULAR CELL

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure

(2015) Anna Postepska-Igielska et al.   MOLECULAR CELL

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells

(2015) Hongjae Sunwoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson 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

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

(2015) Vincent J. Lynch et al.   Cell Reports

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

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

(2014) Thomas Trimarchi et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Universality of core promoter elements?

(2014) Matthias Siebert et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2013) Baohui Chen et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

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

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

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

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

(2013) Liuqing Yang et al.   NATURE

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

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

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

(2012) Guoliang Li et al.   CELL

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2011) Kevin C. Wang et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias 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

Inhibition of ERK1/2 prevents neural and mesendodermal differentiation and promotes human embryonic stem cell self-renewal

(2010) Jie Na et al.   Stem Cell Research

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

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

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

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

A model for transmission of the H3K27me3 epigenetic mark

(2008) Klaus H. Hansen et al.   NATURE CELL BIOLOGY