A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation

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

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator

(2016) J. Patrick Pett et al.   PLoS Computational Biology

Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression

(2016) Yichi Xu et al.   PLoS Genetics

Oscillating primary transcripts harbor miRNAs with circadian functions

(2016) Haifang Wang et al.   Scientific Reports

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

Pancreatic   cell enhancers regulate rhythmic transcription of genes controlling insulin secretion

(2015) M. Perelis et al.   SCIENCE

Circadian control of bile acid synthesis by a KLF15-Fgf15 axis

(2015) Shuxin Han et al.   Nature Communications

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

Liver Med23 ablation improves glucose and lipid metabolism through modulating FOXO1 activity

(2014) Yajing Chu et al.   CELL RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Transcriptional interference by antisense RNA is required for circadian clock function

(2014) Zhihong Xue et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

An update on LNCipedia: a database for annotated human lncRNA sequences

(2014) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional regulatory functions of nuclear long noncoding RNAs

(2014) Keith W. Vance et al.   TRENDS IN GENETICS

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

(2014) Han Wu et al.   PLoS Genetics

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Correction of a Genetic Disease in Mouse via Use of CRISPR-Cas9

(2013) Yuxuan Wu et al.   Cell Stem 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

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

(2013) Liuqing Yang et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Cycles in spatial and temporal chromosomal organization driven by the circadian clock

(2013) Lorena Aguilar-Arnal et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish

(2013) Ying Li et al.   PLoS Computational Biology

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Genome Regulation by Long Noncoding RNAs

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

Rev-erb  and Rev-erb  coordinately protect the circadian clock and normal metabolic function

(2012) A. Bugge 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

An RNA-Independent Linkage of Noncoding Transcription to Long-Range Enhancer Function

(2012) E. J. Yoo et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β

(2012) Han Cho et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

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

(2011) Igor Ulitsky et al.   CELL

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

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism

(2011) D. Feng et al.   SCIENCE

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

(2011) Bas Tolhuis et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The mammalian clock component PERIOD2 coordinates circadian output by interaction with nuclear receptors

(2010) I. Schmutz et al.   GENES & DEVELOPMENT

High-throughput analysis of gene expression on tissue sections by in situ hybridization

(2010) Gregor Eichele et al.   METHODS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Circadian Integration of Metabolism and Energetics

(2010) J. Bass et al.   SCIENCE

Comprehensive analysis of microRNA-mRNA co-expression in circadian rhythm

(2009) Young-Ji Na et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

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

(2009) Mitchell Guttman et al.   NATURE

Harmonics of Circadian Gene Transcription in Mammals

(2009) Michael E. Hughes et al.   PLoS Genetics

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm

(2008) Jun Yan et al.   PLoS Computational Biology