Identification and function of enhancers in the human genome

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo

(2016) Ezzat El-Sherif et al.   CURRENT BIOLOGY

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen et al.   GENOME RESEARCH

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

(2016) Yasuhiro Murakawa et al.   TRENDS IN GENETICS

3CDB: a manually curated database of chromosome conformation capture data

(2016) Xiaoxiao Yun et al.   Database-The Journal of Biological Databases and Curation

A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation

(2016) Shigeki Iwase et al.   Cell Reports

New Insights Into Intellectual Disability Caused by Mutations in a Chromatin Regulator

(2016) Emily Brookes   EBioMedicine

De Novo Nonsense Mutations in KAT6A, a Lysine Acetyl-Transferase Gene, Cause a Syndrome Including Microcephaly and Global Developmental Delay

(2015) Valerie A. Arboleda et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

(2015) Olgert Denas et al.   BMC GENOMICS

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Chromatin deregulation in disease

(2015) Anne C. Mirabella et al.   CHROMOSOMA

Tumour exosome integrins determine organotropic metastasis

(2015) Ayuko Hoshino et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Good laboratory practice for clinical next-generation sequencing informatics pipelines

(2015) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

(2015) Jenny C Taylor et al.   NATURE GENETICS

Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin

(2015) Kosuke Izumi et al.   NATURE GENETICS

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

(2015) Sándor Spisák et al.   NATURE MEDICINE

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

(2015) Stephan J. Sanders et al.   NEURON

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

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 Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Identification of altered cis-regulatory elements in human disease

(2015) Anthony Mathelier et al.   TRENDS IN GENETICS

Mutant cohesin affects RNA polymerase II regulation in Cornelia de Lange syndrome

(2015) Linda Mannini et al.   Scientific Reports

Genetic variation in the non-coding genome: Involvement of micro-RNAs and long non-coding RNAs in disease

(2014) Barbara Hrdlickova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Enhancer Activation Requires trans-Recruitment of a Mega Transcription Factor Complex

(2014) Zhijie Liu et al.   CELL

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

(2014) Yan Li et al.   PLoS One

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Getting "function" right

(2014) T. D. P. Brunet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Comparative genomics as a tool to understand evolution and disease

(2013) J. Alfoldi et al.   GENOME RESEARCH

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Locus-specific editing of histone modifications at endogenous enhancers

(2013) Eric M Mendenhall et al.   NATURE BIOTECHNOLOGY

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

(2013) Michael N Weedon et al.   NATURE GENETICS

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

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

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

Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation

(2012) Zhaoyu Li et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest

(2012) Alvaro Rada-Iglesias et al.   Cell Stem Cell

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Complex effects of nucleotide variants in a mammalian cis-regulatory element

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

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

(2012) Manching Ku et al.   GENOME BIOLOGY

Multilineage Priming of Enhancer Repertoires Precedes Commitment to the B and Myeloid Cell Lineages in Hematopoietic Progenitors

(2011) Elinore M. Mercer et al.   IMMUNITY

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS

(2010) Eric Pasmant et al.   FASEB JOURNAL

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

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

(2010) Axel Visel et al.   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Annotating non-coding regions of the genome

(2010) Roger P. Alexander et al.   NATURE REVIEWS GENETICS

A Systematic Enhancer Screen Using Lentivector Transgenesis Identifies Conserved and Non-Conserved Functional Elements at the Olig1 and Olig2 Locus

(2010) Marc Friedli et al.   PLoS One

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) D. Schmidt 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

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

(2009) Randy S. Daughters et al.   PLoS Genetics

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE