Transcription factor-dependent ‘anti-repressive’ mammalian enhancers exclude H3K27me3 from extended genomic domains

Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements

(2017) Jelena Erceg et al.   GENES & DEVELOPMENT

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells

(2016) Unmesh Jadhav et al.   CELL

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Histone demethylases in physiology and cancer: a tale of two enzymes, JMJD3 and UTX

(2016) Kelly Marie Arcipowski et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis

(2016) Jialiang Huang et al.   DEVELOPMENTAL CELL

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

(2016) Justin S. Becker et al.   TRENDS IN GENETICS

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Targeting Polycomb systems to regulate gene expression: modifications to a complex story

(2015) Neil P. Blackledge et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns

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

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

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

(2013) Warren A. Whyte et al.   CELL

Polycomb Repressive Complex 2 Regulates Normal Hematopoietic Stem Cell Function in a Developmental-Stage-Specific Manner

(2013) Huafeng Xie et al.   Cell Stem Cell

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

(2013) Esteban O Mazzoni et al.   NATURE NEUROSCIENCE

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cdx function is required for maintenance of intestinal identity in the adult

(2012) Alexa Hryniuk et al.   DEVELOPMENTAL BIOLOGY

Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding

(2012) M. P. Verzi et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2012) Yin Shen et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Cdx2 determines the fate of postnatal intestinal endoderm

(2011) E. J. Stringer et al.   DEVELOPMENT

UTX, a Histone H3-Lysine 27 Demethylase, Acts as a Critical Switch to Activate the Cardiac Developmental Program

(2011) Seunghee Lee et al.   DEVELOPMENTAL CELL

Polycomb eviction as a new distant enhancer function

(2011) D. Vernimmen et al.   GENES & DEVELOPMENT

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Nucleosomes and the accessibility problem

(2011) Xin Wang et al.   TRENDS IN GENETICS

Genome-wide transcription factor binding: beyond direct target regulation

(2011) Kyle L. MacQuarrie et al.   TRENDS IN GENETICS

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2

(2010) Michael P. Verzi et al.   DEVELOPMENTAL CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias 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

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Establishment of Intestinal Identity and Epithelial-Mesenchymal Signaling by Cdx2

(2009) Nan Gao et al.   DEVELOPMENTAL CELL

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq

(2008) Yong Zhang et al.   BMC GENOMICS

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY