Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

Coolpup.py: versatile pile-up analysis of Hi-C data

(2020) Ilya M Flyamer et al.   BIOINFORMATICS

The regulatory landscapes of developmental genes

(2020) Christopher Chase Bolt et al.   DEVELOPMENT

Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping

(2020) V. Loubiere et al.   Science Advances

A central role for canonical PRC1 in shaping the 3D nuclear landscape

(2020) Shelagh Boyle et al.   GENES & DEVELOPMENT

Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers

(2020) Robin Steinhaus et al.   NUCLEIC ACIDS RESEARCH

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

CG dinucleotides enhance promoter activity independent of DNA methylation

(2019) Dominik Hartl et al.   GENOME RESEARCH

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs

(2019) Magdalena Laugsch et al.   Cell Stem Cell

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

(2019) Anne H Turberfield et al.   NUCLEIC ACIDS RESEARCH

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule

(2019) Francisco Requena et al.   Scientific Reports

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing

(2019) Jean-Pierre Etchegaray et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements

(2019) Shigeki Hirabayashi et al.   NATURE GENETICS

Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers

(2018) Jian Yan et al.   CELL RESEARCH

Tild-CRISPR Allows for Efficient and Precise Gene Knockin in Mouse and Human Cells

(2018) Xuan Yao et al.   DEVELOPMENTAL CELL

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

(2018) Rui R. Catarino et al.   GENES & DEVELOPMENT

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding

(2018) Matteo Perino et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Implications of CpG islands on chromosomal architectures and modes of global gene regulation

(2018) Samuel Beck et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies

(2018) Lori L. O’Brien et al.   PLoS Genetics

FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment

(2018) Emilia Dimitrova et al.   eLife

Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

(2018) Jing Wang et al.   BMC GENOMICS

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

(2018) Bjørt K. Kragesteen et al.   NATURE GENETICS

The RNA exosome contributes to gene expression regulation during stem cell differentiation

(2018) Marta Lloret-Llinares et al.   NUCLEIC ACIDS RESEARCH

GADD45A binds R-loops and recruits TET1 to CpG island promoters

(2018) Khelifa Arab et al.   NATURE GENETICS

Orphan CpG islands define a novel class of highly active enhancers

(2017) Joshua S. K. Bell et al.   Epigenetics

Identification of H3K4me1-associated proteins at mammalian enhancers

(2017) Andrea Local et al.   NATURE GENETICS

Intragenic CpG islands play important roles in bivalent chromatin assembly of developmental genes

(2017) Sun-Min Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

The role of Polycomb in stem cell genome architecture

(2016) Gloria Mas et al.   CURRENT OPINION IN CELL BIOLOGY

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

(2016) Manuel Beltran et al.   GENOME RESEARCH

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Darío G. Lupiáñez et al.   CELL

Using transgenic reporter assays to functionally characterize enhancers in animals

(2015) Evgeny Z. Kvon   GENOMICS

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

(2015) Carlos Gómez-Marín et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

(2015) Jan J Zylicz et al.   eLife

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Variant PRC1 Complex-Dependent H2A Ubiquitylation Drives PRC2 Recruitment and Polycomb Domain Formation

(2014) Neil P. Blackledge et al.   CELL

Dkk1-dependent inhibition of Wnt signaling activatesHesx1expression through its 5′ enhancer and directs forebrain precursor development

(2014) Kazunari Matsuda et al.   GENES TO CELLS

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

In Vitro Generation of Neuromesodermal Progenitors Reveals Distinct Roles for Wnt Signalling in the Specification of Spinal Cord and Paraxial Mesoderm Identity

(2014) Mina Gouti et al.   PLOS BIOLOGY

ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection

(2013) Hannah K. Long et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

(2013) Ehsan Habibi et al.   Cell Stem Cell

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

(2013) Kyoichi Isono et al.   DEVELOPMENTAL CELL

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

CpG island chromatin

(2011) Neil P. Blackledge et al.   Epigenetics

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes

(2011) J. S. You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR 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

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH