High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells

(2020) James D.P. Rhodes et al.   Cell Reports

Alteration of genome folding via contact domain boundary insertion

(2020) Di Zhang et al.   NATURE GENETICS

LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice

(2019) Kevin Monahan et al.   NATURE

Multiplex chromatin interactions with single-molecule precision

(2019) Meizhen Zheng et al.   NATURE

Fine mapping chromatin contacts in capture Hi-C data

(2019) Christiaan Q Eijsbouts et al.   BMC GENOMICS

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

HiChIRP reveals RNA-associated chromosome conformation

(2019) Maxwell R. Mumbach et al.   NATURE METHODS

Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

(2019) Judith Hyle et al.   NUCLEIC ACIDS RESEARCH

DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation

(2019) Laura Godfrey et al.   Nature Communications

PRC1 Catalytic Activity Is Central to Polycomb System Function

(2019) Neil P. Blackledge et al.   MOLECULAR CELL

Impaired DNA demethylation of C/EBP sites causes premature aging

(2018) Andrea Schäfer et al.   GENES & DEVELOPMENT

The Ftx Noncoding Locus Controls X Chromosome Inactivation Independently of Its RNA Products

(2018) Giulia Furlan et al.   MOLECULAR CELL

peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

(2018) Geert Geeven et al.   NUCLEIC ACIDS RESEARCH

Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

(2018) Matthias Thurner et al.   eLife

Population snapshots predict early haematopoietic and erythroid hierarchies

(2018) Betsabeh Khoramian Tusi et al.   NATURE

A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions

(2018) Jill M. Brown et al.   Nature Communications

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

(2018) A. Marieke Oudelaar et al.   NATURE GENETICS

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies et al.   NATURE METHODS

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

(2017) Benedikt Zacher et al.   PLoS One

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

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

(2016) Deborah Hay et al.   NATURE GENETICS

UMI-4C for quantitative and targeted chromosomal contact profiling

(2016) Omer Schwartzman et al.   NATURE METHODS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

FourCSeq: analysis of 4C sequencing data

(2015) Felix A. Klein et al.   BIOINFORMATICS

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

(2015) James O J Davies et al.   NATURE METHODS

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application

(2015) Guoliang Li et al.   BMC GENOMICS

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

(2014) Muhammad A. Zabidi et al.   NATURE

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

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

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

The hypersensitive sites of the murine  -globin locus control region act independently to affect nuclear localization and transcriptional elongation

(2012) M. A. Bender et al.   BLOOD

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE