Technological advances in probing 4D genome organization

Loop stacking organizes genome folding from TADs to chromosomes

(2023) Antonina Hafner et al.   MOLECULAR CELL

Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

(2023) Viraat Y. Goel et al.   NATURE GENETICS

Transcription shapes 3D chromatin organization by interacting with loop extrusion

(2023) Edward J. Banigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding

(2023) Jia-Yong Zhong et al.   Nature Communications

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

(2023) David B. Brückner et al.   SCIENCE

Single nucleosome tracking to study chromatin plasticity

(2022) Melike Lakadamyali   CURRENT OPINION IN CELL BIOLOGY

Genome organization controls transcriptional dynamics during development

(2022) Philippe J. Batut et al.   SCIENCE

HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization

(2022) Xiaolin Wei et al.   MOLECULAR CELL

Transcriptional coupling of distant regulatory genes in living embryos

(2022) Michal Levo et al.   NATURE

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

(2022) Aditya S. Deshpande et al.   NATURE BIOTECHNOLOGY

Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

(2022) Michele Gabriele et al.   SCIENCE

HiCuT: An efficient and low input method to identify protein-directed chromatin interactions

(2022) Satish Sati et al.   PLoS Genetics

Coming full circle: On the origin and evolution of the looping model for enhancer–promoter communication

(2022) Tessa M. Popay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

(2022) Chiara Anania et al.   NATURE GENETICS

Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells

(2022) Shiori Iida et al.   Science Advances

New insights into genome folding by loop extrusion from inducible degron technologies

(2022) Elzo de Wit et al.   NATURE REVIEWS GENETICS

Cohesin and CTCF control the dynamics of chromosome folding

(2022) Pia Mach et al.   NATURE GENETICS

Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

(2022) Tsung-Han S. Hsieh et al.   NATURE GENETICS

Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription

(2022) Isabel N. Goronzy et al.   Cell Reports

Order and stochasticity in the folding of individual Drosophila genomes

(2021) Sergey V. Ulianov et al.   Nature Communications

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

(2021) Damien J. Downes et al.   Nature Communications

Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation

(2021) Pablo Aurelio Gómez-García et al.   Cell Reports

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics

(2021) Houda Belaghzal et al.   NATURE GENETICS

Defining genome architecture at base-pair resolution

(2021) Peng Hua et al.   NATURE

Single-cell measurement of higher-order 3D genome organization with scSPRITE

(2021) Mary V. Arrastia et al.   NATURE BIOTECHNOLOGY

Systematic evaluation of chromosome conformation capture assays

(2021) Betul Akgol Oksuz et al.   NATURE METHODS

Essential Roles for RNA in Shaping Nuclear Organization

(2021) Sofia A. Quinodoz et al.   Cold Spring Harbor Perspectives in Biology

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Cell-type specialization is encoded by specific chromatin topologies

(2021) Warren Winick-Ng et al.   NATURE

Single-cell nuclear architecture across cell types in the mouse brain

(2021) Yodai Takei et al.   SCIENCE

Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP)

(2020) Berkley E. Gryder et al.   Nature Protocols

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

GPSeq reveals the radial organization of chromatin in the cell nucleus

(2020) Gabriele Girelli et al.   NATURE BIOTECHNOLOGY

Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization

(2020) Paweł Trzaskoma et al.   Nature Communications

Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin

(2020) Jonathan Lerner et al.   MOLECULAR CELL

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Conformation of sister chromatids in the replicated human genome

(2020) Michael Mitter et al.   NATURE

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

(2020) Liguo Zhang et al.   GENOME RESEARCH

Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging

(2020) Hugo B. Brandão et al.   CURRENT OPINION IN CELL BIOLOGY

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

Multiplex chromatin interactions with single-molecule precision

(2019) Meizhen Zheng et al.   NATURE

HiChIRP reveals RNA-associated chromosome conformation

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

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

Chromatin folding and nuclear architecture: PRC1 function in 3D

(2019) Robert S Illingworth   CURRENT OPINION IN GENETICS & DEVELOPMENT

Structural and Dynamical Signatures of Local DNA Damage in Live Cells

(2019) Jonah A. Eaton et al.   BIOPHYSICAL JOURNAL

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

FISH-ing for captured contacts: towards reconciling FISH and 3C

(2017) Geoffrey Fudenberg et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

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

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

(2016) Simeon Carstens et al.   PLoS Computational Biology

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

(2015) Borbala Mifsud et al.   NATURE GENETICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

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

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

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

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