The era of 3D and spatial genomics

RNA gradients: Shapers of 3D genome architecture

(2022) Britta A.M. Bouwman et al.   CURRENT OPINION IN CELL BIOLOGY

Spatially resolved single-cell genomics and transcriptomics by imaging

(2021) Xiaowei Zhuang   NATURE METHODS

Spatially resolved transcriptomics adds a new dimension to genomics

(2021) Ludvig Larsson et al.   NATURE METHODS

Genome oligopaint via local denaturation fluorescence in situ hybridization

(2021) Yanbo Wang et al.   MOLECULAR CELL

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue

(2021) Miao Liu et al.   Nature Protocols

Understanding 3D genome organization by multidisciplinary methods

(2021) Ivana Jerkovic´ et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chorus2: design of genome‐scale oligonucleotide‐based probes for fluorescence in situ hybridization

(2021) Tao Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

Single‐cell imaging of genome organization and dynamics

(2021) Liangqi Xie et al.   Molecular Systems Biology

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

PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments

(2021) Elliot A. Hershberg et al.   NATURE METHODS

Distinct nuclear compartment-associated genome architecture in the developing mammalian brain

(2021) Sajad Hamid Ahanger et al.   NATURE NEUROSCIENCE

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

The CRISPR-Cas toolbox and gene editing technologies

(2021) Guanwen Liu et al.   MOLECULAR CELL

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues

(2021) Tongtong Zhao et al.   NATURE

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

(2021) Yodai Takei et al.   SCIENCE

The two waves in single-cell 3D genomics

(2021) Sergey V. Ulianov et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A Shift in Paradigms: Spatial Genomics Approaches to Reveal Single-Cell Principles of Genome Organization

(2021) Andres M. Cardozo Gizzi   Frontiers in Genetics

FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains

(2021) Antonina Maslova et al.   Frontiers in Cell and Developmental Biology

Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide

(2020) Keerthivasan Raanin Chandradoss et al.   BMC GENOMICS

Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos

(2020) Ahilya N. Sawh et al.   MOLECULAR CELL

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

Visualizing the genome in high resolution challenges our textbook understanding

(2020) Melike Lakadamyali et al.   NATURE METHODS

Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies

(2020) Carlo Vermeulen et al.   Nature Protocols

Monitoring the spatio-temporal organization and dynamics of the genome

(2020) Haitham A Shaban et al.   NUCLEIC ACIDS RESEARCH

Advances in Chromatin Imaging at Kilobase-Scale Resolution

(2020) Alistair Boettiger et al.   TRENDS IN GENETICS

Radial Organization in the Mammalian Nucleus

(2020) Nicola Crosetto et al.   Frontiers in Genetics

GPSeq reveals the radial organization of chromatin in the cell nucleus

(2020) Gabriele Girelli et al.   NATURE BIOTECHNOLOGY

Simultaneous quantification of protein–DNA interactions and transcriptomes in single cells with scDam&T-seq

(2020) Corina M. Markodimitraki et al.   Nature Protocols

Evolving methodologies and concepts in 4D nucleome research

(2020) Thomas M. Sparks et al.   CURRENT OPINION IN CELL BIOLOGY

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

(2020) Huy Q. Nguyen et al.   NATURE METHODS

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

(2020) Miao Liu et al.   Nature Communications

Coupling chromatin structure and dynamics by live super-resolution imaging

(2020) R. Barth et al.   Science Advances

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

(2020) Jun-Han Su et al.   CELL

High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection

(2020) Pranitha Vangala et al.   MOLECULAR CELL

Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

(2020) Qiancheng You et al.   NATURE BIOTECHNOLOGY

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

Chromatin Tracing: Imaging 3D Genome and Nucleome

(2020) Mengwei Hu et al.   TRENDS IN CELL BIOLOGY

ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization

(2020) Mengwei Hu et al.   Scientific Reports

Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture

(2020) Sjoerd JD Tjalsma et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

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

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

(2019) Andrés M. Cardozo Gizzi et al.   MOLECULAR CELL

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

(2019) Josef Redolfi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans

(2019) Brandon D Fields et al.   eLife

Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells

(2019) Koos Rooijers et al.   NATURE BIOTECHNOLOGY

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

(2019) Eleni Gelali et al.   Nature Communications

CRISPR-mediated live imaging of genome editing and transcription

(2019) Haifeng Wang et al.   SCIENCE

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

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

(2018) Sofia A. Quinodoz et al.   CELL

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

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

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

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag

(2018) Baohui Chen et al.   Nature Communications

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

(2017) Houda Belaghzal et al.   METHODS

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

(Po)STAC (Polycistronic SunTAg modified CRISPR) enables live-cell and fixed-cell super-resolution imaging of multiple genes

(2017) Maria V Neguembor et al.   NUCLEIC ACIDS RESEARCH

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow

(2016) Hanhui Ma et al.   NATURE BIOTECHNOLOGY

Mapping the 3D genome: Aiming for consilience

(2016) Job Dekker   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci

(2016) Yi Fu et al.   Nature Communications

An RNA-aptamer-based two-color CRISPR labeling system

(2016) Siyuan Wang et al.   Scientific Reports

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

(2015) Wulan Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

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

(2014) Suhas S.P. Rao et al.   CELL

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Implementing personalized cancer care

(2014) Richard L. Schilsky   Nature Reviews Clinical Oncology

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

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

(2013) Takashi Nagano et al.   NATURE

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

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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

(2012) Magda Bienko et al.   NATURE METHODS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

(2011) Shelagh Boyle et al.   CHROMOSOME RESEARCH

Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH

(2011) N.A. Yamada et al.   CYTOGENETIC AND GENOME RESEARCH

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Genome organization in and around the nucleolus

(2011) Attila Németh et al.   TRENDS IN GENETICS

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

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

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

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE