Plant 3D genomics: the exploration and application of chromatin organization

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

(2020) Sean A. Montgomery et al.   CURRENT BIOLOGY

The Cohesin Complex Subunit ZmSMC Participates in Meiotic Centromere Pairing in Maize

(2020) Jing Zhang et al.   PLANT CELL

Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize

(2020) Yalin Liu et al.   PLOS BIOLOGY

Plant and animal chromatin three-dimensional organization: similar structures but different functions

(2020) Pengfei Dong et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide Characterization of DNase I-hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses

(2020) Jinlei Han et al.   PLANT CELL

Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis

(2020) Linhua Sun et al.   Nature Communications

UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize

(2020) Yanfang Du et al.   PLoS Genetics

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states

(2020) Hans-Wilhelm Nützmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Technologies for Capturing 3D Genome Architecture in Plants

(2020) Weizhi Ouyang et al.   TRENDS IN PLANT SCIENCE

Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships

(2019) Patrice S. Albert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex chromatin interactions with single-molecule precision

(2019) Meizhen Zheng et al.   NATURE

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

(2019) Pengfei Dong et al.   Journal of Integrative Plant Biology

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2019) Yongdae Shin et al.   CELL

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

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

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

The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation

(2019) Hui Zhang et al.   NUCLEIC ACIDS RESEARCH

Chromatin interaction maps reveal genetic regulation for quantitative traits in maize

(2019) Yong Peng et al.   Nature Communications

Long-range interactions between proximal and distal regulatory regions in maize

(2019) En Li et al.   Nature Communications

Global Quantitative Mapping of Enhancers in Rice by STARR-seq

(2019) Jialei Sun et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Cut-C: cleavage under tethered nuclease for conformational capture

(2019) Takashi Shimbo et al.   BMC GENOMICS

BAT Hi-C maps global chromatin interactions in an efficient and economical way

(2019) Jie Huang et al.   METHODS

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

(2019) Dong-Sung Lee et al.   NATURE METHODS

Joint profiling of DNA methylation and chromatin architecture in single cells

(2019) Guoqiang Li et al.   NATURE METHODS

Decrosslinking enabled visualization of RGEN-ISL signals for DNA sequences in plant tissues

(2019) Kiyotaka Nagaki et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cell-type–specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage

(2019) Laura R. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering essential cistromes using genome-wide CRISPR screens

(2019) Teng Fei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

(2019) Lun Zhao et al.   Nature Communications

Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques

(2019) Alessandra M. Sullivan et al.   Frontiers in Plant Science

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

(2018) Sofia A. Quinodoz et al.   CELL

Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture

(2018) Da Lin et al.   NATURE GENETICS

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks

(2018) Paja Sijacic et al.   PLANT JOURNAL

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice

(2018) Qianli Dong et al.   PLANT JOURNAL

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Gene Expression Dominance in Allopolyploids: Hypotheses and Models

(2018) Samuel Bottani et al.   TRENDS IN PLANT SCIENCE

Entering the Next Dimension: Plant Genomes in 3D

(2018) Mariana Sotelo-Silveira et al.   TRENDS IN PLANT SCIENCE

Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

(2018) Qi Wang et al.   Nature Communications

Single-cell variability in multicellular organisms

(2018) Stephen Smith et al.   Nature Communications

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Trac-looping measures genome structure and chromatin accessibility

(2018) Binbin Lai et al.   NATURE METHODS

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants

(2017) Axel Poulet et al.   JOURNAL OF CELL SCIENCE

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

(2017) Pengfei Dong et al.   Molecular Plant

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

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

(2017) Tim J. Stevens et al.   NATURE

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Live-cell CRISPR imaging in plants reveals dynamic telomere movements

(2017) Steven Dreissig et al.   PLANT JOURNAL

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

(2017) Horng D. Ou et al.   SCIENCE

Live cell imaging of single genomic loci with quantum dot-labeled TALEs

(2017) Yingxin Ma et al.   Nature Communications

BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions

(2017) Zhengyu Liang et al.   Nature Communications

Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9

(2017) Peiwu Qin et al.   Nature Communications

Super-resolution Microscopy – Applications in Plant Cell Research

(2017) Veit Schubert   Frontiers in Plant Science

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Visualization of specific repetitive genomic sequences with fluorescent TALEs inArabidopsis thaliana

(2016) Satoru Fujimoto et al.   JOURNAL OF EXPERIMENTAL BOTANY

Put your 3D glasses on: plant chromatin is on show

(2016) Natalia Y. Rodriguez-Granados et al.   JOURNAL OF EXPERIMENTAL BOTANY

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

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

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation

(2016) Maojun Wang et al.   NUCLEIC ACIDS RESEARCH

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

On TADs and LADs: Spatial Control Over Gene Expression

(2016) Adriana Gonzalez-Sandoval et al.   TRENDS IN GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Exploring chromatin organization mechanisms through its dynamic properties

(2016) Irena Bronshtein et al.   Nucleus

Exploring chromatin organization mechanisms through its dynamic properties

(2016) Irena Bronshtein et al.   Nucleus

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

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

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

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus

(2015) Joana Sequeira-Mendes et al.   CHROMOSOMA

Non-coding genetic variants in human disease: Figure 1.

(2015) Feng Zhang et al.   HUMAN MOLECULAR GENETICS

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

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

(2015) Borbala Mifsud et al.   NATURE GENETICS

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

(2015) Bo Zhu et al.   PLANT 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

Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

(2015) Xiang Li et al.   Nature Communications

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

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

(2014) Suhas S.P. Rao et al.   CELL

Genome-wide analysis of local chromatin packing inArabidopsis thaliana

(2014) Congmao Wang et al.   GENOME RESEARCH

Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila

(2014) Stefan Grob et al.   MOLECULAR CELL

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

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

(2014) Jim R Hughes et al.   NATURE GENETICS

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

(2014) Wenxiu Ma et al.   NATURE METHODS

Hypomethylated Pollen Bypasses the Interploidy Hybridization Barrier in Arabidopsis

(2014) N. Schatlowski et al.   PLANT CELL

A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis in Arabidopsis Intraspecific Hybrids

(2014) D. W.- K. Ng et al.   PLANT CELL

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

(2014) A. Li et al.   PLANT CELL

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids

(2014) M. R. Woodhouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements

(2014) Petros Kolovos et al.   Epigenetics & Chromatin

Chromatin associations in Arabidopsis interphase nuclei

(2014) Veit Schubert et al.   Frontiers in Genetics

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Chromatin reprogramming during the somatic-to-reproductive cell fate transition in plants

(2013) Wenjing She et al.   DEVELOPMENT

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

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

(2013) Takashi Nagano et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

MADS Domain Transcription Factors Mediate Short-Range DNA Looping That Is Essential for Target Gene Expression in Arabidopsis

(2013) M. A. Mendes et al.   PLANT CELL

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture

(2013) Stefan Grob et al.   GENOME BIOLOGY

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

(2012) Veit Schubert et al.   CHROMOSOMA

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Transposon integration enhances expression of stress response genes

(2012) Gang Feng et al.   NUCLEIC ACIDS RESEARCH

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

The chromatin insulator CTCF and the emergence of metazoan diversity

(2012) P. Heger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Abiotic Stress and Induced DNA Hypomethylation Cause Interphase Chromatin Structural Changes in Rice rDNA Loci

(2011) A.P. Santos et al.   CYTOGENETIC AND GENOME RESEARCH

Light Sheet Fluorescence Microscopy

(2011) Peter A. Santi   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

From nucleosome to chromosome: a dynamic organization of genetic information

(2011) Paul Fransz et al.   PLANT JOURNAL

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

(2011) Z. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization and dynamics of plant interphase chromosomes

(2011) Ingo Schubert et al.   TRENDS IN PLANT SCIENCE

Widefield microscopy for live imaging of lipid domains and membrane dynamics

(2010) Guy Wheeler et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Direct fluorescence in situ hybridization (FISH) in Escherichia coli with a target-specific quantum dot-based molecular beacon

(2010) Sheng-Mei Wu et al.   BIOSENSORS & BIOELECTRONICS

FISH Applications for Genomics and Plant Breeding Strategies in Tomato and Other Solanaceous Crops

(2010) D. Szinay et al.   CYTOGENETIC AND GENOME RESEARCH

Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice

(2010) Gui-Sheng Song et al.   Molecular Plant

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Super-Resolution Imaging of Plasmodesmata Using Three-Dimensional Structured Illumination Microscopy

(2010) J. Fitzgibbon et al.   PLANT PHYSIOLOGY

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Tissue- and Expression Level-Specific Chromatin Looping at Maize b1 Epialleles

(2009) M. Louwers et al.   PLANT CELL

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE