标题
Plant 3D genomics: the exploration and application of chromatin organization
作者
关键词
-
出版物
NEW PHYTOLOGIST
Volume -, Issue -, Pages -
出版商
Wiley
发表日期
2021-02-10
DOI
10.1111/nph.17262
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- 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
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started