3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering
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Title
3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering
Authors
Keywords
Chromosome conformation capture (3C), Topologically associating domains (TADs), Hi-C, C-technologies, Chromosome territory
Journal
Molecular Cytogenetics
Volume 11, Issue 1, Pages -
Publisher
Springer Nature
Online
2018-03-09
DOI
10.1186/s13039-018-0368-2
References
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Note: Only part of the references are listed.- Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy
- (2017) Volker J. Schmid et al. METHODS
- The genome of Chenopodium quinoa
- (2017) David E. Jarvis et al. NATURE
- Complex multi-enhancer contacts captured by genome architecture mapping
- (2017) Robert A. Beagrie 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
- Cell-cycle dynamics of chromosomal organization at single-cell resolution
- (2017) Takashi Nagano et al. NATURE
- A chromosome conformation capture ordered sequence of the barley genome
- (2017) Martin Mascher et al. NATURE
- Native chromosome conformation
- (2017) Nicole Rusk NATURE METHODS
- How best to identify chromosomal interactions: a comparison of approaches
- (2017) James O J Davies et al. NATURE METHODS
- Comparison of computational methods for Hi-C data analysis
- (2017) Mattia Forcato et al. NATURE METHODS
- FISH-ing for captured contacts: towards reconciling FISH and 3C
- (2017) Geoffrey Fudenberg et al. NATURE METHODS
- Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions
- (2017) Xingwang Li et al. Nature Protocols
- Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes
- (2017) François Aymard et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
- (2017) Olga Dudchenko et al. SCIENCE
- Wild emmer genome architecture and diversity elucidate wheat evolution and domestication
- (2017) Raz Avni et al. SCIENCE
- 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations
- (2017) Pengze Wu et al. Nature Communications
- Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes
- (2017) François Aymard et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- The 3D Genome as Moderator of Chromosomal Communication
- (2016) Job Dekker et al. CELL
- Chromosome conformation capture technologies and their impact in understanding genome function
- (2016) Satish Sati et al. CHROMOSOMA
- Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations
- (2016) Phillippa C. Taberlay et al. GENOME RESEARCH
- Exploiting native forces to capture chromosome conformation in mammalian cell nuclei
- (2016) Lilija Brant et al. Molecular Systems Biology
- Chromosome conformation elucidates regulatory relationships in developing human brain
- (2016) Hyejung Won et al. NATURE
- Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast
- (2016) Kyoung-Dong Kim et al. NATURE GENETICS
- Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
- (2016) Tsung-Han S Hsieh et al. NATURE METHODS
- 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
- Organization and function of the 3D genome
- (2016) Boyan Bonev et al. NATURE REVIEWS GENETICS
- 3D solutions to complex gene regulation
- (2016) Edith Heard NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Mapping the 3D genome: Aiming for consilience
- (2016) Job Dekker NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Regulation of disease-associated gene expression in the 3D genome
- (2016) Peter Hugo Lodewijk Krijger et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Genome-wide mapping and analysis of chromosome architecture
- (2016) Anthony D. Schmitt et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Understanding Spatial Genome Organization: Methods and Insights
- (2016) Vijay Ramani et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C
- (2015) Ferhat Ay et al. BMC GENOMICS
- Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
- (2015) Tsung-Han S. Hsieh et al. CELL
- The Hitchhiker’s guide to Hi-C analysis: Practical guidelines
- (2015) Bryan R. Lajoie et al. METHODS
- An Overview of Genome Organization and How We Got There: from FISH to Hi-C
- (2015) James Fraser et al. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
- 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
- Multiplexed analysis of chromosome conformation at vastly improved sensitivity
- (2015) James O J Davies et al. NATURE METHODS
- Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell
- (2015) Takashi Nagano et al. Nature Protocols
- Moving a TAD closer to unravelling chromosome architecture
- (2015) Joana Osório NATURE REVIEWS GENETICS
- The effects of chromatin organization on variation in mutation rates in the genome
- (2015) Kateryna D. Makova et al. NATURE REVIEWS GENETICS
- Unraveling the 3D genome: genomics tools for multiscale exploration
- (2015) Viviana I. Risca et al. TRENDS IN GENETICS
- Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
- (2015) Roland Jäger 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
- A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia
- (2014) Stefan Gröschel et al. CELL
- Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
- (2014) Iain Williamson et al. GENES & DEVELOPMENT
- Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
- (2014) F. Ay et al. GENOME RESEARCH
- Genome-wide map of regulatory interactions in the human genome
- (2014) Nastaran Heidari et al. GENOME RESEARCH
- 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
- 3D genome reconstruction from chromosomal contacts
- (2014) Annick Lesne et al. NATURE METHODS
- Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
- (2014) Wenxiu Ma et al. NATURE METHODS
- Genome Architecture: Domain Organization of Interphase Chromosomes
- (2013) Wendy A. Bickmore et al. CELL
- Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
- (2013) Takashi Nagano et al. NATURE
- A high-resolution map of the three-dimensional chromatin interactome in human cells
- (2013) Fulai Jin et al. NATURE
- Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
- (2013) Joshua N Burton et al. NATURE BIOTECHNOLOGY
- Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
- (2013) Siddarth Selvaraj et al. NATURE BIOTECHNOLOGY
- Exploring long-range genome interactions using the WashU Epigenome Browser
- (2013) Xin Zhou et al. NATURE METHODS
- Singled out for sequencing
- (2013) Kelly Rae Chi NATURE METHODS
- Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions
- (2013) Ralph Stadhouders et al. Nature Protocols
- Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
- (2013) Job Dekker et al. NATURE REVIEWS GENETICS
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- (2013) T. B. K. Le et al. SCIENCE
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- (2013) G. Andrey et al. SCIENCE
- Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture
- (2013) Stefan Grob et al. GENOME BIOLOGY
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- (2012) Ming Hu et al. BIOINFORMATICS
- SnapShot: Chromosome Conformation Capture
- (2012) Ofir Hakim et al. CELL
- A map of the cis-regulatory sequences in the mouse genome
- (2012) Yin Shen et al. NATURE
- 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
- Iterative correction of Hi-C data reveals hallmarks of chromosome organization
- (2012) Maxim Imakaev et al. NATURE METHODS
- Robust 4C-seq data analysis to screen for regulatory DNA interactions
- (2012) Harmen J G van de Werken et al. NATURE METHODS
- Complexity of chromatin folding is captured by the strings and binders switch model
- (2012) M. Barbieri et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing
- (2012) G. Moissiard et al. SCIENCE
- Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis
- (2011) Shelagh Boyle et al. CHROMOSOME RESEARCH
- The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA
- (2011) E. Splinter et al. GENES & DEVELOPMENT
- Tumour evolution inferred by single-cell sequencing
- (2011) Nicholas Navin et al. NATURE
- A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
- (2011) Kevin C. Wang et al. NATURE
- Variegated gene expression caused by cell-specific long-range DNA interactions
- (2011) Daan Noordermeer et al. NATURE CELL BIOLOGY
- Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
- (2011) Eitan Yaffe et al. NATURE GENETICS
- CTCF-mediated functional chromatin interactome in pluripotent cells
- (2011) Lusy Handoko et al. NATURE GENETICS
- Single-cell methods
- (2011) Natalie de Souza NATURE METHODS
- A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber
- (2011) I. Comet et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution
- (2011) E. H. Rego et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome
- (2010) Thomas M Asbury et al. BMC BIOINFORMATICS
- A three-dimensional model of the yeast genome
- (2010) Zhijun Duan et al. NATURE
- Genomics tools for unraveling chromosome architecture
- (2010) Bas van Steensel et al. NATURE BIOTECHNOLOGY
- The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules
- (2010) Davide Baù et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene
- (2010) Nele Gheldof et al. NUCLEIC ACIDS RESEARCH
- The three-dimensional architecture of Hox cluster silencing
- (2010) Maria A. Ferraiuolo et al. NUCLEIC ACIDS RESEARCH
- Stable Morphology, but Dynamic Internal Reorganisation, of Interphase Human Chromosomes in Living Cells
- (2010) Iris Müller et al. PLoS One
- Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization
- (2010) Manfred Bohn et al. PLoS One
- Genome organization influences partner selection for chromosomal rearrangements
- (2010) Patrick J. Wijchers et al. TRENDS IN GENETICS
- An oestrogen-receptor-α-bound human chromatin interactome
- (2009) Melissa J. Fullwood et al. NATURE
- High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology
- (2009) Marieke Simonis et al. NATURE METHODS
- Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)
- (2009) Marieke Louwers et al. Nature Protocols
- Spatially confined folding of chromatin in the interphase nucleus
- (2009) J. Mateos-Langerak 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
- Yeast Silent Mating Type Loci Form Heterochromatic Clusters through Silencer Protein-Dependent Long-Range Interactions
- (2009) Adriana Miele et al. PLoS Genetics
- Chromatin conformation signatures of cellular differentiation
- (2009) James Fraser et al. GENOME BIOLOGY
- Association between active genes occurs at nuclear speckles and is modulated by chromatin environment
- (2008) Jill M. Brown et al. JOURNAL OF CELL BIOLOGY
- Dynamic interactions between the promoter and terminator regions of the mammalianBRCA1gene
- (2008) Sue Mei Tan-Wong et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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