标题
Three-dimensional genome architecture and emerging technologies: looping in disease
作者
关键词
-
出版物
Genome Medicine
Volume 9, Issue 1, Pages -
出版商
Springer Nature
发表日期
2017-09-30
DOI
10.1186/s13073-017-0477-2
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。- 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
- Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells
- (2017) Shiqi Xie et al. MOLECULAR CELL
- Complex multi-enhancer contacts captured by genome architecture mapping
- (2017) Robert A. Beagrie 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
- CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
- (2017) Tyler S Klann et al. NATURE BIOTECHNOLOGY
- Promoting transcription over long distances
- (2017) Rui R Catarino et al. NATURE GENETICS
- Genome-wide characterization of mammalian promoters with distal enhancer functions
- (2017) Lan T M Dao et al. NATURE GENETICS
- 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
- A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
- (2017) Yarui Diao et al. NATURE METHODS
- Massively multiplex single-cell Hi-C
- (2017) Vijay Ramani et al. NATURE METHODS
- De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
- (2017) Olga Dudchenko et al. SCIENCE
- Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
- (2017) Paula Freire-Pritchett et al. eLife
- Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
- (2016) Biola M. Javierre et al. CELL
- Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
- (2016) Denes Hnisz et al. CELL
- Editing DNA Methylation in the Mammalian Genome
- (2016) X. Shawn Liu et al. CELL
- Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
- (2016) Rongxin Fang et al. CELL RESEARCH
- Chromosome conformation capture technologies and their impact in understanding genome function
- (2016) Satish Sati et al. CHROMOSOMA
- Capture‐C reveals preformed chromatin interactions between HIF‐binding sites and distant promoters
- (2016) James L Platt et al. EMBO REPORTS
- A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening
- (2016) Yarui Diao et al. GENOME RESEARCH
- Chromosome conformation elucidates regulatory relationships in developing human brain
- (2016) Hyejung Won et al. NATURE
- Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow
- (2016) Hanhui Ma et al. NATURE BIOTECHNOLOGY
- High-throughput mapping of regulatory DNA
- (2016) Nisha Rajagopal et al. NATURE BIOTECHNOLOGY
- Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry
- (2016) Olivia Corradin et al. NATURE GENETICS
- 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
- Targeting the cancer epigenome for therapy
- (2016) Peter A. Jones et al. NATURE REVIEWS GENETICS
- Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
- (2016) Jesse M. Engreitz et al. 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
- Spatial genome organization and cognition
- (2016) Prashanth Rajarajan et al. NATURE REVIEWS NEUROSCIENCE
- ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis
- (2016) Guipeng Li et al. NUCLEIC ACIDS RESEARCH
- Activation of proto-oncogenes by disruption of chromosome neighborhoods
- (2016) D. Hnisz et al. SCIENCE
- High-resolution interrogation of functional elements in the noncoding genome
- (2016) N. E. Sanjana et al. SCIENCE
- Systematic mapping of functional enhancer–promoter connections with CRISPR interference
- (2016) Charles P. Fulco et al. SCIENCE
- Breaking TADs: How Alterations of Chromatin Domains Result in Disease
- (2016) Darío G. Lupiáñez et al. TRENDS IN GENETICS
- A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
- (2016) Anthony D. Schmitt et al. Cell Reports
- Nuclear organization and 3D chromatin architecture in cognition and neuropsychiatric disorders
- (2016) Alejandro Medrano-Fernández et al. Molecular Brain
- Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
- (2016) Neva C. Durand et al. Cell Systems
- Understanding Spatial Genome Organization: Methods and Insights
- (2016) Vijay Ramani et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Mango: a bias-correcting ChIA-PET analysis pipeline
- (2015) Douglas H. Phanstiel et al. BIOINFORMATICS
- FourCSeq: analysis of 4C sequencing data
- (2015) Felix A. Klein et al. BIOINFORMATICS
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
- (2015) Suhas S.P. Rao 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
- Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency
- (2015) Onkar Joshi et al. Cell Stem Cell
- C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization
- (2015) A. Rasim Barutcu et al. JOURNAL OF CELLULAR PHYSIOLOGY
- Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation
- (2015) J. Fraser et al. Molecular Systems Biology
- Insulator dysfunction and oncogene activation in IDH mutant gliomas
- (2015) William A. Flavahan et al. NATURE
- Cell-of-origin chromatin organization shapes the mutational landscape of cancer
- (2015) Paz Polak et al. NATURE
- Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
- (2015) Silvana Konermann et al. NATURE
- Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
- (2015) Borbala Mifsud et al. NATURE GENETICS
- The effects of chromatin organization on variation in mutation rates in the genome
- (2015) Kateryna D. Makova et al. NATURE REVIEWS GENETICS
- Multicolor CRISPR labeling of chromosomal loci in human cells
- (2015) Hanhui Ma et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci
- (2015) Paul Martin et al. Nature Communications
- Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
- (2015) Roland Jäger et al. Nature Communications
- Epigenetic silencing of the XAF1 gene is mediated by the loss of CTCF binding
- (2015) Georgina Victoria-Acosta et al. Scientific Reports
- Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription
- (2014) Luca Giorgetti et al. CELL
- Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus
- (2014) Jian-Feng Xiang et al. CELL RESEARCH
- Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
- (2014) Nicola H. Dryden et al. GENOME RESEARCH
- Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
- (2014) F. Ay et al. GENOME RESEARCH
- Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping
- (2014) Paula J P de Vree et al. NATURE BIOTECHNOLOGY
- Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment
- (2014) Jim R Hughes et al. NATURE GENETICS
- Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants
- (2014) Lorenzo Pasquali 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
- CTCF: an architectural protein bridging genome topology and function
- (2014) Chin-Tong Ong et al. NATURE REVIEWS GENETICS
- Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units
- (2014) F. Song et al. SCIENCE
- 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
- Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system
- (2013) Albert W Cheng et al. CELL RESEARCH
- Regional chromatin decompaction in Cornelia de Lange syndrome associated with NIPBL disruption can be uncoupled from cohesin and CTCF
- (2013) Leisha D. Nolen et al. HUMAN MOLECULAR GENETICS
- Novel Higher-Order Epigenetic Regulation of the Bdnf Gene upon Seizures
- (2013) A. Walczak et al. JOURNAL OF NEUROSCIENCE
- Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
- (2013) Takashi Nagano et al. NATURE
- Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
- (2013) Fan Lai 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
- Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
- (2013) J. Zuin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Organization of the Mitotic Chromosome
- (2013) N. Naumova et al. SCIENCE
- Methods for Identifying Higher-Order Chromatin Structure
- (2012) Samin A. Sajan et al. Annual Review of Genomics and Human Genetics
- Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations
- (2012) Yu Zhang et al. CELL
- Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome
- (2012) R. P. McCord et al. GENOME RESEARCH
- Linking disease associations with regulatory information in the human genome
- (2012) M. A. Schaub et al. GENOME RESEARCH
- A misplaced lncRNA causes brachydactyly in humans
- (2012) Philipp G. Maass et al. JOURNAL OF CLINICAL INVESTIGATION
- Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation
- (2012) Erik Splinter et al. METHODS
- Chromatin organization is a major influence on regional mutation rates in human cancer cells
- (2012) Benjamin Schuster-Böckler et al. NATURE
- The long-range interaction landscape of gene promoters
- (2012) Amartya Sanyal et al. NATURE
- The accessible chromatin landscape of the human genome
- (2012) Robert E. Thurman 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
- Robust 4C-seq data analysis to screen for regulatory DNA interactions
- (2012) Harmen J G van de Werken et al. NATURE METHODS
- A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity
- (2012) M. Jinek et al. SCIENCE
- Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
- (2012) M. T. Maurano et al. SCIENCE
- Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene
- (2011) Lucy J. Davison et al. HUMAN MOLECULAR GENETICS
- Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
- (2011) Reza Kalhor et al. NATURE BIOTECHNOLOGY
- CTCF-mediated functional chromatin interactome in pluripotent cells
- (2011) Lusy Handoko et al. NATURE GENETICS
- Mediator and cohesin connect gene expression and chromatin architecture
- (2010) Michael H. Kagey et al. NATURE
- Cohesin: Its Roles and Mechanisms
- (2009) Kim Nasmyth et al. Annual Review of 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
- 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
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started