Revisiting 3D chromatin architecture in cancer development and progression
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Revisiting 3D chromatin architecture in cancer development and progression
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-09-04
DOI
10.1093/nar/gkaa747
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression
- (2020) Maria Fasolino et al. IMMUNITY
- TADs or no TADS: Lessons From Single-cell Imaging of Chromosome Architecture
- (2020) Andrés M. Cardozo Gizzi et al. JOURNAL OF MOLECULAR BIOLOGY
- Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development
- (2020) Chew Yee Ngan et al. NATURE GENETICS
- Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping
- (2020) V. Loubiere et al. Science Advances
- The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
- (2020) Orit Rozenblatt-Rosen et al. CELL
- Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria
- (2020) Kohta Ikegami et al. DEVELOPMENTAL CELL
- RIC-seq for global in situ profiling of RNA–RNA spatial interactions
- (2020) Zhaokui Cai et al. NATURE
- Dynamics of the 4D genome during in vivo lineage specification and differentiation
- (2020) A. Marieke Oudelaar et al. Nature Communications
- LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice
- (2019) Kevin Monahan et al. NATURE
- Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly
- (2019) Sreejith J. Nair et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Transposable elements drive widespread expression of oncogenes in human cancers
- (2019) Hyo Sik Jang et al. NATURE GENETICS
- Multiplex chromatin interactions with single-molecule precision
- (2019) Meizhen Zheng et al. NATURE
- Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance
- (2019) Jessica A. Bertolini et al. Cell Stem Cell
- Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
- (2019) Jeffrey M Alexander et al. eLife
- The Polycomb Repressor Complex 1 Drives Double-Negative Prostate Cancer Metastasis by Coordinating Stemness and Immune Suppression
- (2019) Wenjing Su et al. CANCER CELL
- LADL: light-activated dynamic looping for endogenous gene expression control
- (2019) Ji Hun Kim et al. NATURE METHODS
- The role of 3D genome organization in development and cell differentiation
- (2019) Hui Zheng et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- CUT&Tag for efficient epigenomic profiling of small samples and single cells
- (2019) Hatice S. Kaya-Okur et al. Nature Communications
- RNA Interactions Are Essential for CTCF-Mediated Genome Organization
- (2019) Ricardo Saldaña-Meyer et al. MOLECULAR CELL
- Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation
- (2019) Nezha S. Benabdallah et al. MOLECULAR CELL
- BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells
- (2019) David N. Debruyne et al. NATURE
- Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion
- (2019) Ansuman T. Satpathy et al. NATURE BIOTECHNOLOGY
- A compendium of promoter-centered long-range chromatin interactions in the human genome
- (2019) Inkyung Jung et al. NATURE GENETICS
- NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements
- (2019) Shigeki Hirabayashi et al. NATURE GENETICS
- Transposable elements in human genetic disease
- (2019) Lindsay M. Payer et al. NATURE REVIEWS GENETICS
- Functional Enhancers Shape Extrachromosomal Oncogene Amplifications
- (2019) Andrew R. Morton et al. CELL
- CoBATCH for High-Throughput Single-Cell Epigenomic Profiling
- (2019) Qianhao Wang et al. MOLECULAR CELL
- Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs
- (2019) William A. Flavahan et al. NATURE
- Circular ecDNA promotes accessible chromatin and high oncogene expression
- (2019) Sihan Wu et al. NATURE
- Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia
- (2019) Jeffrey M. Granja et al. NATURE BIOTECHNOLOGY
- Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
- (2018) Sofia A. Quinodoz et al. CELL
- Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation
- (2018) Jason D. Buenrostro et al. CELL
- Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element
- (2018) Seung Woo Cho et al. CELL
- A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer
- (2018) David Y. Takeda et al. CELL
- PRC1 Fine-tunes Gene Repression and Activation to Safeguard Skin Development and Stem Cell Specification
- (2018) Idan Cohen et al. Cell Stem Cell
- A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans
- (2018) Pei-Fang Tsai et al. MOLECULAR CELL
- Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements
- (2018) Bo Gu et al. SCIENCE
- Coactivator condensation at super-enhancers links phase separation and gene control
- (2018) Benjamin R. Sabari et al. SCIENCE
- Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
- (2018) Jason C Bell et al. eLife
- Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids
- (2018) Anthony M. D'Ippolito et al. Cell Systems
- A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
- (2018) Darren A. Cusanovich et al. CELL
- Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies
- (2018) Briana Van Treeck et al. CELL
- Interchromosomal interactions: A genomic love story of kissing chromosomes
- (2018) Philipp G. Maass et al. JOURNAL OF CELL BIOLOGY
- Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments
- (2018) Jill J. Bouchard et al. MOLECULAR CELL
- Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies
- (2018) Carsten Bahr et al. NATURE
- Enhancer redundancy provides phenotypic robustness in mammalian development
- (2018) Marco Osterwalder et al. NATURE
- The cis-regulatory dynamics of embryonic development at single-cell resolution
- (2018) Darren A. Cusanovich et al. NATURE
- Joint profiling of chromatin accessibility and gene expression in thousands of single cells
- (2018) Junyue Cao et al. SCIENCE
- Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication
- (2018) Jiao Sima et al. CELL
- Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains
- (2018) Ann Boija et al. CELL
- Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
- (2018) Bogdan Bintu et al. SCIENCE
- Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator
- (2018) Jung Kim et al. Cell Reports
- CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression
- (2017) Gang Ren et al. MOLECULAR CELL
- Phase separation drives heterochromatin domain formation
- (2017) Amy R. Strom et al. NATURE
- Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity
- (2017) Kristen M. Turner et al. NATURE
- Complex multi-enhancer contacts captured by genome architecture mapping
- (2017) Robert A. Beagrie et al. NATURE
- Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin
- (2017) Adam G. Larson et al. NATURE
- GRID-seq reveals the global RNA–chromatin interactome
- (2017) Xiao Li et al. NATURE BIOTECHNOLOGY
- Copy number alterations unmasked as enhancer hijackers
- (2017) Rameen Beroukhim et al. NATURE GENETICS
- Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
- (2017) Adam J Rubin et al. NATURE GENETICS
- Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
- (2017) Maxwell R Mumbach et al. NATURE GENETICS
- An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
- (2017) M Ryan Corces 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
- Programmable DNA looping using engineered bivalent dCas9 complexes
- (2017) Nan Hao et al. Nature Communications
- Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping
- (2017) Stefanie L. Morgan et al. Nature Communications
- Polycomb repressive complex 1 modifies transcription of active genes
- (2017) Michelle Pherson et al. Science Advances
- Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
- (2016) Denes Hnisz et al. CELL
- Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
- (2016) Rongxin Fang et al. CELL RESEARCH
- Replication timing and transcriptional control: beyond cause and effect — part III
- (2016) Juan Carlos Rivera-Mulia et al. CURRENT OPINION IN CELL BIOLOGY
- High-throughput functional comparison of promoter and enhancer activities
- (2016) Thomas A. Nguyen et al. GENOME RESEARCH
- Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping
- (2016) Caroline R. Bartman et al. MOLECULAR CELL
- Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
- (2016) M Ryan Corces et al. NATURE GENETICS
- Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
- (2016) Vincent Loubiere et al. NATURE GENETICS
- 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
- Isolation of the protein and RNA content of active sites of transcription from mammalian cells
- (2016) Svitlana Melnik et al. Nature Protocols
- Enhancers as non-coding RNA transcription units: recent insights and future perspectives
- (2016) Wenbo Li et al. NATURE REVIEWS GENETICS
- Activation of proto-oncogenes by disruption of chromosome neighborhoods
- (2016) D. Hnisz et al. SCIENCE
- CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
- (2015) Zhonghui Tang et al. CELL
- Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms
- (2015) Lluis Morey et al. Cell Stem Cell
- Single-cell chromatin accessibility reveals principles of regulatory variation
- (2015) Jason D. Buenrostro et al. NATURE
- Insulator dysfunction and oncogene activation in IDH mutant gliomas
- (2015) William A. Flavahan et al. NATURE
- Multiplexed analysis of chromosome conformation at vastly improved sensitivity
- (2015) James O J Davies et al. NATURE METHODS
- 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
- Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
- (2015) Adrian L. Sanborn et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Transcription factor trapping by RNA in gene regulatory elements
- (2015) A. A. Sigova et al. SCIENCE
- Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
- (2015) Erik Arner et al. SCIENCE
- Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
- (2015) D. A. Cusanovich et al. SCIENCE
- Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping
- (2014) Wulan Deng et al. CELL
- A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia
- (2014) Stefan Gröschel et al. CELL
- Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
- (2014) Jill M. Dowen et al. CELL
- An atlas of active enhancers across human cell types and tissues
- (2014) Robin Andersson et al. NATURE
- Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
- (2014) Paul A. Northcott et al. NATURE
- Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment
- (2014) Jim R Hughes et al. NATURE GENETICS
- Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation
- (2014) C.-L. Hsieh et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci
- (2013) Kambiz Mousavi et al. MOLECULAR CELL
- Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
- (2013) Wenbo Li et al. NATURE
- Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
- (2013) Michael T. Y. Lam 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
- Expression of the cancer-testis antigen BORIS correlates with prostate cancer
- (2013) Zubair Cheema et al. PROSTATE
- Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
- (2013) C. D. Arnold et al. SCIENCE
- Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor
- (2012) Wulan Deng et al. CELL
- Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
- (2012) Guoliang Li et al. CELL
- Landscape of transcription in human cells
- (2012) Sarah Djebali et al. NATURE
- The accessible chromatin landscape of the human genome
- (2012) Robert E. Thurman et al. NATURE
- Hallmarks of Cancer: The Next Generation
- (2011) Douglas Hanahan et al. CELL
- BORIS Binding to the Promoters of Cancer Testis Antigens, MAGEA2, MAGEA3, and MAGEA4, Is Associated with Their Transcriptional Activation in Lung Cancer
- (2011) S. Bhan et al. CLINICAL CANCER RESEARCH
- Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
- (2010) T. Ryba et al. GENOME RESEARCH
- Phenotypic robustness conferred by apparently redundant transcriptional enhancers
- (2010) Nicolás Frankel et al. NATURE
- Widespread transcription at neuronal activity-regulated enhancers
- (2010) Tae-Kyung Kim et al. NATURE
- A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
- (2010) Francesca De Santa et al. PLOS BIOLOGY
- Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture
- (2010) Eitan Yaffe et al. PLoS Genetics
- A Model for all Genomes: The Role of Transcription Factories
- (2009) Peter R. Cook JOURNAL OF MOLECULAR BIOLOGY
- BORIS, a paralogue of the transcription factor, CTCF, is aberrantly expressed in breast tumours
- (2008) V D'Arcy et al. BRITISH JOURNAL OF CANCER
- Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules
- (2008) Q. Hu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More