Enhancers dysfunction in the 3D genome of cancer cells

Recent progress and challenges in single-cell imaging of enhancer–promoter interaction

(2023) Liang-Fu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

When 3D genome changes cause disease: the impact of structural variations in congenital disease and cancer

(2023) Joachim Weischenfeldt et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

(2023) Christopher M. Uyehara et al.   Cell Reports

Computational methods for analysing multiscale 3D genome organization

(2023) Yang Zhang et al.   NATURE REVIEWS GENETICS

Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer

(2023) Kyukwang Kim et al.   Cell Reports

Three‐dimensional genome structure and function

(2023) Hao Liu et al.   MedComm

Somatic structural variant formation is guided by and influences genome architecture

(2022) Nikos Sidiropoulos et al.   GENOME RESEARCH

Structural Variation in Cancer: Role, Prevalence, and Mechanisms

(2022) Marco Raffaele Cosenza et al.   Annual Review of Genomics and Human Genetics

Dangerous RNA links pave the way to glioblastoma

(2022) Magda Bienko   MOLECULAR CELL

Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

(2022) Michele Gabriele et al.   SCIENCE

High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation

(2022) Daniel Rico et al.   GENOME RESEARCH

Coming full circle: On the origin and evolution of the looping model for enhancer–promoter communication

(2022) Tessa M. Popay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The era of 3D and spatial genomics

(2022) Britta A.M. Bouwman et al.   TRENDS IN GENETICS

Subtype-specific 3D genome alteration in acute myeloid leukaemia

(2022) Jie Xu et al.   NATURE

Structural variants drive context-dependent oncogene activation in cancer

(2022) Zhichao Xu et al.   NATURE

Cohesin and CTCF control the dynamics of chromosome folding

(2022) Pia Mach et al.   NATURE GENETICS

Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ

(2021) Giulia Della Chiara et al.   Nature Communications

High-resolution Hi-C maps highlight multiscale 3D epigenome reprogramming during pancreatic cancer metastasis

(2021) Bo Ren et al.   Journal of Hematology & Oncology

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

(2021) Xiaotao Wang et al.   NATURE METHODS

Global in situ profiling of RNA-RNA spatial interactions with RIC-seq

(2021) Changchang Cao et al.   Nature Protocols

3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia

(2021) Lu Yang et al.   Nature Communications

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

(2021) Rebeca San Martin et al.   JOURNAL OF CELL BIOLOGY

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Radial Organization in the Mammalian Nucleus

(2020) Nicola Crosetto et al.   Frontiers in Genetics

Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia

(2020) Andreas Kloetgen et al.   NATURE GENETICS

Three-dimensional chromatin in disease: What holds us together and what drives us apart?

(2020) Daniel M. Ibrahim et al.   CURRENT OPINION IN CELL BIOLOGY

Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging

(2020) Hugo B. Brandão et al.   CURRENT OPINION IN CELL BIOLOGY

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma

(2019) Wen Fong Ooi et al.   GUT

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

(2019) Priscillia Lhoumaud et al.   Nature Communications

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

(2018) Yu Amanda Guo et al.   Nature Communications

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

(2016) Pratiti Bandopadhayay et al.   NATURE GENETICS

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

(2015) Darío G. Lupiáñez et al.   CELL

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott 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

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

Chromosome Territories

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

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

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