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

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

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

Visualizing the genome in high resolution challenges our textbook understanding

(2020) Melike Lakadamyali et al.   NATURE METHODS

Advances in Chromatin Imaging at Kilobase-Scale Resolution

(2020) Alistair Boettiger et al.   TRENDS IN GENETICS

Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression

(2020) Hanae Sato et al.   Annual Review of Biochemistry

Chromosome organization by one-sided and two-sided loop extrusion

(2020) Edward J Banigan et al.   eLife

Cohesin and condensin extrude DNA loops in a cell-cycle dependent manner

(2020) Stefan Golfier et al.   eLife

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

(2020) Michiel J. Thiecke et al.   Cell Reports

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

Cell cycle– and genomic distance–dependent dynamics of a discrete chromosomal region

(2019) Hanhui Ma et al.   JOURNAL OF CELL BIOLOGY

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

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

(2019) Jeffrey M Alexander et al.   eLife

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells

(2019) Jieru Li et al.   CELL

Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions

(2019) Nimish Khanna et al.   Nature Communications

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

(2019) Laila El Khattabi et al.   CELL

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

(2019) Mustafa Mir et al.   DEVELOPMENT

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Chromatinopathies: A focus on Cornelia de Lange syndrome

(2019) Laura Avagliano et al.   CLINICAL GENETICS

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Dynamics of sister chromatid resolution during cell cycle progression

(2018) Rugile Stanyte et al.   JOURNAL OF CELL BIOLOGY

Fractal Folding and Medium Viscoelasticity Contribute Jointly to Chromosome Dynamics

(2018) K. E. Polovnikov et al.   PHYSICAL REVIEW LETTERS

The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes

(2018) Michele Gabriele et al.   PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy

(2018) Atsushi Matsuda et al.   Scientific Reports

Robust model-based analysis of single-particle tracking experiments with Spot-On

(2018) Anders S Hansen et al.   eLife

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Super-resolution microscopy demystified

(2018) Lothar Schermelleh et al.   NATURE CELL BIOLOGY

A general method to fine-tune fluorophores for live-cell and in vivo imaging

(2017) Jonathan B Grimm et al.   NATURE METHODS

The origin of Metazoa: a unicellular perspective

(2017) Arnau Sebé-Pedrós et al.   NATURE REVIEWS GENETICS

Multiplexed sgRNA Expression Allows Versatile Single Nonrepetitive DNA Labeling and Endogenous Gene Regulation

(2017) Shipeng Shao et al.   ACS Synthetic Biology

Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories

(2017) Assaf Amitai et al.   Cell Reports

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Recent evidence that TADs and chromatin loops are dynamic structures

(2017) Anders S. Hansen et al.   Nucleus

Recent evidence that TADs and chromatin loops are dynamic structures

(2017) Anders S. Hansen et al.   Nucleus

Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration

(2017) Ofir Shukron et al.   Scientific Reports

Enhancer deregulation in cancer and other diseases

(2016) Hans-Martin Herz   BIOESSAYS

Physical Modeling of Dynamic Coupling between Chromosomal Loci

(2016) Thomas J. Lampo et al.   BIOPHYSICAL JOURNAL

A quick guide to light microscopy in cell biology

(2016) Kurt Thorn   MOLECULAR BIOLOGY OF THE CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Objective comparison of particle tracking methods

(2014) Nicolas Chenouard et al.   NATURE METHODS

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA