Molecular basis and biological function of variability in spatial genome organization

LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice

(2019) Kevin Monahan et al.   NATURE

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

(2019) Leslie J. Mateo et al.   NATURE

Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

(2019) Elizabeth H. Finn et al.   CELL

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

(2019) Jeffrey M Alexander et al.   eLife

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

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

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

(2018) Won-Ki Cho et al.   SCIENCE

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Interphase human chromosome exhibits out of equilibrium glassy dynamics

(2018) Guang Shi et al.   Nature Communications

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

Frequent monoallelic or skewed expression for developmental genes in CNS-derived cells and evidence for balancing selection

(2018) Sergio Branciamore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Uniform gene expression in embryos is achieved by temporal averaging of transcription noise

(2017) L. Carine Stapel et al.   GENES & DEVELOPMENT

Genome organization in the nucleus: From dynamic measurements to a functional model

(2017) Anat Vivante et al.   METHODS

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic

(2017) A D Marshall et al.   ONCOGENE

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons

(2017) Kevin Monahan et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Transcription Dynamics in Living Cells

(2016) Tineke L. Lenstra et al.   Annual Review of Biophysics

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains

(2016) Guido Tiana et al.   BIOPHYSICAL JOURNAL

Droplet organelles?

(2016) Edward M Courchaine et al.   EMBO JOURNAL

Tissue-of-origin-specific gene repositioning in breast and prostate cancer

(2016) Karen J. Meaburn et al.   HISTOCHEMISTRY AND CELL BIOLOGY

What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism

(2016) Orsolya Symmons et al.   MOLECULAR CELL

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity

(2016) C. M. Torres et al.   SCIENCE

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

(2016) C.-K. Chen et al.   SCIENCE

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

(2014) Eirene Markenscoff-Papadimitriou et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT BIOLOGY

Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells

(2014) Pierre Therizols et al.   SCIENCE

Ultrastructural fingerprints of avian influenza A (H7N9) virus in infected human lung cells

(2014) Olivier Terrier et al.   VIROLOGY

Contribution of RNA polymerase concentration variation to protein expression noise

(2014) Sora Yang et al.   Nature Communications

Heterochromatin-Mediated Gene Silencing Facilitates the Diversification of Olfactory Neurons

(2014) David B. Lyons et al.   Cell Reports

Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity

(2013) Shawn C. Little et al.   CELL

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Spatial Dynamics of Chromosome Translocations in Living Cells

(2013) V. Roukos et al.   SCIENCE

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

(2012) E. Josephine Clowney et al.   CELL

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

(2012) Jacob Stewart-Ornstein et al.   MOLECULAR CELL

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loop domain organization of the p53 locus in normal and breast cancer cells correlates with the transcriptional status of the TP53 and the neighboring genes

(2011) Andrea C.S. Goes et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Single-allele analysis of transcription kinetics in living mammalian cells

(2010) Sharon Yunger et al.   NATURE METHODS

The three-dimensional architecture of Hox cluster silencing

(2010) Maria A. Ferraiuolo et al.   NUCLEIC ACIDS RESEARCH

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Visualization of Individual Scr mRNAs during Drosophila Embryogenesis Yields Evidence for Transcriptional Bursting

(2009) Adam Paré et al.   CURRENT BIOLOGY

Nonallelic transvection of multiple imprinted loci is organized by theH19imprinting control region during germline development

(2009) Kuljeet Singh Sandhu et al.   GENES & DEVELOPMENT

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Probing the Dynamic Organization of Transcription Compartments and Gene Loci within the Nucleus of Living Cells

(2008) Deepak Kumar Sinha et al.   BIOPHYSICAL JOURNAL

Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression

(2008) Effie Apostolou et al.   CELL

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE