Nuclear organization of RNA polymerase II transcription

The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture

(2012) Yolanda Markaki et al.   BIOESSAYS

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

(2012) Chih-yu Chen et al.   BMC GENOMICS

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

(2012) Yu Zhang et al.   CELL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs

(2012) Emily Brookes et al.   Cell Stem Cell

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation

(2012) T. Muramoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF, cohesin, and histone variants: connecting the genome

(2011) Jean-François Millau et al.   Biochemistry and Cell Biology

Discovering genome regulation with 3C and 3C-related technologies

(2011) Sylvain D. Ethier et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

(2011) Mathieu Rousseau et al.   BMC BIOINFORMATICS

Live-Cell Chromosome Dynamics and Outcome of X Chromosome Pairing Events during ES Cell Differentiation

(2011) Osamu Masui et al.   CELL

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

(2011) Shelagh Boyle et al.   CHROMOSOME RESEARCH

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA

(2011) E. Splinter et al.   GENES & DEVELOPMENT

Ultrastructural study of transcription factories in mouse erythroblasts

(2011) C. H. Eskiw et al.   JOURNAL OF CELL SCIENCE

Proteomic Analysis of Mitotic RNA Polymerase II Reveals Novel Interactors and Association With Proteins Dysfunctional in Disease

(2011) André Möller et al.   MOLECULAR & CELLULAR PROTEOMICS

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

A transgenic mouse for in vivo detection of endogenous labeled mRNA

(2011) Timothée Lionnet et al.   NATURE METHODS

The proteomes of transcription factories containing RNA polymerases I, II or III

(2011) Svitlana Melnik et al.   NATURE METHODS

Innate Structure of DNA Foci Restricts the Mixing of DNA from Different Chromosome Territories

(2011) Pedro Olivares-Chauvet et al.   PLoS One

Genome organization in and around the nucleolus

(2011) Attila Németh et al.   TRENDS IN GENETICS

A Dynamical Model Reveals Gene Co-Localizations in Nucleus

(2011) Jing Kang et al.   PLoS Computational Biology

Bursts and pulses: insights from single cell studies into transcriptional mechanisms

(2010) Jonathan R Chubb et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The three-dimensional architecture of Hox cluster silencing

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

Stable Morphology, but Dynamic Internal Reorganisation, of Interphase Human Chromosomes in Living Cells

(2010) Iris Müller et al.   PLoS One

Cell type specificity of chromatin organization mediated by CTCF and cohesin

(2010) Chunhui Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

Active RNA Polymerases: Mobile or Immobile Molecular Machines?

(2010) Argyris Papantonis et al.   PLOS BIOLOGY

Poised Transcription Factories Prime Silent uPA Gene Prior to Activation

(2010) Carmelo Ferrai et al.   PLOS BIOLOGY

Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts

(2010) Ishita S Mehta et al.   GENOME BIOLOGY

A Model for all Genomes: The Role of Transcription Factories

(2009) Peter R. Cook   JOURNAL OF MOLECULAR BIOLOGY

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

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

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

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

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

Transcription factories are nuclear subcompartments that remain in the absence of transcription

(2008) J. A. Mitchell et al.   GENES & DEVELOPMENT

RNA polymerase II activity is located on the surface of protein-rich transcription factories

(2008) C. H. Eskiw et al.   JOURNAL OF CELL SCIENCE

Transcriptional heterogeneity in mouse embryonic stem cells

(2008) Tetsuya S. Tanaka   REPRODUCTION FERTILITY AND DEVELOPMENT