Communication of genome regulatory elements in a folded chromosome

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

Long distance relationships: Enhancer–promoter communication and dynamic gene transcription

(2012) Judith Marsman et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2012) Wulan Deng et al.   CELL

Nuclear architecture by RNA

(2012) Maïwen Caudron-Herger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin organization — The 30nm fiber

(2012) Sergei A. Grigoryev et al.   EXPERIMENTAL CELL RESEARCH

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Relationship between DNA replication and the nuclear matrix

(2012) Rosemary H. C. Wilson et al.   GENES TO CELLS

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

Genome-wide Studies of CCCTC-binding Factor (CTCF) and Cohesin Provide Insight into Chromatin Structure and Regulation: FIGURE 1.

(2012) Bum-Kyu Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Super-resolution imaging reveals three-dimensional folding dynamics of the  -globin locus upon gene activation

(2012) M. P. C. van de Corput et al.   JOURNAL OF CELL SCIENCE

Chromatin dynamics in living cells: Identification of oscillatory motion

(2012) Artem Pliss et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

(2012) Natalia Naumova et al.   METHODS

Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation

(2012) Rui Xiao et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

(2012) Xun Lan et al.   NUCLEIC ACIDS RESEARCH

The Role of Nuclear Matrix Proteins Binding to Matrix Attachment Regions (MARs) in Prostate Cancer Cell Differentiation

(2012) Paola Barboro et al.   PLoS One

CTCF/cohesin-mediated DNA looping is required for protocadherin   promoter choice

(2012) Y. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleolar disruption leads to the spatial separation of key 18S rRNA processing factors

(2012) Amy Jane Turner et al.   RNA Biology

Enhancers and silencers: an integrated and simple model for their function

(2012) Petros Kolovos et al.   Epigenetics & Chromatin

Chromatin loops, gene positioning, and gene expression

(2012) Sjoerd Holwerda et al.   Frontiers in Genetics

The CTCF insulator protein forms an unusual DNA structure

(2011) Melissa J MacPherson et al.   BMC MOLECULAR BIOLOGY

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

SAF-A Has a Role in Transcriptional Regulation of Oct4 in ES Cells Through Promoter Binding

(2011) Dzeneta Vizlin-Hodzic et al.   Cellular Reprogramming

Human telomeric G-quadruplexes undergo dynamic conversion in a molecular crowding environment

(2011) Liang Xu et al.   CHEMICAL COMMUNICATIONS

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Chromatin higher-order structures and gene regulation

(2011) Guohong Li et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A view of nuclear Polycomb bodies

(2011) Vincenzo Pirrotta et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Human tRNA genes function as chromatin insulators

(2011) Jesse R Raab et al.   EMBO JOURNAL

Architectural roles of long noncoding RNAs in the intranuclear formation of functional paraspeckles

(2011) Tetsuya Kawaguchi   Frontiers in Bioscience-Landmark

Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene

(2011) Elena N. Markova et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Structure of Human Telomeric DNA in Crowded Solution

(2011) Brahim Heddi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Direct Interactions of OCA-B and TFII-I Regulate Immunoglobulin Heavy-Chain Gene Transcription by Facilitating Enhancer-Promoter Communication

(2011) Xiaodi Ren et al.   MOLECULAR CELL

The nucleoskeleton as a genome-associated dynamic 'network of networks'

(2011) Dan N. Simon et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription factories in the context of the nuclear and genome organization

(2011) S. V. Razin et al.   NUCLEIC ACIDS RESEARCH

The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3′-UTR

(2011) Feiran Gong et al.   NUCLEIC ACIDS RESEARCH

SAF-A Forms a Complex with BRG1 and Both Components Are Required for RNA Polymerase II Mediated Transcription

(2011) Dzeneta Vizlin-Hodzic et al.   PLoS One

A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber

(2011) I. Comet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting the function of nuclear scaffold/matrix binding proteins in X chromosome inactivation

(2011) Yuko Hasegawa et al.   RNA Biology

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

HMGB proteins: Interactions with DNA and chromatin

(2010) Michal Štros   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin

(2010) Rolf Ohlsson et al.   CHROMOSOMA

The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

Gamma Interferon-Dependent Transcriptional Memory via Relocalization of a Gene Locus to PML Nuclear Bodies

(2010) M. Gialitakis et al.   MOLECULAR AND CELLULAR BIOLOGY

Insulators, Not Polycomb Response Elements, Are Required for Long-Range Interactions between Polycomb Targets in Drosophila melanogaster

(2010) H.-B. Li et al.   MOLECULAR AND CELLULAR BIOLOGY

A mini review of MAR-binding proteins

(2010) Tian-Yun Wang et al.   MOLECULAR BIOLOGY REPORTS

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide

(2010) Marco Botta et al.   Molecular Systems Biology

Insulators and promoters: closer than we think

(2010) Jesse R. Raab et al.   NATURE REVIEWS GENETICS

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The three-dimensional architecture of Hox cluster silencing

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

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

NuMA after 30 years: the matrix revisited

(2010) Andreea E. Radulescu et al.   TRENDS IN CELL BIOLOGY

Chromosome Territories

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

Active RNA Polymerases: Mobile or Immobile Molecular Machines?

(2010) Argyris Papantonis et al.   PLOS BIOLOGY

Interactions between the nuclear matrix and an enhancer of the tryptophan oxygenase gene

(2009) Hidenori Kaneoka et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Does CTCF mediate between nuclear organization and gene expression?

(2009) Rolf Ohlsson et al.   BIOESSAYS

Chromosome looping at the human  -globin locus is mediated via the major upstream regulatory element (HS -40)

(2009) D. Vernimmen et al.   BLOOD

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

CCCTC-binding factor: to loop or to bridge

(2009) J. Zlatanova et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Entropic organization of interphase chromosomes

(2009) Peter R. Cook et al.   JOURNAL OF CELL BIOLOGY

A Model for all Genomes: The Role of Transcription Factories

(2009) Peter R. Cook   JOURNAL OF MOLECULAR BIOLOGY

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

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

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Transcription factories: gene expression in unions?

(2009) Heidi Sutherland et al.   NATURE REVIEWS GENETICS

TMEM8 – a non-globin gene entrapped in the globin web

(2009) Elena S. Philonenko et al.   NUCLEIC ACIDS RESEARCH

Inter-MAR Association Contributes to Transcriptionally Active Looping Events in Human β-globin Gene Cluster

(2009) Li Wang et al.   PLoS One

Transcription factors mediate long-range enhancer-promoter interactions

(2009) I. K. Nolis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

EZH2-dependent chromatin looping controls INK4a and INK4b, but not ARF, during human progenitor cell differentiation and cellular senescence

(2009) Sima Kheradmand Kia et al.   Epigenetics & Chromatin

Transcription factories

(2008) David R.F. Carter et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Macromolecular crowding and its potential impact on nuclear function

(2008) Karsten Richter et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Self-association of polynucleosome chains by macromolecular crowding

(2008) Ronald Hancock   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Proteomic analysis of the nuclear matrix in the early stages of rat liver carcinogenesis: Identification of differentially expressed and MAR-binding proteins

(2008) Paola Barboro et al.   EXPERIMENTAL CELL RESEARCH

Joining the loops: β-Globin gene regulation

(2008) Daan Noordermeer et al.   IUBMB LIFE

Similar active genes cluster in specialized transcription factories

(2008) Meng Xu et al.   JOURNAL OF CELL BIOLOGY

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

Spatial configuration of the chicken α-globin gene domain: immature and active chromatin hubs

(2008) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

(2008) Vijay K Tiwari et al.   PLOS BIOLOGY