Functional implications of genome topology

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

(2012) Joseph M. Zullo et al.   CELL

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

(2012) Yu Zhang et al.   CELL

Step-Wise Methylation of Histone H3K9 Positions Heterochromatin at the Nuclear Periphery

(2012) Benjamin D. Towbin et al.   CELL

SnapShot: Chromosome Conformation Capture

(2012) Ofir Hakim et al.   CELL

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

(2012) Wulan Deng 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

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

(2012) E. Josephine Clowney et al.   CELL

Mapping of lamin A- and progerin-interacting genome regions

(2012) Nard Kubben et al.   CHROMOSOMA

A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

(2012) Hua Wong et al.   CURRENT BIOLOGY

DNA damage, chromatin, and transcription: the trinity of aging

(2012) Rebecca C Burgess et al.   CURRENT OPINION IN CELL BIOLOGY

Insulators, long-range interactions, and genome function

(2012) Jingping Yang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Nature and function of insulator protein binding sites in the Drosophila genome

(2012) Y. B. Schwartz et al.   GENOME RESEARCH

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

(2012) H. Tjong et al.   GENOME RESEARCH

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

(2012) K. Van Bortle et al.   GENOME RESEARCH

Genome-scale identification of active DNA replication origins

(2012) Christelle Cayrou et al.   METHODS

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman 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

Increased chromosome mobility facilitates homology search during recombination

(2012) Judith Miné-Hattab et al.   NATURE CELL BIOLOGY

Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery

(2012) Vincent Dion et al.   NATURE CELL BIOLOGY

3D chromatin conformation correlates with replication timing and is conserved in resting cells

(2012) Benoit Moindrot et al.   NUCLEIC ACIDS RESEARCH

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding

(2012) S.-i. Takebayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

Concise Review: Chromatin and Genome Organization in Reprogramming

(2012) Alva Biran et al.   STEM CELLS

The great unravelling: chromatin as a modulator of the aging process

(2012) Roderick J. O'Sullivan et al.   TRENDS IN BIOCHEMICAL SCIENCES

Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion

(2012) Thierry Cheutin et al.   PLoS Genetics

Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair

(2011) Irene Chiolo et al.   CELL

Translocation-Capture Sequencing Reveals the Extent and Nature of Chromosomal Rearrangements in B Lymphocytes

(2011) Isaac A. Klein et al.   CELL

Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

(2011) Roberto Chiarle et al.   CELL

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

(2011) Osamu Masui et al.   CELL

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

Throwing transcription for a loop: expression of the genome in the 3D nucleus

(2011) Chunhui Hou et al.   CHROMOSOMA

Gene positioning and expression

(2011) Defne Egecioglu et al.   CURRENT OPINION IN CELL BIOLOGY

Constitutive heterochromatin reorganization during somatic cell reprogramming

(2011) Eden Fussner et al.   EMBO JOURNAL

Polycomb eviction as a new distant enhancer function

(2011) D. Vernimmen et al.   GENES & DEVELOPMENT

Transcriptional repression and DNA looping associated with a novel regulatory element in the final exon of the lymphotoxin-β gene

(2011) K Wicks et al.   GENES AND IMMUNITY

On emerging nuclear order

(2011) Indika Rajapakse et al.   JOURNAL OF CELL BIOLOGY

Principles of chromosomal organization: lessons from yeast

(2011) Christophe Zimmer et al.   JOURNAL OF CELL BIOLOGY

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

(2011) Lena Ho et al.   NATURE CELL BIOLOGY

Variegated gene expression caused by cell-specific long-range DNA interactions

(2011) Daan Noordermeer et al.   NATURE CELL BIOLOGY

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Noncoding RNAs and enhancers: complications of a long-distance relationship

(2011) Ulf Andersson Ørom et al.   TRENDS IN GENETICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Genome–nuclear lamina interactions and gene regulation

(2010) Jop Kind et al.   CURRENT OPINION IN CELL BIOLOGY

The spatial dynamics of tissue-specific promoters during C. elegans development

(2010) P. Meister et al.   GENES & DEVELOPMENT

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping

(2010) P.-Y. Hsu et al.   GENOME RESEARCH

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

Cell fate transitions and the replication timing decision point: Figure 1.

(2010) David M. Gilbert   JOURNAL OF CELL BIOLOGY

Elevated Histone Expression Promotes Life Span Extension

(2010) Jason Feser et al.   MOLECULAR CELL

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Genomics tools for unraveling chromosome architecture

(2010) Bas van Steensel et al.   NATURE BIOTECHNOLOGY

Eukaryotic DNA replication origins: many choices for appropriate answers

(2010) Marcel Méchali   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres

(2010) Roderick J O'Sullivan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Biogenesis of Nuclear Bodies

(2010) M. Dundr et al.   Cold Spring Harbor Perspectives in Biology

Alternative Epigenetic Chromatin States of Polycomb Target Genes

(2010) Yuri B. Schwartz et al.   PLoS Genetics

Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer

(2009) Chunru Lin et al.   CELL

Replication timing and transcriptional control: beyond cause and effect—part II

(2009) Ichiro Hiratani et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome

(2009) M. Schwaiger et al.   GENES & DEVELOPMENT

Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex

(2009) Sue Mei Tan-Wong et al.   GENES & DEVELOPMENT

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

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

Disease-specific gene repositioning in breast cancer

(2009) Karen J. Meaburn et al.   JOURNAL OF CELL BIOLOGY

Ageing-related chromatin defects through loss of the NURD complex

(2009) Gianluca Pegoraro et al.   NATURE CELL BIOLOGY

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

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology

(2009) Marieke Simonis et al.   NATURE METHODS

Gene deregulation and spatial genome reorganization near breakpoints prior to formation of translocations in anaplastic large cell lymphoma

(2009) S. Mathas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G9a selectively represses a class of late-replicating genes at the nuclear periphery

(2009) T. Yokochi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SIRT1 Redistribution on Chromatin Promotes Genomic Stability but Alters Gene Expression during Aging

(2008) Philipp Oberdoerffer et al.   CELL

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

(2008) Effie Apostolou et al.   CELL

Global Transcription in Pluripotent Embryonic Stem Cells

(2008) Sol Efroni et al.   Cell Stem Cell

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations

(2008) V. K. Tiwari et al.   GENOME RESEARCH

A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence

(2008) R. Ileng Kumaran et al.   JOURNAL OF CELL BIOLOGY

Chromatin position in human HepG2 cells: Although being non-random, significantly changed in daughter cells

(2008) Zuzana Cvačková et al.   JOURNAL OF STRUCTURAL BIOLOGY

ATM Signaling Facilitates Repair of DNA Double-Strand Breaks Associated with Heterochromatin

(2008) Aaron A. Goodarzi et al.   MOLECULAR CELL

Progesterone-Dependent Deoxyribonucleic Acid Looping between RUSH/SMARCA3 and Egr-1 Mediates Repression by c-Rel

(2008) Aveline Hewetson et al.   MOLECULAR ENDOCRINOLOGY

HP1-β mobilization promotes chromatin changes that initiate the DNA damage response

(2008) Nabieh Ayoub et al.   NATURE

Role for perinuclear chromosome tethering in maintenance of genome stability

(2008) Karim Mekhail et al.   NATURE

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos

(2008) Mareike Puschendorf et al.   NATURE GENETICS

Genome-wide studies highlight indirect links between human replication origins and gene regulation

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

Dynamic interactions between the promoter and terminator regions of the mammalianBRCA1gene

(2008) Sue Mei Tan-Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY

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

(2008) Vijay K Tiwari et al.   PLOS BIOLOGY

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics