3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome

HP1 maintains protein stability of H3K9 methyltransferases and demethylases

(2022) Ryo Maeda et al.   EMBO REPORTS

A Mediator-cohesin axis controls heterochromatin domain formation

(2022) Judith H. I. Haarhuis et al.   Nature Communications

H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats

(2022) Francesco Gualdrini et al.   GENES & DEVELOPMENT

Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression

(2022) William Garland et al.   MOLECULAR CELL

Heterochromatic repeat clustering imposes a physical barrier on homologous recombination to prevent chromosomal translocations

(2022) Ioanna Mitrentsi et al.   MOLECULAR CELL

Histone post-translational modifications — cause and consequence of genome function

(2022) Gonzalo Millán-Zambrano et al.   NATURE REVIEWS GENETICS

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

(2022) Savannah J. Hoyt et al.   SCIENCE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains

(2022) Cristiana Bersaglieri et al.   Nature Communications

Cohesin-mediated loop anchors confine the locations of human replication origins

(2022) Daniel J. Emerson et al.   NATURE

TFs for TEs: the transcription factor repertoire of mammalian transposable elements

(2021) Clara Hermant et al.   GENES & DEVELOPMENT

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Sequence, Chromatin and Evolution of Satellite DNA

(2021) Jitendra Thakur et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

HP1 drives de novo 3D genome reorganization in early Drosophila embryos

(2021) Fides Zenk et al.   NATURE

Genome folding through loop extrusion by SMC complexes

(2021) Iain F. Davidson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes

(2021) Yuanlong Liu et al.   Nature Communications

Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats

(2021) Meredith M. Course et al.   GENOME RESEARCH

Communication between chromatin and homologous recombination

(2021) Priyanka Verma et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

(2020) Vasavi Sundaram et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Telomeric Chromatin and TERRA

(2020) Amandine Barral et al.   JOURNAL OF MOLECULAR BIOLOGY

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

(2020) Jonathan A. Beagan et al.   NATURE NEUROSCIENCE

Histone H3K9 methylation promotes formation of genome compartments inCaenorhabditis elegansvia chromosome compaction and perinuclear anchoring

(2020) Qian Bian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes

(2020) Adam G. Diehl et al.   Nature Communications

Evolution of a Human-Specific Tandem Repeat Associated with ALS

(2020) Meredith M. Course et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Loop extrusion: theory meets single-molecule experiments

(2020) Edward J. Banigan et al.   CURRENT OPINION IN CELL BIOLOGY

Histone methyltransferase activity programs nuclear peripheral genome positioning

(2020) Kelvin See et al.   DEVELOPMENTAL BIOLOGY

Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview

(2020) Franziska K. Geis et al.   Viruses-Basel

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

The nucleolus as a multiphase liquid condensate

(2020) Denis L. J. Lafontaine et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification

(2019) Dario Nicetto et al.   SCIENCE

Telomeres and telomerase: three decades of progress

(2019) Jerry W. Shay et al.   NATURE REVIEWS GENETICS

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

(2019) Leslie J. Mateo et al.   NATURE

Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development

(2019) Bo Fu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs

(2019) Christ Leemans et al.   CELL

PRC2 is high maintenance

(2019) Jia-Ray Yu et al.   GENES & DEVELOPMENT

Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin

(2019) Anastassiia Vertii et al.   GENOME RESEARCH

LADL: light-activated dynamic looping for endogenous gene expression control

(2019) Ji Hun Kim et al.   NATURE METHODS

The nucleolus functions as a phase-separated protein quality control compartment

(2019) F. Frottin et al.   SCIENCE

The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse

(2019) Lucas J.T. Kaaij et al.   CELL

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Positioning Heterochromatin at the Nuclear Periphery Suppresses Histone Turnover to Promote Epigenetic Inheritance

(2019) Sahana Holla et al.   CELL

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

(2018) Chenfei Wang et al.   NATURE CELL BIOLOGY

Detecting hierarchical genome folding with network modularity

(2018) Heidi K Norton et al.   NATURE METHODS

Tandem repeats mediating genetic plasticity in health and disease

(2018) Anthony J. Hannan   NATURE REVIEWS GENETICS

Shelterin-Mediated Telomere Protection

(2018) Titia de Lange   Annual Review of Genetics

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

(2018) James H. Sun et al.   CELL

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Nuclear F-actin and myosins drive relocalization of heterochromatic breaks

(2018) Christopher P. Caridi et al.   NATURE

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

Alu insertion variants alter mRNA splicing

(2018) Lindsay M Payer et al.   NUCLEIC ACIDS RESEARCH

Bottom–up modeling of chromatin segregation due to epigenetic modifications

(2018) Quinn MacPherson 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

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

Crossed wires: 3D genome misfolding in human disease

(2017) Heidi K. Norton et al.   JOURNAL OF CELL BIOLOGY

Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance

(2017) Satoshi Ishiyama et al.   MOLECULAR CELL

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes

(2017) Justin S. Becker et al.   MOLECULAR CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

(2017) Oscar Velazquez Camacho et al.   eLife

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin

(2017) Whitney L Johnson et al.   eLife

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming

(2016) Jonathan A. Beagan et al.   Cell Stem Cell

Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues

(2016) Gabriela Ecco et al.   DEVELOPMENTAL CELL

Rapid movement and transcriptional re‐localization of human cohesin on DNA

(2016) Iain F Davidson et al.   EMBO JOURNAL

Temporal and Spatial Uncoupling of DNA Double Strand Break Repair Pathways within Mammalian Heterochromatin

(2016) Katerina Tsouroula et al.   MOLECULAR CELL

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

(2016) Justin S. Becker et al.   TRENDS IN GENETICS

Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

(2016) Jian Fang et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Restricting retrotransposons: a review

(2016) John L. Goodier   Mobile DNA

Roles for retrotransposon insertions in human disease

(2016) Dustin C. Hancks et al.   Mobile DNA

Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells

(2015) M. Amendola et al.   EMBO REPORTS

Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins

(2015) Jennifer C. Harr et al.   JOURNAL OF CELL BIOLOGY

Abundant contribution of short tandem repeats to gene expression variation in humans

(2015) Melissa Gymrek et al.   NATURE GENETICS

The molecular basis for centromere identity and function

(2015) Kara L. McKinley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Control of telomerase action at human telomeres

(2015) Dirk Hockemeyer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells

(2015) I. A. Tchasovnikarova et al.   SCIENCE

Germline and Pluripotent Stem Cells

(2015) Wolf Reik et al.   Cold Spring Harbor Perspectives in Biology

Constitutive heterochromatin formation and transcription in mammals

(2015) Nehmé Saksouk et al.   Epigenetics & Chromatin

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

(2015) Dhaval Varshney et al.   Nature Communications

Control of telomerase action at human telomeres

(2015) Dirk Hockemeyer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2014) Suhas S.P. Rao et al.   CELL

Unraveling architecture of the pluripotent genome

(2014) Jennifer E Phillips-Cremins   CURRENT OPINION IN CELL BIOLOGY

Setdb1is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

(2014) Sheng Liu et al.   GENES & DEVELOPMENT

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation

(2013) Irina Solovei et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

β-Globin cis-elements determine differential nuclear targeting through epigenetic modifications

(2013) Qian Bian et al.   JOURNAL OF CELL BIOLOGY

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

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

(2012) Dominic Schmidt et al.   CELL

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

(2012) Benjamin D. Towbin et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

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

(2012) Tom Sexton et al.   CELL

Human Transposon Tectonics

(2012) Kathleen H. Burns et al.   CELL

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

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

Molecular mechanisms and potential functions of histone demethylases

(2012) Susanne Marije Kooistra et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation

(2012) Scott B Rothbart et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The SRA protein UHRF1 promotes epigenetic crosstalks and is involved in prostate cancer progression

(2012) F Babbio et al.   ONCOGENE

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

(2012) Julia Arand et al.   PLoS Genetics

LINE-1 Elements in Structural Variation and Disease

(2011) Christine R. Beck et al.   Annual Review of Genomics and Human Genetics

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

(2011) Irene Chiolo et al.   CELL

An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

(2011) Angeliki Magklara et al.   CELL

SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin

(2011) Christèle Maison et al.   NATURE GENETICS

The distribution of repressive histone modifications on silenced FMR1 alleles provides clues to the mechanism of gene silencing in fragile X syndrome

(2010) D. Kumari et al.   HUMAN MOLECULAR GENETICS

High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

(2010) Silvana van Koningsbruggen et al.   MOLECULAR BIOLOGY OF THE CELL

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres

(2009) Zhong Deng et al.   MOLECULAR CELL

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

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

Instability and chromatin structure of expanded trinucleotide repeats

(2009) Vincent Dion et al.   TRENDS IN GENETICS

Active Alu retrotransposons in the human genome

(2008) E. A. Bennett et al.   GENOME RESEARCH

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

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

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