Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency

Cohesin Removal Reprograms Gene Expression upon Mitotic Entry

(2020) Carlos Perea-Resa et al.   MOLECULAR CELL

On the existence and functionality of topologically associating domains

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

Polycomb regulation is coupled to cell cycle transition in pluripotent stem cells

(2020) Helena G. Asenjo et al.   Science Advances

Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment

(2020) Celeste D. Rosencrance et al.   MOLECULAR CELL

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

(2020) Marco Di Stefano et al.   Nature Communications

Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation

(2020) Hyeseon Kang et al.   GENES & DEVELOPMENT

Alteration of genome folding via contact domain boundary insertion

(2020) Di Zhang et al.   NATURE GENETICS

Transcription factor activity and nucleosome organization in mitosis

(2019) Nicola Festuccia et al.   GENOME RESEARCH

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

(2019) Marlies E. Oomen et al.   GENOME RESEARCH

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription

(2019) Vivek Behera et al.   Cell Reports

The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming

(2019) Georgina Peñalosa-Ruiz et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D

(2019) Michael I. Robson et al.   MOLECULAR CELL

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

(2019) Ji Hun Kim et al.   NATURE METHODS

Mitotic Chromosome Mechanics: How Cells Segregate Their Genome

(2019) Paul Batty et al.   TRENDS IN CELL BIOLOGY

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks

(2019) Dafne Campigli Di Giammartino et al.   NATURE CELL BIOLOGY

CRISPR-mediated live imaging of genome editing and transcription

(2019) Haifeng Wang et al.   SCIENCE

The multiscale effects of polycomb mechanisms on 3D chromatin folding

(2019) Thierry Cheutin et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Reprogramming: identifying the mechanisms that safeguard cell identity

(2019) Justin Brumbaugh et al.   DEVELOPMENT

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

Modes of phase separation affecting chromatin regulation

(2019) Spiros Palikyras et al.   Open Biology

CTCF confers local nucleosome resiliency after DNA replication and during mitosis

(2019) Nick Owens et al.   eLife

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Cellular trajectories and molecular mechanisms of iPSC reprogramming

(2018) Effie Apostolou et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C

(2018) Philipp G. Maass et al.   MOLECULAR CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Shasha Chong et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

(2018) Clara Lopes Novo et al.   Cell Reports

A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes

(2018) Sheila S Teves et al.   eLife

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

(2018) Jose Luis Sardina et al.   Cell Stem Cell

Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns

(2018) Elisheva Javasky et al.   GENOME RESEARCH

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

(2018) Roubina Tatavosian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods

(2018) Fei Sun et al.   MOLECULAR CELL

A changing paradigm of transcriptional memory propagation through mitosis

(2018) Katherine C. Palozola et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

New Insights into Genome Structure: Genes of a Feather Stick Together

(2017) Denes Hnisz et al.   MOLECULAR CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

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

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells

(2017) Jin Xu et al.   NATURE GENETICS

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map

(2017) Kyle P. Eagen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Mitotic transcription and waves of gene reactivation during mitotic exit

(2017) Katherine C. Palozola et al.   SCIENCE

Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells

(2017) Yiyuan Liu et al.   Cell Reports

Quantitative Cell Cycle Analysis Based on an Endogenous All-in-One Reporter for Cell Tracking and Classification

(2017) Thomas Zerjatke et al.   Cell Reports

Mitotic phosphorylation of CCCTC-binding factor (CTCF) reduces its DNA binding activity

(2017) Takeshi Sekiya et al.   FEBS Open Bio

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

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

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

(2016) Peter Hugo Lodewijk Krijger et al.   Cell Stem Cell

Cycling through developmental decisions: how cell cycle dynamics control pluripotency, differentiation and reprogramming

(2016) Abdenour Soufi et al.   DEVELOPMENT

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

(2016) Cédric Deluz et al.   GENES & DEVELOPMENT

A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

(2016) Chris C.-S. Hsiung et al.   GENES & DEVELOPMENT

Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D

(2016) Siim Pauklin et al.   GENES & DEVELOPMENT

Bromodomain 4: a cellular Swiss army knife

(2016) Ballachanda N. Devaiah et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

(2016) Nicola Festuccia et al.   NATURE CELL BIOLOGY

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Concise Review: Control of Cell Fate Through Cell Cycle and Pluripotency Networks

(2016) Ben Boward et al.   STEM CELLS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Chromosomes Progress to Metaphase in Multiple Discrete Steps via Global Compaction/Expansion Cycles

(2015) Zhangyi Liang et al.   CELL

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency

(2015) Onkar Joshi et al.   Cell Stem Cell

Chromatin remodeling and bivalent histone modifications in embryonic stem cells

(2015) A. Harikumar et al.   EMBO REPORTS

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

(2015) Vishnu Dileep et al.   GENOME RESEARCH

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

(2015) Kaiwei Liang et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

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

Linking the Cell Cycle to Cell Fate Decisions

(2015) Stephen Dalton   TRENDS IN CELL BIOLOGY

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

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

(2014) Suhas S.P. Rao et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

The 3D Genome in Transcriptional Regulation and Pluripotency

(2014) David U. Gorkin et al.   Cell Stem Cell

Genome accessibility is widely preserved and locally modulated during mitosis

(2014) Chris C.-S. Hsiung et al.   GENOME RESEARCH

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

Pluripotent stem cells in regenerative medicine: challenges and recent progress

(2014) Viviane Tabar et al.   NATURE REVIEWS GENETICS

RNA and dynamic nuclear organization

(2014) J. Rinn et al.   SCIENCE

Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture

(2014) Job Dekker   Epigenetics & Chromatin

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity

(2013) Siim Pauklin et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

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

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

Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

(2013) Zong Wei et al.   Cell Stem Cell

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

The Hierarchy of the 3D Genome

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

Chromatin dynamics during cellular reprogramming

(2013) Effie Apostolou et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Genome-wide promoter methylation analysis identifies epigenetic silencing ofMAPK13in primary cutaneous melanoma

(2013) Linda Gao et al.   Pigment Cell & Melanoma Research

Aurora B and Cdk1 mediate Wapl activation and release of acetylated cohesin from chromosomes by phosphorylating Sororin

(2013) T. Nishiyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Mitotic bookmarking by transcription factors

(2013) Stephan Kadauke et al.   Epigenetics & Chromatin

Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells

(2013) Amar M. Singh et al.   Stem Cell Reports

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

(2012) Stephan Kadauke 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

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

(2012) Abdenour Soufi et al.   CELL

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

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

(2012) Tom Sexton et al.   CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2

(2012) Claudia A. Doege et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

A short G1 phase is an intrinsic determinant of naïve embryonic stem cell pluripotency

(2012) Diana Coronado et al.   Stem Cell Research

Human Embryonic Stem Cells Exhibit Increased Propensity to Differentiate During the G1 Phase Prior to Phosphorylation of Retinoblastoma Protein

(2012) Yogev Sela et al.   STEM CELLS

Lengthened G1 Phase Indicates Differentiation Status in Human Embryonic Stem Cells

(2012) Ashley Calder et al.   STEM CELLS AND DEVELOPMENT

Histone modifications and mitosis: countermarks, landmarks, and bookmarks

(2012) Fangwei Wang et al.   TRENDS IN CELL BIOLOGY

Protein intrinsic disorder and induced pluripotent stem cells

(2011) Bin Xue et al.   Molecular BioSystems

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Discovering pluripotency: 30 years of mouse embryonic stem cells

(2011) Martin Evans   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells

(2010) Debbie L.C. van den Berg et al.   Cell Stem Cell

An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease

(2010) Mercedes Pardo et al.   Cell Stem Cell

H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes

(2010) Theresa K. Kelly et al.   MOLECULAR CELL

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Brd4 Marks Select Genes on Mitotic Chromatin and Directs Postmitotic Transcription

(2009) Anup Dey et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

The Bromodomain Protein Brd4 Stimulates G1Gene Transcription and Promotes Progression to S Phase

(2008) Kazuki Mochizuki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2008) Lars Guelen et al.   NATURE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE