H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization

Gene expression and cell identity controlled by anaphase-promoting complex

(2020) Eugene Oh et al.   NATURE

Mechanisms and Functions of Chromosome Compartmentalization

(2020) Erica M. Hildebrand et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

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

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

Cohesin and condensin extrude DNA loops in a cell-cycle dependent manner

(2020) Stefan Golfier et al.   eLife

Transcription factors: building hubs in the 3D space

(2020) Dafne Campigli Di Giammartino et al.   CELL CYCLE

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

(2020) Hyeseon Kang et al.   GENES & DEVELOPMENT

Differential contribution of p300 and CBP to regulatory element acetylation in mESCs

(2020) Sara Martire et al.   BMC Molecular and Cell Biology

Alteration of genome folding via contact domain boundary insertion

(2020) Di Zhang et al.   NATURE GENETICS

Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency

(2020) Bobbie Pelham-Webb et al.   Stem Cell Reports

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

4C-seq from start to end: a detailed protocol for sample preparation and data analysis

(2019) Peter H.L. Krijger et al.   METHODS

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim 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

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

(2019) Judhajeet Ray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

CTCF confers local nucleosome resiliency after DNA replication and during mitosis

(2019) Nick Owens et al.   eLife

Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome

(2018) Brian T. Weinert et al.   CELL

Forces driving the three‐dimensional folding of eukaryotic genomes

(2018) Alvaro Rada‐Iglesias et al.   Molecular Systems 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

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

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

(2018) Sheila S Teves et al.   eLife

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

(2018) James T. Robinson et al.   Cell Systems

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   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

Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation

(2018) Ryan Raisner et al.   Cell Reports

Identification of regulatory elements from nascent transcription using dREG

(2018) Zhong Wang et al.   GENOME RESEARCH

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

A changing paradigm of transcriptional memory propagation through mitosis

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

Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours

(2017) Loren M. Lasko et al.   NATURE

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger et al.   NATURE

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

(2017) Takashi Nagano et al.   NATURE

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

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

Transcriptional landscape of the human cell cycle

(2017) Yin Liu 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

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

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

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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 dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

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

(2015) Zhangyi Liang et al.   CELL

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

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

(2015) Kaiwei Liang et al.   MOLECULAR CELL

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

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

Cell-Cycle Control of Bivalent Epigenetic Domains Regulates the Exit from Pluripotency

(2015) Amar M. Singh et al.   Stem Cell Reports

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

Fucci2a:A bicistronic cell cycle reporter that allows Cre mediated tissue specific expression in mice

(2014) Richard Lester Mort et al.   CELL CYCLE

GATA6 Levels Modulate Primitive Endoderm Cell Fate Choice and Timing in the Mouse Blastocyst

(2014) Nadine Schrode et al.   DEVELOPMENTAL CELL

Genome accessibility is widely preserved and locally modulated during mitosis

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

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Pluripotent stem cells in regenerative medicine: challenges and recent progress

(2014) Viviane Tabar et al.   NATURE REVIEWS GENETICS

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

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

Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes

(2013) J. M. Caravaca et al.   GENES & DEVELOPMENT

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Discovering pluripotency: 30 years of mouse embryonic stem cells

(2011) Martin Evans   NATURE REVIEWS MOLECULAR CELL BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Mitotic bookmarking of genes: a novel dimension to epigenetic control

(2010) Sayyed K. Zaidi et al.   NATURE REVIEWS GENETICS

Chromatin structure and the inheritance of epigenetic information

(2010) Raphaël Margueron et al.   NATURE REVIEWS GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Brd4 Marks Select Genes on Mitotic Chromatin and Directs Postmitotic Transcription

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

A Reconfigured Pattern of MLL Occupancy within Mitotic Chromatin Promotes Rapid Transcriptional Reactivation Following Mitotic Exit

(2009) Gerd A. Blobel et al.   MOLECULAR CELL

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

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

A High-Efficiency System for the Generation and Study of Human Induced Pluripotent Stem Cells

(2008) Nimet Maherali et al.   Cell Stem Cell

Induced Pluripotent Stem Cell Generation Using a Single Lentiviral Stem Cell Cassette

(2008) Cesar A. Sommer et al.   STEM CELLS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY