4.6 Article

Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics

Houda Belaghzal et al.

Summary: Liquid chromatin Hi-C technique reveals the stability of interactions between chromatin loci, showing that compartmentalization is stabilized when fragments are larger than 10-25 kb and smaller chromatin fragments can lead to gradual loss of genome organization. Lamin-associated domains are more stable compared to speckle- and polycomb-associated loci, and cohesin-mediated loops dissolve after fragmentation. This technique provides a genome-wide view of chromosome interaction dynamics.

NATURE GENETICS (2021)

Review Biochemistry & Molecular Biology

Higher-Order Chromosomal Structures Mediate Genome Function

Ivana Jerkovic et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Article Biology

Role of nucleosome positioning in 3D chromatin organization and loop formation

Hungyo Kharerin et al.

JOURNAL OF BIOSCIENCES (2020)

Review Biochemistry & Molecular Biology

Higher-order Chromosome Structures Investigated by Polymer Physics in Cellular Morphogenesis and Differentiation

Andrea Esposito et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

PRC1 Catalytic Activity Is Central to Polycomb System Function

Neil P. Blackledge et al.

MOLECULAR CELL (2020)

Review Cell Biology

Chromosome dynamics during interphase: a biophysical perspective

Maxime M. C. Tortora et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2020)

Article Cell Biology

A central role for canonical PRC1 in shaping the 3D nuclear landscape

Shelagh Boyle et al.

GENES & DEVELOPMENT (2020)

Article Biotechnology & Applied Microbiology

Chromatin rigidity provides mechanical and genome protection

Andrew D. Stephens

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS (2020)

Review Biochemistry & Molecular Biology

Nucleosome positioning and chromatin organization

Jyotsana J. Parmar et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

Review Cell Biology

Two major mechanisms of chromosome organization

Leonid A. Mirny et al.

CURRENT OPINION IN CELL BIOLOGY (2019)

Review Cell Biology

Chromatin's physical properties shape the nucleus and its functions

Andrew D. Stephens et al.

CURRENT OPINION IN CELL BIOLOGY (2019)

Article Multidisciplinary Sciences

Nucleosome positions alone can be used to predict domains in yeast chromosomes

Oliver Wiese et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Review Biochemistry & Molecular Biology

The multiscale effects of polycomb mechanisms on 3D chromatin folding

Thierry Cheutin et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs

Masae Ohno et al.

Article Biochemistry & Molecular Biology

Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays

Mikhail V. Bass et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2019)

Article Biochemistry & Molecular Biology

Single-molecule compaction of megabase-long chromatin molecules by multivalent cations

Anatoly Zinchenko et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Cell Biology

Subnuclear distribution of proteins: Links with genome architecture

Fouziya R. Shah et al.

NUCLEUS (2018)

Review Cell Biology

Subnuclear distribution of proteins: Links with genome architecture

Fouziya R. Shah et al.

NUCLEUS (2018)

Article Cell Biology

Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins

Andrew D. Stephens et al.

MOLECULAR BIOLOGY OF THE CELL (2018)

Article Multidisciplinary Sciences

Chromatin organization by an interplay of loop extrusion and compartmental segregation

Johannes Nuebler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemical Research Methods

How epigenome drives chromatin folding and dynamics, insights from efficient coarse grained models of chromosomes

Surya K. Ghosh et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Multidisciplinary Sciences

TADs are 3D structural units of higher-order chromosome organization in Drosophila

Quentin Szabo et al.

SCIENCE ADVANCES (2018)

Article Biochemistry & Molecular Biology

Polycomb repressive complex l shapes the nucleosome landscape but not accessibility at target genes

Hamish W. King et al.

GENOME RESEARCH (2018)

Article Multidisciplinary Sciences

Interphase human chromosome exhibits out of equilibrium glassy dynamics

Guang Shi et al.

NATURE COMMUNICATIONS (2018)

Editorial Material Multidisciplinary Sciences

Top-down causation and quantum physics

George F. R. Ellis

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Genetics & Heredity

Polycomb and Trithorax Group Genes in Drosophila

Judith A. Kassis et al.

GENETICS (2017)

Review Cell Biology

Emerging roles of mechanical forces in chromatin regulation

Yekaterina A. Miroshnikova et al.

JOURNAL OF CELL SCIENCE (2017)

Article Biochemistry & Molecular Biology

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

Sharmistha Kundu et al.

MOLECULAR CELL (2017)

Article Multidisciplinary Sciences

Two independent modes of chromatin organization revealed by cohesin removal

Wibke Schwarzer et al.

NATURE (2017)

Article Genetics & Heredity

Polycomb and Trithorax Group Genes in Drosophila

Judith A. Kassis et al.

GENETICS (2017)

Article Multidisciplinary Sciences

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Alistair N. Boettiger et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

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

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Transferable model for chromosome architecture

Michele Di Pierro et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

Jakub Mieczkowski et al.

NATURE COMMUNICATIONS (2016)

Article Multidisciplinary Sciences

Chromatin topology is coupled to Polycomb group protein subnuclear organization

Ajazul H. Wani et al.

NATURE COMMUNICATIONS (2016)

Article Biochemistry & Molecular Biology

CTCF Binding Polarity Determines Chromatin Looping

Elzo de Wit et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changesin cellular differentiation

James Fraser et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Article Multidisciplinary Sciences

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

Carlos Gomez-Marin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biophysics

Changing Chromatin Fiber Conformation by Nucleosome Repositioning

Oliver Mueller et al.

BIOPHYSICAL JOURNAL (2014)

Article Cell Biology

O-GlcNAcylation Prevents Aggregation of the Polycomb Group Repressor Polyhomeotic

Maria Cristina Gambetta et al.

DEVELOPMENTAL CELL (2014)

Review Cell Biology

What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory

Philipp A. Steffen et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression

Reinhard Kalb et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

Daniel Jost et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biotechnology & Applied Microbiology

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

Sarah K. Bowman et al.

BMC GENOMICS (2013)

Article Cell Biology

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

Kyoichi Isono et al.

DEVELOPMENTAL CELL (2013)

Review Biochemistry & Molecular Biology

The Hierarchy of the 3D Genome

Johan H. Gibcus et al.

MOLECULAR CELL (2013)

Article Multidisciplinary Sciences

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Chris A. Brackley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

Short nucleosome repeats impose rotational modulations on chromatin fibre folding

Sarah J. Correll et al.

EMBO JOURNAL (2012)

Article Multidisciplinary Sciences

A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence

Leslie Y. Beh et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Review Biology

Top-down causation and emergence: some comments on mechanisms

George F. R. Ellis

INTERFACE FOCUS (2012)

Article Biochemistry & Molecular Biology

Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure

Heather J. Szerlong et al.

BIOCHEMISTRY AND CELL BIOLOGY-BIOCHIMIE ET BIOLOGIE CELLULAIRE (2011)

Review Cell Biology

Trithorax group proteins: switching genes on and keeping them active

Bernd Schuettengruber et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

Michael Y. Tolstorukov et al.

GENOME RESEARCH (2009)

Article Multidisciplinary Sciences

Chromatin compaction by a polycomb group protein complex

NJ Francis et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Histone methyltransferase activity of a Drosophila polycomb group repressor complex

J Müller et al.