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Transcription organizes euchromatin similar to an active microemulsion

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-4939-1594-1_10openalex-snapshot

Visualization of Epigenetic Modifications in Preimplantation Embryos

inferredcites →https://doi.org/10.1016/j.ceb.2015.04.003openalex-snapshot

Nuclear bodies: the emerging biophysics of nucleoplasmic phases

inferredcites →https://doi.org/10.1016/j.ceb.2015.04.007openalex-snapshot

Emerging properties of nuclear RNP biogenesis and export

inferredcites →https://doi.org/10.1016/j.cell.2012.05.022openalex-snapshot

Getting RNA and Protein in Phase

inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2015.04.004openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2015.11.018openalex-snapshot

Control of Transcript Variability in Single Mammalian Cells

inferredcites →https://doi.org/10.1016/j.cell.2017.03.024openalex-snapshot

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription

inferredcites →https://doi.org/10.1016/j.cell.2017.05.029openalex-snapshot

SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs

inferredcites →https://doi.org/10.1016/j.celrep.2013.12.030openalex-snapshot

The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species

inferredcites →https://doi.org/10.1016/j.celrep.2015.11.036openalex-snapshot

Nuclear Retention of mRNA in Mammalian Tissues

inferredcites →https://doi.org/10.1016/j.devcel.2015.09.014openalex-snapshot

A Temporal Window for Signal Activation Dictates the Dimensions of a Nodal Signaling Domain

inferredcites →https://doi.org/10.1016/j.devcel.2016.10.015openalex-snapshot

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

inferredcites →https://doi.org/10.1016/j.febslet.2015.05.037openalex-snapshot

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co‐aligned active and inactive nuclear compartments

inferredcites →https://doi.org/10.1016/j.gde.2007.08.008openalex-snapshot

Functional organisation of the genome during interphase

inferredcites →https://doi.org/10.1016/j.molcel.2017.07.022openalex-snapshot

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

inferredcites →https://doi.org/10.1016/j.ymeth.2014.08.002openalex-snapshot

Quantifying histone and RNA polymerase II post-translational modification dynamics in mother and daughter cells

inferredcites →https://doi.org/10.1038/35046510openalex-snapshot

Visualization of gene activity in living cells

inferredcites →https://doi.org/10.1038/emboj.2012.288openalex-snapshot

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

inferredcites →https://doi.org/10.1038/nature12632openalex-snapshot

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

inferredcites →https://doi.org/10.1038/nature13714openalex-snapshot

Regulation of RNA polymerase II activation by histone acetylation in single living cells

inferredcites →https://doi.org/10.1038/nature16490openalex-snapshot

Insulator dysfunction and oncogene activation in IDH mutant gliomas

inferredcites →https://doi.org/10.1038/nature16496openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature21411openalex-snapshot

Complex multi-enhancer contacts captured by genome architecture mapping

inferredcites →https://doi.org/10.1038/nature21429openalex-snapshot

3D structures of individual mammalian genomes studied by single-cell Hi-C

inferredcites →https://doi.org/10.1038/nature22822openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature22989openalex-snapshot

Phase separation drives heterochromatin domain formation

inferredcites →https://doi.org/10.1038/nmeth.2019openalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41467-019-08487-5openalex-snapshot

A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation

inferredcites →https://doi.org/10.1038/s41586-018-0174-3openalex-snapshot

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

inferredcites →https://doi.org/10.1063/1.449286openalex-snapshot

Monte Carlo simulation of model amphiphile-oil–water systems

inferredcites →https://doi.org/10.1080/15476286.2016.1255397openalex-snapshot

Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos

inferredcites →https://doi.org/10.1083/jcb.200011069openalex-snapshot

Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter

inferredcites →https://doi.org/10.1093/emboj/18.10.2855openalex-snapshot

Inefficient processing impairs release of RNA from the site of transcription

inferredcites →https://doi.org/10.1093/nar/gkr343openalex-snapshot

Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling

inferredcites →https://doi.org/10.1101/244038openalex-snapshot

Heterochromatin drives organization of conventional and inverted nuclei

inferredcites →https://doi.org/10.1101/369231openalex-snapshot

Brd4 and P300 regulate zygotic genome activation through histone acetylation

inferredcites →https://doi.org/10.1101/gad.292104openalex-snapshot

Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription

inferredcites →https://doi.org/10.1101/gad.305078.117openalex-snapshot

Dense Bicoid hubs accentuate binding along the morphogen gradient

inferredcites →https://doi.org/10.1126/science.1172046openalex-snapshot

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.aad9024openalex-snapshot

Activation of proto-oncogenes by disruption of chromosome neighborhoods

inferredcites →https://doi.org/10.1126/science.aaf8084openalex-snapshot

Spatial organization of chromatin domains and compartments in single chromosomes

inferredcites →https://doi.org/10.1126/science.aag0025openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.aar2555openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.aar3958openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.aar4199openalex-snapshot

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

inferredcites →https://doi.org/10.1146/annurev-cellbio-100913-013325openalex-snapshot

Liquid-Liquid Phase Separation in Biology

inferredcites →https://doi.org/10.1186/gb-2005-6-5-r47openalex-snapshot

The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

inferredcites →https://doi.org/10.1242/jcs.109.6.1427openalex-snapshot

Active RNA polymerases are localized within discrete transcription ‘factories’ in human nuclei

inferredcites →https://doi.org/10.1242/jcs.113.9.1565openalex-snapshot

Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei

inferredcites →https://doi.org/10.1371/journal.pbio.1000270openalex-snapshot

Poised Transcription Factories Prime Silent uPA Gene Prior to Activation

inferredcites →https://doi.org/10.7554/elife.02407openalex-snapshot

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

inferredcites →https://doi.org/10.7554/elife.04236openalex-snapshot

3D imaging of Sox2 enhancer clusters in embryonic stem cells

inferredcites →https://doi.org/10.7554/elife.23326openalex-snapshot

Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos

inferredcites →https://doi.org/10.7554/elife.27240openalex-snapshot

A tunable refractive index matching medium for live imaging cells, tissues and model organisms

inferredcites →https://doi.org/10.7554/elife.28975openalex-snapshot

Nuclear microenvironments modulate transcription from low-affinity enhancers

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/bs.ctdb.2020.02.002openalex-snapshot

From mother to embryo: A molecular perspective on zygotic genome activation

inferred← citeshttps://doi.org/10.1016/j.gde.2020.12.001openalex-snapshot

Single-molecule tracking of transcription protein dynamics in living cells: seeing is believing, but what are we seeing?

inferred← citeshttps://doi.org/10.1016/j.molcel.2020.10.001openalex-snapshot

Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging

inferred← citeshttps://doi.org/10.1016/j.tcb.2019.10.006openalex-snapshot

Mechanisms for Active Regulation of Biomolecular Condensates

inferred← citeshttps://doi.org/10.1016/j.tcb.2019.12.008openalex-snapshot

Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals

inferred← citeshttps://doi.org/10.1016/j.tibs.2020.01.002openalex-snapshot

Mechanisms and Functions of Chromosome Compartmentalization

inferred← citeshttps://doi.org/10.1016/j.tig.2018.09.002openalex-snapshot

The Birth of the 3D Genome during Early Embryonic Development

inferred← citeshttps://doi.org/10.1021/acsnano.0c07397openalex-snapshot

Genome-in-a-Box: Building a Chromosome from the Bottom Up

inferred← citeshttps://doi.org/10.1038/s41467-019-12208-3openalex-snapshot

Highly structured homolog pairing reflects functional organization of the Drosophila genome

inferred← citeshttps://doi.org/10.1038/s41586-019-1275-3openalex-snapshot

Heterochromatin drives compartmentalization of inverted and conventional nuclei

inferred← citeshttps://doi.org/10.1038/s41592-020-0758-3openalex-snapshot

Visualizing the genome in high resolution challenges our textbook understanding

inferred← citeshttps://doi.org/10.1038/s41598-018-26307-6openalex-snapshot

The live cell DNA stain SiR-Hoechst induces DNA damage responses and impairs cell cycle progression

inferred← citeshttps://doi.org/10.1088/1361-6463/ab3200openalex-snapshot

Super-resolution imaging of densely packed DNA in nuclei of zebrafish embryos using stimulated emission double depletion microscopy

inferred← citeshttps://doi.org/10.1093/nar/gkab275openalex-snapshot

Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates

inferred← citeshttps://doi.org/10.1101/2021.02.03.429626openalex-snapshot

RNA polymerase II clusters form in line with liquid phase wetting of chromatin

inferred← citeshttps://doi.org/10.1101/2021.02.16.431394openalex-snapshot

Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates

inferred← citeshttps://doi.org/10.1101/244038openalex-snapshot

Heterochromatin drives organization of conventional and inverted nuclei

inferred← citeshttps://doi.org/10.1101/601393openalex-snapshot

Quantitative measurements of chromatin modification dynamics during zygotic genome activation

inferred← citeshttps://doi.org/10.1103/physrevlett.123.228101openalex-snapshot

Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

inferred← citeshttps://doi.org/10.1186/s13100-020-0202-3openalex-snapshot

Integrating transposable elements in the 3D genome

inferred← citeshttps://doi.org/10.1242/dev.161471openalex-snapshot

The maternal-to-zygotic transition revisited

inferred← citeshttps://doi.org/10.1242/dev.179127openalex-snapshot

Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis

inferred← citeshttps://doi.org/10.12688/f1000research.13842.1openalex-snapshot

Enhancer functions in three dimensions: beyond the flat world perspective

inferred← citeshttps://doi.org/10.12688/f1000research.21809.1openalex-snapshot

Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model

inferred← citeshttps://doi.org/10.1292/jvms.18-0019openalex-snapshot

Morphometric analysis of cornea in the Slc39a13/Zip13-knockout mice

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008974openalex-snapshot

The hierarchical packing of euchromatin domains can be described as multiplicative cascades

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008546openalex-snapshot

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

inferred← citeshttps://doi.org/10.3410/f.735906976.793572893openalex-snapshot

Faculty Opinions recommendation of Heterochromatin drives compartmentalization of inverted and conventional nuclei.

inferred← citeshttps://doi.org/10.3410/f.737214548.793573559openalex-snapshot

Faculty Opinions recommendation of Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation.

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