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Temporal scaling in developmental gene networks by epigenetic timing control
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Modeling transcriptional regulatory networks
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Interspecies Exchange of a Hoxd Enhancer in Vivo Induces Premature Transcription and Anterior Shift of the Sacrum
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An Intrinsic Timer That Controls Cell-Cycle Withdrawal in Cultured Cardiac Myocytes
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The Polycomb Group Protein SUZ12 regulates histone H3 lysine 9 methylation and HP1α distribution
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Tellurium: An extensible python-based modeling environment for systems and synthetic biology
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Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
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Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification
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Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
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Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells
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Regulation of the Probability of Mouse Odorant Receptor Gene Choice
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Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity
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Information Integration and Energy Expenditure in Gene Regulation
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An Optimized microRNA Backbone for Effective Single-Copy RNAi
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Lack of Transcription Triggers H3K27me3 Accumulation in the Gene Body
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Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells
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Slow Chromatin Dynamics Allow Polycomb Target Genes to Filter Fluctuations in Transcription Factor Activity
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Timing temporal transitions during brain development
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Polyphasic feedback enables tunable cellular timers
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SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing
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Enzyme kinetic studies of histone demethylases KDM4C and KDM6A: Towards understanding selectivity of inhibitors targeting oncogenic histone demethylases
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Transcriptional regulation by the numbers: models
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Scaling of morphogen gradients
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Expansion of the polycomb system and evolution of complexity
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Ring1B Compacts Chromatin Structure and Represses Gene Expression Independent of Histone Ubiquitination
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription
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Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide
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SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers
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Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation
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Pyramidal Neurons Derived from Human Pluripotent Stem Cells Integrate Efficiently into Mouse Brain Circuits In Vivo
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Polycomb repression in the regulation of growth and development in Arabidopsis
inferredcites →https://doi.org/10.1016/j.stem.2008.09.002openalex-snapshot
Self-Organized Formation of Polarized Cortical Tissues from ESCs and Its Active Manipulation by Extrinsic Signals
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2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size
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Thinking out of the dish: what to learn about cortical development using pluripotent stem cells
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Ezh2 maintains retinal progenitor proliferation, transcriptional integrity, and the timing of late differentiation
inferredcites →https://doi.org/10.1016/j.ydbio.2017.02.002openalex-snapshot
Species-specific developmental timing is maintained by pluripotent stem cells ex utero
inferredcites →https://doi.org/10.1016/j.ydbio.2017.11.004openalex-snapshot
Polycomb repression complex 2 is required for the maintenance of retinal progenitor cells and balanced retinal differentiation
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The role of subunit entropy in cooperative assembly. Nucleation of microtubules and other two-dimensional polymers
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Brownian motion in a field of force and the diffusion model of chemical reactions
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Oligodendrocyte precursor cells count time but not cell divisions before differentiation
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Size and shape in ontogeny and phylogeny
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c-Myc regulates mammalian body size by controlling cell number but not cell size
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UTX mediates demethylation of H3K27me3 at muscle‐specific genes during myogenesis
inferredcites →https://doi.org/10.1038/nature04733openalex-snapshot
Polycomb complexes repress developmental regulators in murine embryonic stem cells
inferredcites →https://doi.org/10.1038/nature06145openalex-snapshot
UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development
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An intrinsic mechanism of corticogenesis from embryonic stem cells
inferredcites →https://doi.org/10.1038/nature08398openalex-snapshot
Role of the polycomb protein EED in the propagation of repressive histone marks
inferredcites →https://doi.org/10.1038/nature09645openalex-snapshot
Emerging properties of animal gene regulatory networks
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Morphological evolution caused by many subtle-effect substitutions in regulatory DNA
inferredcites →https://doi.org/10.1038/nature10241openalex-snapshot
A Polycomb-based switch underlying quantitative epigenetic memory
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A critical role for TCF-1 in T-lineage specification and differentiation
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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/nature23875openalex-snapshot
Discovery of stimulation-responsive immune enhancers with CRISPR activation
inferredcites →https://doi.org/10.1038/ncomms13343openalex-snapshot
BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization
inferredcites →https://doi.org/10.1038/ncomms6077openalex-snapshot
Dynamic scaling of morphogen gradients on growing domains
inferredcites →https://doi.org/10.1038/ncomms9108openalex-snapshot
An intrinsic timer specifies distal structures of the vertebrate limb
inferredcites →https://doi.org/10.1038/ng.3734openalex-snapshot
Dynamics of BAF–Polycomb complex opposition on heterochromatin in normal and oncogenic states
inferredcites →https://doi.org/10.1038/ni.3514openalex-snapshot
Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment
inferredcites →https://doi.org/10.1038/ni.3598openalex-snapshot
A Myc-dependent division timer complements a cell-death timer to regulate T cell and B cell responses
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
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Targeted in situ genome-wide profiling with high efficiency for low cell numbers
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Network motifs: theory and experimental approaches
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Histone variants on the move: substrates for chromatin dynamics
inferredcites →https://doi.org/10.1038/nrn3618openalex-snapshot
Temporal fate specification and neural progenitor competence during development
inferredcites →https://doi.org/10.1038/s41588-017-0035-2openalex-snapshot
Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate
inferredcites →https://doi.org/10.1038/s41590-018-0238-4openalex-snapshot
Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16
inferredcites →https://doi.org/10.1038/srep41669openalex-snapshot
The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features
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Contingent gene regulatory networks and B cell fate specification
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A gene regulatory network armature for T lymphocyte specification
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Some Unexpected Results of the Heteroplastic Transplantation of Limbs
inferredcites →https://doi.org/10.1073/pnas.1002530107openalex-snapshot
Ezh2, the histone methyltransferase of PRC2, regulates the balance between self-renewal and differentiation in the cerebral cortex
inferredcites →https://doi.org/10.1073/pnas.1012525107openalex-snapshot
Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas
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T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling
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Chromatin organization by an interplay of loop extrusion and compartmental segregation
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High mobility group A2 (HMGA2) deficiency in pigs leads to dwarfism, abnormal fetal resource allocation, and cryptorchidism
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Bottom–up modeling of chromatin segregation due to epigenetic modifications
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Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy
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Nucleation and the kinetics of microtubule assembly.
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Quantitative model for gene regulation by lambda phage repressor.
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Formation of stable transcription complexes as assayed by analysis of individual templates.
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Enhancers increase the probability but not the level of gene expression.
inferredcites →https://doi.org/10.1074/jbc.m307344200openalex-snapshot
Polycomb Group Suppressor of Zeste 12 Links Heterochromatin Protein 1α and Enhancer of Zeste 2
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Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation
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Kinetics of Steady-state Differentiation and Mapping of Intrathymic-signaling Environments by Stem Cell Transplantation in Nonirradiated Mice
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In Vitro Differentiation of Adult Bone Marrow Progenitors into Antigen-Specific CD4 Helper T Cells Using Engineered Stromal Cells Expressing a Notch Ligand and a Major Histocompatibility Complex Class II Protein
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Compare and contrast actin filaments and microtubules.
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/nar/gkw701openalex-snapshot
Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements
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The Encyclopedia of DNA elements (ENCODE): data portal update
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Computational modelling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence
inferredcites →https://doi.org/10.1101/467316openalex-snapshot
Phase separation and nucleosome compaction are governed by the same domain of Polycomb Repressive Complex 1
inferredcites →https://doi.org/10.1101/cshperspect.a018366openalex-snapshot
Regulation of the X Chromosomes in Caenorhabditis elegans
inferredcites →https://doi.org/10.1101/gad.247940.114openalex-snapshot
Nascent RNA interaction keeps PRC2 activity poised and in check
inferredcites →https://doi.org/10.1101/gad.256354.114openalex-snapshot
Two distinct modes for propagation of histone PTMs across the cell cycle
inferredcites →https://doi.org/10.1103/physrevlett.112.068101openalex-snapshot
Statistical Mechanics Model for the Dynamics of Collective Epigenetic Histone Modification
inferredcites →https://doi.org/10.1111/dgd.12337openalex-snapshot
Scaling of pattern formations and morphogen gradients
inferredcites →https://doi.org/10.1126/science.1100576openalex-snapshot
Chromatin Compaction by a Polycomb Group Protein Complex
inferredcites →https://doi.org/10.1126/science.1188063openalex-snapshot
Reprogramming of T Cells to Natural Killer–Like Cells upon Bcl11b Deletion
inferredcites →https://doi.org/10.1126/science.1188989openalex-snapshot
An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b
inferredcites →https://doi.org/10.1126/science.1188995openalex-snapshot
An Essential Developmental Checkpoint for Production of the T Cell Lineage
inferredcites →https://doi.org/10.1126/science.1248559openalex-snapshot
Timing Mechanism Dependent on Cell Division Is Invoked by Polycomb Eviction in Plant Stem Cells
inferredcites →https://doi.org/10.1126/science.aab2956openalex-snapshot
Dynamics of epigenetic regulation at the single-cell level
inferredcites →https://doi.org/10.1126/science.aad8786openalex-snapshot
A beak size locus in Darwin’s finches facilitated character displacement during a drought
inferredcites →https://doi.org/10.1126/science.aai8236openalex-snapshot
Causal role for inheritance of H3K27me3 in maintaining the OFF state of a Drosophila HOX gene
inferredcites →https://doi.org/10.1126/science.aau0583openalex-snapshot
H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification
inferredcites →https://doi.org/10.1128/mcb.00205-14openalex-snapshot
Polycomb Repressive Complex 2 and H3K27me3 Cooperate with H3K9 Methylation To Maintain Heterochromatin Protein 1α at Chromatin
inferredcites →https://doi.org/10.1128/mcb.22.22.8026-8034.2002openalex-snapshot
Transcription through Intergenic Chromosomal Memory Elements of the Drosophila Bithorax Complex Correlates with an Epigenetic Switch
inferredcites →https://doi.org/10.1146/annurev-biophys-051013-022819openalex-snapshot
Mechanisms of ATP-Dependent Chromatin Remodeling Motors
inferredcites →https://doi.org/10.1146/annurev-cellbio-092910-154148openalex-snapshot
Morphogen Gradients: From Generation to Interpretation
inferredcites →https://doi.org/10.1146/annurev-conmatphys-031214-014558openalex-snapshot
Napoleon Is in Equilibrium
inferredcites →https://doi.org/10.1182/blood-2002-06-1862openalex-snapshot
Combined effects of Notch signaling and cytokines induce a multiple log increase in precursors with lymphoid and myeloid reconstituting ability
inferredcites →https://doi.org/10.1182/blood-2002-08-2517openalex-snapshot
Of mice and men … and elephants
inferredcites →https://doi.org/10.1182/blood-2004-04-1293openalex-snapshot
Induction of T-cell development from human cord blood hematopoietic stem cells by Delta-like 1 in vitro
inferredcites →https://doi.org/10.1182/blood-2012-06-440065openalex-snapshot
GATA-3 promotes T-cell specification by repressing B-cell potential in pro–T cells in mice
inferredcites →https://doi.org/10.1186/gb-2013-14-10-r121openalex-snapshot
Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3
inferredcites →https://doi.org/10.1186/s13059-017-1199-xopenalex-snapshot
Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations
inferredcites →https://doi.org/10.1242/dev.078345openalex-snapshot
Genome-wide analysis reveals that Smad3 and JMJD3 HDM co-activate the neural developmental program
inferredcites →https://doi.org/10.1242/dev.091553openalex-snapshot
Polycomb complexes in stem cells and embryonic development
inferredcites →https://doi.org/10.1242/dev.106831openalex-snapshot
Diffusible signals and epigenetic timing cooperate in late proximo-distal limb patterning
inferredcites →https://doi.org/10.1242/dev.107011openalex-snapshot
Scaling morphogen gradients during tissue growth by a cell division rule
inferredcites →https://doi.org/10.1242/dev.129452openalex-snapshot
Morphogen rules: design principles of gradient-mediated embryo patterning
inferredcites →https://doi.org/10.1242/dev.139360openalex-snapshot
Transient ectopic expression of the histone demethylase JMJD3 accelerates the differentiation of human pluripotent stem cells
inferredcites →https://doi.org/10.1242/dev.164368openalex-snapshot
What does time mean in development?
inferredcites →https://doi.org/10.1371/journal.pone.0096545openalex-snapshot
The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner
inferredcites →https://doi.org/10.1515/9783110848281openalex-snapshot
Generelle Morphologie der Organismen
inferredcites →https://doi.org/10.3389/fcell.2014.00005openalex-snapshot
HMGA proteins as modulators of chromatin structure during transcriptional activation
inferredcites →https://doi.org/10.4049/jimmunol.1700319openalex-snapshot
EZH2 Regulates the Developmental Timing of Effectors of the Pre–Antigen Receptor Checkpoints
inferredcites →https://doi.org/10.7554/elife.21064openalex-snapshot
PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes
inferredcites →https://doi.org/10.7554/elife.21064.031openalex-snapshot
Author response: PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes
inferredcites →https://doi.org/10.7554/elife.37851openalex-snapshot
A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.celrep.2021.108888openalex-snapshot
Tunable, division-independent control of gene activation timing by a polycomb switch
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