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Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells

https://doi.org/10.1101/122135
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What this work says

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

inferredcites →https://doi.org/10.1002/stem.1144openalex-snapshot
A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals
inferredcites →https://doi.org/10.1007/978-1-61779-980-8_13openalex-snapshot
FACS Analysis of the Planarian Stem Cell Compartment as a Tool to Understand Regenerative Mechanisms
inferredcites →https://doi.org/10.1007/bf00026179openalex-snapshot
Quantitative analysis of cell types during growth, degrowth and regeneration in the planarians Dugesia mediterranea and Dugesia tigrina
inferredcites →https://doi.org/10.1007/s00427-012-0426-4openalex-snapshot
Stem cell systems and regeneration in planaria
inferredcites →https://doi.org/10.1016/j.cell.2005.10.023openalex-snapshot
Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription
inferredcites →https://doi.org/10.1016/j.cell.2006.02.041openalex-snapshot
A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2016.03.034openalex-snapshot
The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity
inferredcites →https://doi.org/10.1016/j.celrep.2013.04.032openalex-snapshot
Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo
inferredcites →https://doi.org/10.1016/j.celrep.2013.05.043openalex-snapshot
Chromatin Modifications as Determinants of Muscle Stem Cell Quiescence and Chronological Aging
inferredcites →https://doi.org/10.1016/j.celrep.2014.10.018openalex-snapshot
Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome
inferredcites →https://doi.org/10.1016/j.celrep.2015.11.059openalex-snapshot
Set1 and MLL1/2 Target Distinct Sets of Functionally Different Genomic Loci In Vivo
inferredcites →https://doi.org/10.1016/j.celrep.2017.07.046openalex-snapshot
Dynamics of RNA Polymerase II Pausing and Bivalent Histone H3 Methylation during Neuronal Differentiation in Brain Development
inferredcites →https://doi.org/10.1016/j.devcel.2009.08.005openalex-snapshot
A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos
inferredcites →https://doi.org/10.1016/j.devcel.2015.11.004openalex-snapshot
A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians
inferredcites →https://doi.org/10.1016/j.devcel.2016.04.009openalex-snapshot
Inheritance of a Nuclear PIWI from Pluripotent Stem Cells by Somatic Descendants Ensures Differentiation by Silencing Transposons in Planarian
inferredcites →https://doi.org/10.1016/j.molcel.2005.11.021openalex-snapshot
Eaf3 Chromodomain Interaction with Methylated H3-K36 Links Histone Deacetylation to Pol II Elongation
inferredcites →https://doi.org/10.1016/j.molcel.2013.01.038openalex-snapshot
Modification of Enhancer Chromatin: What, How, and Why?
inferredcites →https://doi.org/10.1016/j.molcel.2014.02.032openalex-snapshot
A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers
inferredcites →https://doi.org/10.1016/j.semcdb.2018.04.007openalex-snapshot
Planarian flatworms as a new model system for understanding the epigenetic regulation of stem cell pluripotency and differentiation
inferredcites →https://doi.org/10.1016/j.stem.2008.11.011openalex-snapshot
Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation
inferredcites →https://doi.org/10.1016/j.stem.2011.12.017openalex-snapshot
Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs
inferredcites →https://doi.org/10.1016/j.stem.2014.06.007openalex-snapshot
Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment
inferredcites →https://doi.org/10.1016/j.stemcr.2014.06.001openalex-snapshot
Neoblast Specialization in Regeneration of the Planarian Schmidtea mediterranea
inferredcites →https://doi.org/10.1016/j.tcb.2011.01.005openalex-snapshot
Planarian stem cells: a simple paradigm for regeneration
inferredcites →https://doi.org/10.1016/j.ydbio.2013.09.020openalex-snapshot
Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation
inferredcites →https://doi.org/10.1016/j.ydbio.2017.07.023openalex-snapshot
The abrogation of condensin function provides independent evidence for defining the self-renewing population of pluripotent stem cells
inferredcites →https://doi.org/10.1016/j.ydbio.2017.10.010openalex-snapshot
EvoRegen in animals: Time to uncover deep conservation or convergence of adult stem cell evolution and regenerative processes
inferredcites →https://doi.org/10.1021/cr400158hopenalex-snapshot
RNA Polymerase II C-Terminal Domain: Tethering Transcription to Transcript and Template
inferredcites →https://doi.org/10.1038/cr.2011.146openalex-snapshot
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency
inferredcites →https://doi.org/10.1038/cr.2013.22openalex-snapshot
Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming
inferredcites →https://doi.org/10.1038/emboj.2012.110openalex-snapshot
Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells
inferredcites →https://doi.org/10.1038/nature08866openalex-snapshot
Chromatin signature of embryonic pluripotency is established during genome activation
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/ncb1663openalex-snapshot
Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells
inferredcites →https://doi.org/10.1038/ng.3591openalex-snapshot
Parallel evolution of male germline epigenetic poising and somatic development in animals
inferredcites →https://doi.org/10.1038/nrm3274openalex-snapshot
Understanding the language of Lys36 methylation at histone H3
inferredcites →https://doi.org/10.1038/nsmb.2653openalex-snapshot
The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells
inferredcites →https://doi.org/10.1038/s41467-018-06092-6openalex-snapshot
Conservation of epigenetic regulation by the MLL3/4 tumour suppressor in planarian pluripotent stem cells
inferredcites →https://doi.org/10.1073/pnas.1315204110openalex-snapshot
A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis
inferredcites →https://doi.org/10.1073/pnas.1514789112openalex-snapshot
The ancestral gene repertoire of animal stem cells
inferredcites →https://doi.org/10.1074/jbc.m209294200openalex-snapshot
Association of the Histone Methyltransferase Set2 with RNA Polymerase II Plays a Role in Transcription Elongation
inferredcites →https://doi.org/10.1093/bioinformatics/bti310openalex-snapshot
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btq351openalex-snapshot
BigWig and BigBed: enabling browsing of large distributed datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/nar/gkm684openalex-snapshot
SmedGD: the Schmidtea mediterranea genome database
inferredcites →https://doi.org/10.1093/nar/gkt528openalex-snapshot
Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells
inferredcites →https://doi.org/10.1093/nar/gkv1148openalex-snapshot
PlanMine – a mineable resource of planarian biology and biodiversity
inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot
deepTools2: a next generation web server for deep-sequencing data analysis
inferredcites →https://doi.org/10.1101/gad.219626.113openalex-snapshot
A double take on bivalent promoters
inferredcites →https://doi.org/10.1101/gad.305987.117openalex-snapshot
Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila
inferredcites →https://doi.org/10.1101/gr.080861.108openalex-snapshot
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
inferredcites →https://doi.org/10.1101/gr.113167.110openalex-snapshot
Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm
inferredcites →https://doi.org/10.1101/gr.162529.113openalex-snapshot
Evolutionary conservation of the eumetazoan gene regulatory landscape
inferredcites →https://doi.org/10.1101/gr.185579.114openalex-snapshot
The Release 6 reference sequence of the Drosophila melanogaster genome
inferredcites →https://doi.org/10.1101/gr.6743907openalex-snapshot
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
inferredcites →https://doi.org/10.1111/j.1440-169x.2006.00876.xopenalex-snapshot
Isolation of planarian X‐ray‐sensitive stem cells by fluorescence‐activated cell sorting
inferredcites →https://doi.org/10.1126/science.1116110openalex-snapshot
SMEDWI-2 Is a PIWI-Like Protein That Regulates Planarian Stem Cells
inferredcites →https://doi.org/10.1126/science.aaq1723openalex-snapshot
Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
inferredcites →https://doi.org/10.1126/science.aaq1736openalex-snapshot
Cell type transcriptome atlas for the planarian Schmidtea mediterranea
inferredcites →https://doi.org/10.1186/2041-9139-4-2openalex-snapshot
Closing the circle of germline and stem cells: the Primordial Stem Cell hypothesis
inferredcites →https://doi.org/10.1186/gb-2010-11-4-r42openalex-snapshot
Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophilatestis
inferredcites →https://doi.org/10.1186/gb-2012-13-3-r19openalex-snapshot
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach
inferredcites →https://doi.org/10.1186/s13059-016-0937-9openalex-snapshot
In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians
inferredcites →https://doi.org/10.1242/dev.042051openalex-snapshot
The Mi-2-like Smed-CHD4 gene is required for stem cell differentiation in the planarian Schmidtea mediterranea
inferredcites →https://doi.org/10.1242/dev.047969openalex-snapshot
A conserved germline multipotency program
inferredcites →https://doi.org/10.1242/dev.098152openalex-snapshot
The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation
inferredcites →https://doi.org/10.1242/dev.102681openalex-snapshot
Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant
inferredcites →https://doi.org/10.1242/dev.113027openalex-snapshot
Poised chromatin in the mammalian germ line
inferredcites →https://doi.org/10.1261/rna.1085008openalex-snapshot
The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians
inferredcites →https://doi.org/10.1371/journal.pbio.1000013openalex-snapshot
Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos
inferredcites →https://doi.org/10.1515/1544-6115.1750openalex-snapshot
Normalization, bias correction, and peak calling for ChIP-seq
inferredcites →https://doi.org/10.15252/embr.201541011openalex-snapshot
Chromatin remodeling and bivalent histone modifications in embryonic stem cells
inferredcites →https://doi.org/10.15252/msb.20177754openalex-snapshot
RNA polymerase II primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation
inferredcites →https://doi.org/10.4161/epi.23211openalex-snapshot
Epigenetic regulation of planarian stem cells by the SET1/MLL family of histone methyltransferases
inferredcites →https://doi.org/10.7554/elife.06633openalex-snapshot
Ventromedial hypothalamic neurons control a defensive emotion state
inferredcites →https://doi.org/10.7554/elife.16797openalex-snapshot
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
inferredcites →https://doi.org/10.7554/elife.22194openalex-snapshot
Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-1-4939-7802-1_2openalex-snapshot
Stem Cells, Patterning and Regeneration in Planarians: Self-Organization at the Organismal Scale
inferred← citeshttps://doi.org/10.1016/j.semcdb.2017.08.028openalex-snapshot
Secrets from immortal worms: What can we learn about biological ageing from the planarian model system?
inferred← citeshttps://doi.org/10.1016/j.semcdb.2018.04.007openalex-snapshot
Planarian flatworms as a new model system for understanding the epigenetic regulation of stem cell pluripotency and differentiation
inferred← citeshttps://doi.org/10.1016/j.semcdb.2018.04.009openalex-snapshot
Post-translational regulation of planarian regeneration
inferred← citeshttps://doi.org/10.1016/j.ydbio.2017.07.023openalex-snapshot
The abrogation of condensin function provides independent evidence for defining the self-renewing population of pluripotent stem cells
inferred← citeshttps://doi.org/10.1016/j.ydbio.2017.10.010openalex-snapshot
EvoRegen in animals: Time to uncover deep conservation or convergence of adult stem cell evolution and regenerative processes
inferred← citeshttps://doi.org/10.1038/s41467-018-06092-6openalex-snapshot
Conservation of epigenetic regulation by the MLL3/4 tumour suppressor in planarian pluripotent stem cells
inferred← citeshttps://doi.org/10.1093/bfgp/ely004openalex-snapshot
ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation
inferred← citeshttps://doi.org/10.1242/dev.154971openalex-snapshot
An X-ray shielded irradiation assay reveals EMT transcription factors control pluripotent adult stem cell migration in vivo in planarians
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