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Large-scale dissection suggests that ultraconserved elements are dispensable for mouse embryonic stem cell survival and fitness

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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/(sici)1097-010x(19990615)284:1<67::aid-jez10>3.0.co;2-oopenalex-snapshot

Use of developmental marker genes to define temporal and spatial patterns of differentiation during embryoid body formation

inferredcites →https://doi.org/10.1002/dvdy.21271openalex-snapshot

DRG11 immunohistochemical expression during embryonic development in the mouse

inferredcites →https://doi.org/10.1002/wdev.181openalex-snapshot

Size control: the developmental physiology of body and organ size regulation

inferredcites →https://doi.org/10.1007/978-94-007-6262-6_12openalex-snapshot

Moderate Low Temperature Preserves the Stemness of Neural Stem Cells (Methods)

inferredcites →https://doi.org/10.1007/s00335-008-9152-7openalex-snapshot

Identification and characterization of new long conserved noncoding sequences in vertebrates

inferredcites →https://doi.org/10.1016/0012-1606(75)90330-9openalex-snapshot

Minutes: Mutants of Drosophila autonomously affecting cell division rate

inferredcites →https://doi.org/10.1016/j.cell.2013.03.035openalex-snapshot

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

inferredcites →https://doi.org/10.1016/j.cell.2013.04.037openalex-snapshot

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

inferredcites →https://doi.org/10.1016/j.cell.2017.12.017openalex-snapshot

Ultraconserved Enhancers Are Required for Normal Development

inferredcites →https://doi.org/10.1016/j.celrep.2018.06.031openalex-snapshot

Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization

inferredcites →https://doi.org/10.1016/j.devcel.2013.06.012openalex-snapshot

Competitive Interactions Eliminate Unfit Embryonic Stem Cells at the Onset of Differentiation

inferredcites →https://doi.org/10.1016/j.febslet.2014.08.006openalex-snapshot

Paired related homeobox protein‐like 1 (Prrxl1) controls its own expression by a transcriptional autorepression mechanism

inferredcites →https://doi.org/10.1016/j.jgg.2011.09.006openalex-snapshot

Cell competition and its implications for development and cancer

inferredcites →https://doi.org/10.1016/j.stem.2015.07.005openalex-snapshot

Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming

inferredcites →https://doi.org/10.1016/j.stemcr.2016.01.015openalex-snapshot

Higher-Density Culture in Human Embryonic Stem Cells Results in DNA Damage and Genome Instability

inferredcites →https://doi.org/10.1016/j.tcb.2016.05.009openalex-snapshot

Survival of the Fittest: Essential Roles of Cell Competition in Development, Aging, and Cancer

inferredcites →https://doi.org/10.1016/j.tig.2012.03.006openalex-snapshot

Mechanisms of transcriptional precision in animal development

inferredcites →https://doi.org/10.1038/gt.2011.191openalex-snapshot

A competitive cell growth assay for the detection of subtle effects of gene transduction on cell proliferation

inferredcites →https://doi.org/10.1038/mt.2009.234openalex-snapshot

PiggyBac Transposon-based Inducible Gene Expression In Vivo After Somatic Cell Gene Transfer

inferredcites →https://doi.org/10.1038/nature05295openalex-snapshot

In vivo enhancer analysis of human conserved non-coding sequences

inferredcites →https://doi.org/10.1038/nature05676openalex-snapshot

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

inferredcites →https://doi.org/10.1038/nature09158openalex-snapshot

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

inferredcites →https://doi.org/10.1038/nature10530openalex-snapshot

A high-resolution map of human evolutionary constraint using 29 mammals

inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot

An integrated encyclopedia of DNA elements in the human genome

inferredcites →https://doi.org/10.1038/nbt.1662openalex-snapshot

Discovery and characterization of chromatin states for systematic annotation of the human genome

inferredcites →https://doi.org/10.1038/nbt.3437openalex-snapshot

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

inferredcites →https://doi.org/10.1038/ncomms5000openalex-snapshot

Generation of organized germ layers from a single mouse embryonic stem cell

inferredcites →https://doi.org/10.1038/ng.2007.55openalex-snapshot

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

inferredcites →https://doi.org/10.1038/ng1710openalex-snapshot

Conserved noncoding sequences are selectively constrained and not mutation cold spots

inferredcites →https://doi.org/10.1038/nmeth.1906openalex-snapshot

ChromHMM: automating chromatin-state discovery and characterization

inferredcites →https://doi.org/10.1038/nrg1527openalex-snapshot

Conserved non-genic sequences — an unexpected feature of mammalian genomes

inferredcites →https://doi.org/10.1038/s41598-018-20358-5openalex-snapshot

‘Cold shock’ increases the frequency of homology directed repair gene editing in induced pluripotent stem cells

inferredcites →https://doi.org/10.1073/pnas.0801017105openalex-snapshot

Chromosomal transposition of PiggyBac in mouse embryonic stem cells

inferredcites →https://doi.org/10.1073/pnas.0910383107openalex-snapshot

Multiplexed transposon-mediated stable gene transfer in human cells

inferredcites →https://doi.org/10.1093/database/baaa035openalex-snapshot

MIPPIE: the mouse integrated protein–protein interaction reference

inferredcites →https://doi.org/10.1093/gbe/evy196openalex-snapshot

Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units

inferredcites →https://doi.org/10.1093/hmg/ddl232openalex-snapshot

Conserved distances between vertebrate highly conserved elements

inferredcites →https://doi.org/10.1093/nar/gks1284openalex-snapshot

Integrative annotation of chromatin elements from ENCODE data

inferredcites →https://doi.org/10.1093/nar/gky587openalex-snapshot

Loose ends: almost one in five human genes still have unresolved coding status

inferredcites →https://doi.org/10.1101/gad.1525507openalex-snapshot

Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay

inferredcites →https://doi.org/10.1101/gr.4624306openalex-snapshot

Transposon-free regions in mammalian genomes

inferredcites →https://doi.org/10.1111/ede.12084openalex-snapshot

Functional analysis of limb transcriptional enhancers in the mouse

inferredcites →https://doi.org/10.1111/j.1530-0277.2009.01057.xopenalex-snapshot

Effects of Ethanol on Mouse Embryonic Stem Cells

inferredcites →https://doi.org/10.1126/science.1088328openalex-snapshot

Scanning Human Gene Deserts for Long-Range Enhancers

inferredcites →https://doi.org/10.1126/science.1098119openalex-snapshot

Ultraconserved Elements in the Human Genome

inferredcites →https://doi.org/10.1126/science.1142430openalex-snapshot

Human Genome Ultraconserved Elements Are Ultraselected

inferredcites →https://doi.org/10.1242/dev.87.1.27openalex-snapshot

The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium

inferredcites →https://doi.org/10.1371/journal.pbio.0030007openalex-snapshot

Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development

inferredcites →https://doi.org/10.1371/journal.pbio.0050234openalex-snapshot

Deletion of Ultraconserved Elements Yields Viable Mice

inferredcites →https://doi.org/10.1371/journal.pgen.1004646openalex-snapshot

Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells

inferredcites →https://doi.org/10.1371/journal.pgen.1006441openalex-snapshot

The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6

inferredcites →https://doi.org/10.1371/journal.pone.0115072openalex-snapshot

PiggyBac Mediated Multiplex Gene Transfer in Mouse Embryonic Stem Cell

inferredcites →https://doi.org/10.1371/journal.pone.0132437openalex-snapshot

Spontaneous Cell Competition in Immortalized Mammalian Cell Lines

inferredcites →https://doi.org/10.1371/journal.pone.0176120openalex-snapshot

The analysis of viability for mammalian cells treated at different temperatures and its application in cell shipment

inferredcites →https://doi.org/10.15698/cst2018.12.167openalex-snapshot

Systemic signalling and local effectors in developmental stability, body symmetry, and size

inferredcites →https://doi.org/10.2144/000114065openalex-snapshot

Mild Hypothermia Inhibits Differentiation of Human Embryonic and Induced Pluripotent Stem Cells

inferredcites →https://doi.org/10.3390/ijms21103604openalex-snapshot

On-Target CRISPR/Cas9 Activity Can Cause Undesigned Large Deletion in Mouse Zygotes

inferredcites →https://doi.org/10.3791/825openalex-snapshot

In vitro Differentiation of Mouse Embryonic Stem (mES) Cells Using the Hanging Drop Method

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41588-019-0555-zopenalex-snapshot

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

inferred← citeshttps://doi.org/10.1093/bfgp/elab020openalex-snapshot

Application of CRISPR screens to investigate mammalian cell competition

inferred← citeshttps://doi.org/10.1093/gigascience/giz159openalex-snapshot

A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers

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