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Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

https://doi.org/10.1101/170506
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What this work says

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

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Using MACS to Identify Peaks from ChIP‐Seq Data
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Site specific demethylation in the promoter of human gamma‐globin gene does not alleviate methylation mediated suppression.
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Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl‐CpG binding protein.
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Synchronization of HeLa Cells
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Lessons from comparative analysis of X-chromosome inactivation in mammals
inferredcites →https://doi.org/10.1016/0092-8674(87)90353-9openalex-snapshot
Methylation of the Hprt gene on the inactive X occurs after chromosome inactivation
inferredcites →https://doi.org/10.1016/j.cell.2012.11.014openalex-snapshot
Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development
inferredcites →https://doi.org/10.1016/j.cell.2016.08.056openalex-snapshot
Editing DNA Methylation in the Mammalian Genome
inferredcites →https://doi.org/10.1016/j.cell.2016.09.006openalex-snapshot
Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
inferredcites →https://doi.org/10.1016/j.chembiol.2012.03.010openalex-snapshot
Specificity of Dnmt1 for Methylation of Hemimethylated CpG Sites Resides in Its Catalytic Domain
inferredcites →https://doi.org/10.1016/j.jmb.2012.11.038openalex-snapshot
Targeted Methylation and Gene Silencing of VEGF-A in Human Cells by Using a Designed Dnmt3a–Dnmt3L Single-Chain Fusion Protein with Increased DNA Methylation Activity
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Rapid “Open-Source” Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification
inferredcites →https://doi.org/10.1016/j.molcel.2011.04.005openalex-snapshot
Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.stem.2014.04.006openalex-snapshot
Chromatin and Transcription Transitions of Mammalian Adult Germline Stem Cells and Spermatogenesis
inferredcites →https://doi.org/10.1016/j.tcb.2013.09.001openalex-snapshot
Getting rid of DNA methylation
inferredcites →https://doi.org/10.1016/j.ygeno.2011.05.003openalex-snapshot
Methylation dynamics of IG-DMR and Gtl2-DMR during murine embryonic and placental development
inferredcites →https://doi.org/10.1016/s0960-9822(97)70086-1openalex-snapshot
DNA methylation directs a time-dependent repression of transcription initiation
inferredcites →https://doi.org/10.1038/416552aopenalex-snapshot
DNMT1 and DNMT3b cooperate to silence genes in human cancer cells
inferredcites →https://doi.org/10.1038/83730openalex-snapshot
Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation
inferredcites →https://doi.org/10.1038/cr.2010.156openalex-snapshot
TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine
inferredcites →https://doi.org/10.1038/embor.2011.233openalex-snapshot
DNA methylation: TET proteins—guardians of CpG islands?
inferredcites →https://doi.org/10.1038/nature05987openalex-snapshot
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
inferredcites →https://doi.org/10.1038/nature08514openalex-snapshot
Human DNA methylomes at base resolution show widespread epigenomic differences
inferredcites →https://doi.org/10.1038/nature09798openalex-snapshot
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
inferredcites →https://doi.org/10.1038/nature10716openalex-snapshot
DNA-binding factors shape the mouse methylome at distal regulatory regions
inferredcites →https://doi.org/10.1038/nature13899openalex-snapshot
Structural insight into autoinhibition and histone H3-induced activation of DNMT3A
inferredcites →https://doi.org/10.1038/nature14192openalex-snapshot
Function and information content of DNA methylation
inferredcites →https://doi.org/10.1038/nbt.2450openalex-snapshot
Differential analysis of gene regulation at transcript resolution with RNA-seq
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/ncb1353openalex-snapshot
G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis
inferredcites →https://doi.org/10.1038/ncomms10148openalex-snapshot
Embryonic transcription is controlled by maternally defined chromatin state
inferredcites →https://doi.org/10.1038/ng1297-376openalex-snapshot
Cytosine methylation targetted to pre-determined sequences
inferredcites →https://doi.org/10.1038/ng1719openalex-snapshot
Evidence for an instructive mechanism of de novo methylation in cancer cells
inferredcites →https://doi.org/10.1038/ng1990openalex-snapshot
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nprot.2012.137openalex-snapshot
Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine
inferredcites →https://doi.org/10.1038/nrg3354openalex-snapshot
DNA methylation: roles in mammalian development
inferredcites →https://doi.org/10.1038/onc.2014.470openalex-snapshot
Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer
inferredcites →https://doi.org/10.1038/srep42047openalex-snapshot
Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics
inferredcites →https://doi.org/10.1073/pnas.1415301111openalex-snapshot
Notes on the role of dynamic DNA methylation in mammalian development
inferredcites →https://doi.org/10.1073/pnas.1504199112openalex-snapshot
Reply to Wilkinson: Minor role of programmed methylation and demethylation in mammalian development
inferredcites →https://doi.org/10.1073/pnas.82.9.2560openalex-snapshot
Effect of regional DNA methylation on gene expression.
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/btr490openalex-snapshot
RNA-Seq analysis in MeV
inferredcites →https://doi.org/10.1093/bioinformatics/btr539openalex-snapshot
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
inferredcites →https://doi.org/10.1093/nar/gkl1035openalex-snapshot
Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes
inferredcites →https://doi.org/10.1093/nar/gks360openalex-snapshot
Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer
inferredcites →https://doi.org/10.1093/nar/gkt599openalex-snapshot
Identification of active regulatory regions from DNA methylation data
inferredcites →https://doi.org/10.1093/nar/gku1177openalex-snapshot
The UCSC Genome Browser database: 2015 update
inferredcites →https://doi.org/10.1093/nar/gku154openalex-snapshot
A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data
inferredcites →https://doi.org/10.1093/nar/gku708openalex-snapshot
Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation
inferredcites →https://doi.org/10.1093/nar/gkw159openalex-snapshot
Repurposing the CRISPR-Cas9 system for targeted DNA methylation
inferredcites →https://doi.org/10.1093/nar/gkw258openalex-snapshot
Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved
inferredcites →https://doi.org/10.1093/nar/gkw529openalex-snapshot
A primary role of TET proteins in establishment and maintenance ofDe Novobivalency at CpG islands
inferredcites →https://doi.org/10.1101/gad.2037511openalex-snapshot
CpG islands and the regulation of transcription
inferredcites →https://doi.org/10.1101/gr.114843.110openalex-snapshot
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
inferredcites →https://doi.org/10.1101/gr.125872.111openalex-snapshot
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
inferredcites →https://doi.org/10.1101/gr.132076.111openalex-snapshot
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
inferredcites →https://doi.org/10.1101/gr.133728.111openalex-snapshot
Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
inferredcites →https://doi.org/10.1126/science.1170116openalex-snapshot
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
inferredcites →https://doi.org/10.1126/science.aab2956openalex-snapshot
Dynamics of epigenetic regulation at the single-cell level
inferredcites →https://doi.org/10.1158/0008-5472.can-09-4152openalex-snapshot
The Deubiquitinating Enzyme USP17 Is Highly Expressed in Tumor Biopsies, Is Cell Cycle Regulated, and Is Required for G1-S Progression
inferredcites →https://doi.org/10.1172/jci77321openalex-snapshot
TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts
inferredcites →https://doi.org/10.1186/1471-2164-14-774openalex-snapshot
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/gb-2012-13-10-r84openalex-snapshot
Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns
inferredcites →https://doi.org/10.1186/gb-2012-13-9-r52openalex-snapshot
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-015-0819-6openalex-snapshot
P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis
inferredcites →https://doi.org/10.1186/s13072-015-0002-zopenalex-snapshot
Targeted epigenome editing of an endogenous locus with chromatin modifiers is not stably maintained
inferredcites →https://doi.org/10.1242/bio.019067openalex-snapshot
Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation
inferredcites →https://doi.org/10.1371/journal.pgen.1002604openalex-snapshot
Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions
inferredcites →https://doi.org/10.1371/journal.pone.0087703openalex-snapshot
Targeted Methylation of the Epithelial Cell Adhesion Molecule (EpCAM) Promoter to Silence Its Expression in Ovarian Cancer Cells
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.2174/13892029113149990002openalex-snapshot
KRAB-Zinc Finger Proteins: A Repressor Family Displaying Multiple Biological Functions
inferredcites →https://doi.org/10.4161/cc.6364openalex-snapshot
Synchronization of the cell cycle using Lovastatin
inferredcites →https://doi.org/10.4161/epi.19507openalex-snapshot
Epigenetic reprogramming of cancer cells via targeted DNA methylation

What points at this work

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

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Piecing together cis‐regulatory networks: insights from epigenomics studies in plants
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Bioinformatic and Biostatistic Methods for DNA Methylome Analysis of Obesity
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Reconstructing Denisovan Anatomy Using DNA Methylation Maps
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Epigenetics and postbiotics in Aquaculture: Unlocking sustainable solutions through innovation
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Functional genomic insights into the environmental determinants of mammalian fitness
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Integrative Genome-Scale DNA Methylation Analysis of a Large and Unselected Cohort Reveals 5 Distinct Subtypes of Colorectal Adenocarcinomas
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Association of CHFR Promoter Methylation with Treatment Outcomes of Irinotecan-Based Chemotherapy in Metastatic Colorectal Cancer
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Leveraging brain cortex-derived molecular data to elucidate epigenetic and transcriptomic drivers of complex traits and disease
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Genome-wide tracking of dCas9-methyltransferase footprints
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Retention of paternal DNA methylome in the developing zebrafish germline
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Differential DNA methylation of vocal and facial anatomy genes in modern humans
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Enhancer-associated H3K4 methylation safeguards in vitro germline competence
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Epigenome plasticity in plants
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Sequence determinants, function, and evolution of CpG islands
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Harnessing targeted DNA methylation and demethylation using dCas9
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Enhancer DNA methylation: implications for gene regulation
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Gene activation precedes DNA demethylation in response to infection in human dendritic cells
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Evolution of DNA Methylation in Papio Baboons
inferred← citeshttps://doi.org/10.1093/nar/gkaa1000openalex-snapshot
Epigenome engineering: new technologies for precision medicine
inferred← citeshttps://doi.org/10.1093/nar/gkz1082openalex-snapshot
Epigenetic modification of cytosines fine tunes the stability of i-motif DNA
inferred← citeshttps://doi.org/10.1093/nar/gkz1127openalex-snapshot
SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages
inferred← citeshttps://doi.org/10.1101/2021.11.25.469994openalex-snapshot
Evidence of positive and negative selection associated with DNA methylation
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A modular dCas9-based recruitment platform for combinatorial epigenome editing
inferred← citeshttps://doi.org/10.1101/381145openalex-snapshot
Genome-wide repressive capacity of promoter DNA methylation is revealed through epigenomic manipulation
inferred← citeshttps://doi.org/10.1101/557892openalex-snapshot
Early life DNA methylation profiles are indicative of age-related transcriptome changes
inferred← citeshttps://doi.org/10.1101/gr.233049.117openalex-snapshot
A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
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Connecting the epigenome, metabolome and proteome for a deeper understanding of disease
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Dynamic DNA methylation: In the right place at the right time
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Marine Environmental Epigenetics
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CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness
inferred← citeshttps://doi.org/10.1186/s13059-018-1566-2openalex-snapshot
DNA methylation and de-methylation using hybrid site-targeting proteins
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Detailed insight into the dynamics of the initial phases of de novo RNA-directed DNA methylation in plant cells
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Early-life DNA methylation profiles are indicative of age-related transcriptome changes
inferred← citeshttps://doi.org/10.1186/s13072-021-00428-1openalex-snapshot
Risk-focused differences in molecular processes implicated in SARS-CoV-2 infection: corollaries in DNA methylation and gene expression
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Prioritizing putative influential genes in cardiovascular disease susceptibility by applying tissue-specific Mendelian randomization
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Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4
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A general framework for predicting the transcriptomic consequences of non-coding variation and small molecules
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Enhancer-associated H3K4 methylation safeguards in vitro germline competence
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Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering
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Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease
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DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering
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Investigating Neurodegenerative Disorders
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Neuroimaging and epigenetic machine-learning analyses to predict conversion to psychosis : towards a neurodevelopmental model
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Genome-wide quantification of the effects of DNA methylation on human gene regulation
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