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Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites

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What this work says

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

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Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpA sites

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Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs

inferredcites →https://doi.org/10.1016/j.cell.2011.11.013openalex-snapshot

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

inferredcites →https://doi.org/10.1016/j.cell.2012.04.027openalex-snapshot

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

inferredcites →https://doi.org/10.1016/j.cell.2013.03.011openalex-snapshot

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

inferredcites →https://doi.org/10.1016/j.cell.2014.04.017openalex-snapshot

Programming and Inheritance of Parental DNA Methylomes in Mammals

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Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization

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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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ATRX Partners with Cohesin and MeCP2 and Contributes to Developmental Silencing of Imprinted Genes in the Brain

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

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

inferredcites →https://doi.org/10.1038/nature06397openalex-snapshot

The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA

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

An integrated encyclopedia of DNA elements in the human genome

inferredcites →https://doi.org/10.1038/nature13458openalex-snapshot

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells

inferredcites →https://doi.org/10.1038/nature14319openalex-snapshot

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

inferredcites →https://doi.org/10.1038/ncomms7363openalex-snapshot

Intermediate DNA methylation is a conserved signature of genome regulation

inferredcites →https://doi.org/10.1038/ng.3258openalex-snapshot

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

inferredcites →https://doi.org/10.1038/ng1491openalex-snapshot

Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome

inferredcites →https://doi.org/10.1038/ng1570openalex-snapshot

Integrative analysis of the cancer transcriptome

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nrg2719openalex-snapshot

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

inferredcites →https://doi.org/10.1038/nrg3663openalex-snapshot

CTCF: an architectural protein bridging genome topology and function

inferredcites →https://doi.org/10.1073/pnas.2536758100openalex-snapshot

Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules

inferredcites →https://doi.org/10.1093/bioinformatics/bth349openalex-snapshot

Java Treeview—extensible visualization of microarray data

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

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/btr167openalex-snapshot

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/nar/29.17.3506openalex-snapshot

Enzymatic properties of de novo-type mouse DNA (cytosine-5) methyltransferases

inferredcites →https://doi.org/10.1093/nar/gku365openalex-snapshot

deepTools: a flexible platform for exploring deep-sequencing data

inferredcites →https://doi.org/10.1093/nar/gku564openalex-snapshot

Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping

inferredcites →https://doi.org/10.1101/gr.163147.113openalex-snapshot

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

inferredcites →https://doi.org/10.1111/j.1365-2443.2006.00984.xopenalex-snapshot

Maintenance of self‐renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b

inferredcites →https://doi.org/10.1126/science.1111098openalex-snapshot

How Are Alkynes Scrambled?

inferredcites →https://doi.org/10.1126/science.1147939openalex-snapshot

UHRF1 Plays a Role in Maintaining DNA Methylation in Mammalian Cells

inferredcites →https://doi.org/10.1126/science.187.4173.226openalex-snapshot

DNA Modification Mechanisms and Gene Activity During Development

inferredcites →https://doi.org/10.1126/science.277.5334.1996openalex-snapshot

Human DNA-(Cytosine-5) Methyltransferase-PCNA Complex as a Target for p21 WAF1

inferredcites →https://doi.org/10.1128/mcb.00484-09openalex-snapshot

Selective Anchoring of DNA Methyltransferases 3A and 3B to Nucleosomes Containing Methylated DNA

inferredcites →https://doi.org/10.1128/mcb.22.2.480-491.2002openalex-snapshot

Cooperativity between DNA Methyltransferases in the Maintenance Methylation of Repetitive Elements

inferredcites →https://doi.org/10.1128/mcb.23.16.5594-5605.2003openalex-snapshot

Establishment and Maintenance of Genomic Methylation Patterns in Mouse Embryonic Stem Cells by Dnmt3a and Dnmt3b

inferredcites →https://doi.org/10.1146/annurev-genom-090413-025437openalex-snapshot

Non-CG Methylation in the Human Genome

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1371/journal.pgen.1001286openalex-snapshot

Nucleosomes Containing Methylated DNA Stabilize DNA Methyltransferases 3A/3B and Ensure Faithful Epigenetic Inheritance

inferredcites →https://doi.org/10.1371/journal.pgen.1002750openalex-snapshot

In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

What points at this work

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

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DNA methylation maintenance at heterochromatin

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Considerations for the need of recommendations for the research and publication of DNA methylation results

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Regulation of 3D chromatin organization by CTCF

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RAD21 deficiency drives corneal to scleral differentiation fate switching via upregulating WNT9B

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Epigenetic-mediated positive feedback loop facilitates the progression of lung adenocarcinoma

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Mitotic inheritance of DNA methylation: more than just copy and paste

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Epigenetic silencing of the DAPK1 gene in Egyptian patients with chronic myeloid Leukemia

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Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication

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Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA

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Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications

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Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions

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High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics

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Chromatin replication and epigenetic cell memory

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Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS

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Epigenomic heterogeneity as a source of tumour evolution

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DNA methylation in mammalian development and disease

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Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

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Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance

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Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance

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Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity

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Resolution of the DNA methylation state of single CpG dyads using in silico strand annealing and WGBS data

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Simultaneously measuring the methylation of parent and daughter strands of replicated DNA at the single-molecule level by Hammer-seq

inferred← citeshttps://doi.org/10.1038/s41596-021-00585-3openalex-snapshot

Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq

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CXXC5 as an unmethylated CpG dinucleotide binding protein contributes to estrogen-mediated cellular proliferation

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Chromatin affinity purification coupled with mass spectrometry indetifies novel histone ubiquitylation interactors

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Additional file 1 of Statistical and bioinformatic analysis of hemimethylation patterns in non-small cell lung cancer

inferred← citeshttps://doi.org/10.6084/m9.figshare.14826131openalex-snapshot

Additional file 1 of Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells

inferred← citeshttps://doi.org/10.6084/m9.figshare.14826143openalex-snapshot

Additional file 5 of Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells

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Targets and genomic constraints of ectopic Dnmt3b expression

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