(Q38089266)

28 August 2017

Non-canonical functions of the DNA methylome in gene regulation (English)

1 reference

28 August 2017

James P Reddington

1

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Richard Meehan

object named as

Richard R Meehan

series ordinal

3

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author name string

Sari Pennings

series ordinal

2

1 reference

PubMed ID

23489368

28 August 2017

language of work or name

English

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publication date

1 April 2013

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28 August 2017

1 reference

28 August 2017

451

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28 August 2017

1

1 reference

28 August 2017

13-23

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A gene regulatory network controlling the embryonic specification of endoderm

28 August 2017

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Operating on chromatin, a colorful language where context matters

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Programming of DNA methylation patterns

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genome-wide analysis of DNA methylation patterns

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Human DNA methylomes at base resolution show widespread epigenomic differences

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Dynamic changes in the human methylome during differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The DNA methylome of human peripheral blood mononuclear cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

CpG islands and the regulation of transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

A novel CpG island set identifies tissue-specific methylation at developmental gene loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation dynamics during in vivo differentiation of blood and skin stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNMT1 maintains progenitor function in self-renewing somatic tissue

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Pancreatic β cell identity is maintained by DNA methylation-mediated repression of Arx.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation status predicts cell type-specific enhancer activity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genomic DNA methylation: the mark and its mediators

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Role for DNA methylation in genomic imprinting

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation profiles of human active and inactive X chromosomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Targets and dynamics of promoter DNA methylation during early mouse development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA demethylation and USF regulate the meiosis-specific expression of the mouse Miwi

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation supports intrinsic epigenetic memory in mammalian cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

A human B cell methylome at 100-base pair resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Replication timing-related and gene body-specific methylation of active human genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Gene body-specific methylation on the active X chromosome

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation profiling of human chromosomes 6, 20 and 22

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Orphan CpG islands identify numerous conserved promoters in the mammalian genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Conserved role of intragenic DNA methylation in regulating alternative promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Chromatin and epigenetic regulation of pre-mRNA processing

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genome-wide association between DNA methylation and alternative splicing in an invertebrate

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Alternative chromatin structure at CpG islands

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

CpG islands influence chromatin structure via the CpG-binding protein Cfp1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

CpG islands recruit a histone H3 lysine 36 demethylase

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

CpG island clusters and pro-epigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

A mutant form of MeCP2 protein associated with human Rett syndrome cannot be displaced from methylated DNA by notch in Xenopus embryos

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The accessible chromatin landscape of the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Identification of genetic elements that autonomously determine DNA methylation states.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Large-scale methylation domains mark a functional subset of neuronally expressed genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

5-Hydroxymethylcytosine: a new kid on the epigenetic block?

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The mammalian de novo DNA methyltransferases DNMT3A and DNMT3B are also DNA 5-hydroxymethylcytosine dehydroxymethylases

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Ten-Eleven-Translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Nucleosome-interacting proteins regulated by DNA and histone methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Polycomb group protein complexes exchange rapidly in living Drosophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

RNAi components are required for nuclear clustering of Polycomb group response elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Interactions among Polycomb domains are guided by chromosome architecture

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

A view of nuclear Polycomb bodies

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

TrxG and PcG proteins but not methylated histones remain associated with DNA through replication

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Histone H4K20me3 and HP1α are late heterochromatin markers in development, but present in undifferentiated embryonic stem cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Nucleosome deposition and DNA methylation at coding region boundaries

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation, nucleosome formation and positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Polycomb proteins in mammalian cell differentiation and plasticity

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

DNA methylation patterns and epigenetic memory

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Recruitment of polycomb group complexes and their role in the dynamic regulation of cell fate choice

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The Polycomb complex PRC2 and its mark in life

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Control of developmental regulators by Polycomb in human embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Polycomb complexes repress developmental regulators in murine embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

The Polycomb group protein EZH2 directly controls DNA methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Regulation of mammalian DNA methyltransferases: a route to new mechanisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

A vertebrate Polycomb response element governs segmentation of the posterior hindbrain

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

A region of the human HOXD cluster that confers polycomb-group responsiveness

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

GC-rich sequence elements recruit PRC2 in mammalian ES cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

X Inactivation in the Mouse Embryo Deficient for Dnmt1: Distinct Effect of Hypomethylation on Imprinted and Random X Inactivation

21 January 2018

1 reference

https://api.crossref.org/works/10.1042%2FBJ20121585

21 January 2018

Identifiers

DOI

10.1042/BJ20121585

1 reference

28 August 2017

1 reference

PubMed ID

23489368