Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA unmethylome profiling by covalent capture of CpG sites

ABSTRACT: Here we present an approach for the mapping of unmethylated DNA. Our technique is based on DNA methyltransferase-directed transfer of activated groups (mTAG) and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interogation on tiling microarrays or next generation sequencing. mTAG labeled genomic DNA of one sample

ORGANISM(S): Homo sapiens

SUBMITTER: Viviane Labrie

PROVIDER: E-GEOD-48994 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

DNA unmethylome profiling by covalent capture of CpG sites.

Kriukienė Edita E Labrie Viviane V Labrie Viviane V Khare Tarang T Urbanavičiūtė Giedrė G Lapinaitė Audronė A Koncevičius Karolis K Li Daofeng D Wang Ting T Pai Shraddha S Ptak Carolyn C Gordevičius Juozas J Wang Sun-Chong SC Petronis Artūras A Klimašauskas Saulius S

Nature communications 20130101

Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mapping of unmodified regions of the genome, which we call the unmethylome. Our technique is based on DNA methyltransferase-directed transfer of activated groups and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interrog ...[more]

PMID: 23877302

Similar Datasets

DNA unmethylome profiling by covalent capture of CpG sites (microarray)

Project description:Here we present an approach for the mapping of unmethylated DNA. Our technique is based on DNA methyltransferase-directed transfer of activated groups (mTAG) and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interogation on tiling microarrays or next generation sequencing. mapping of unmethylated DNA

2013-08-27 | E-GEOD-49044 | biostudies-arrayexpress

DNA unmethylome profiling by covalent capture of CpG sites

2013-08-27 | GSE48994 | GEO

DNA unmethylome profiling by covalent capture of CpG sites (microarray)

2013-08-27 | GSE49044 | GEO

DNA unmethylome profiling via covalent capture of CpG sites

Project description:Cytosine 5-modification is a widespread epigenetic mark in eukaryote genomes including humans, but its large scale populational studies are hampered by substantial limitations of the existing analytical techniques. We have developed a new approach for mapping of the unmodified fraction of the genome, i.e. DNA unmethylome, which is based on covalent tagging of unmodified CpG sites with biotin. Sequence-specific tagging of DNA was achieved by using an engineered version of the SssI cytosine-5 methyltransferase and a synthetic analog of the S-adenosylmethionine cofactor carrying a transferable 6-aminohex-2-ynyl group. Analysis of the streptavidin-enriched human unmethylome on tiling DNA microarrays showed that the new approach (named mTAG-chip) offers nanogram sensitivity, a substantially higher precision in the low and medium CpG density regions and added versatility as compared with the existing epigenome profiling techniques.

2012-03-08 | GSE36305 | GEO

DNA unmethylome profiling via covalent capture of CpG sites

2012-03-08 | E-GEOD-36305 | biostudies-arrayexpress

Tethered Oligonucleotide-Primed sequencing (TOP-seq): a high resolution economical approach for DNA epigenome profiling

Project description:We describe the development and thorough validation of a new approach for epigenome analysis (named TOP-seq) that is based on a novel concept – combination of selective covalent tagging and targeted genomic sequencing of the genome. The technique reports the modification status of each genomic CpG site by priming the DNA polymerase action from a tethered oligonucleotide probe that is selectively attached to the unmodified CpG sites.

2017-01-16 | GSE91023 | GEO

ABPP-LC/MS results of covalent inhibitor targeting LC3A/B in HeLa cells

Project description:The autophagic ubiquitin-like protein LC3 functions through interactions with LC3-interaction regions (LIRs) of other autophagy proteins including autophagy receptors, which stands out as a promising protein-protein interaction (PPI) target for the intervention of autophagy. Through screening covalent compounds, we discover a small molecule modulator of LC3A/B that covalently modifies LC3A/B protein at Lys49. Activity-based protein profiling (ABPP) based evaluations reveal that a derivative molecule DC-LC3in-D5 exhibits a potent covalent reactivity and selectivity to LC3A/B in HeLa cells.

2023-03-11 | PXD026874 | Pride

Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape of ESCs revealing changes in lineage specification and chromosomal stability (ChIP-Seq)

Project description:Histone modifications and DNA methylation represent two distinct modes of varying epigenetic landscapes, but whose exact interrelationship remains unclear. Previous studies have shown that histone H3 lysine 4 trimethylation (H3K4me3) inhibits the binding of de novo DNA methyltransferases (Dnmt) through the ATRX-DNMT3-DNMTL (ADD) domain, thus protecting H3K4me3 marked CpG islands (CGI) from DNA methylation. In addition to H3K4me3, we identified antagonistic relationship between H3T3 phosphorylation and the binding of the ADD domain to the unmodified H3 N-terminus. To assess the physiological relevance of these restrictions, we engineered the wild-type ADD domain of Dnmt3a (WT) to permit additional binding to either H3K4me3 (WWD) or H3T3ph (R) and stably introduced FLAG-tagged, full-length normal or mutant Dnmt3a2 into ESCs lacking all Dnmts (TKO; triple knock-out of Dnmt1, Dnmt3a, and Dnmt3b) using the PiggyBac transposon system. For each WT-, WWD-, and R-Dnmt3a2, we generated bulk and clonally-derived ESC lines. We then employed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) to identify the genomic distribution of full-length WT-, WWD-, R-Dnmt3a2, and the H3K4me3 distribution. In parallel, we quantitatively measured genome-wide CpG (cytosine) methylation at base-pair resolution using an enhanced form of reduced representation bisulfite sequencing (RRBS), and performed RNA-seq to assess transcription in matched ESC lines. Examination of wild-type/mutant Dnmt3a2 and matched H3K4me3 distributions in TKO-ESCs.

2015-06-22 | E-GEOD-57574 | biostudies-arrayexpress

Unified analysis of DNA methylation, hydroxymethylation and chromatin accessibility through targeted DNA labeling [TOP-Seq]

Project description:Epigenetic regulation depends on complex interactions between different epigenetic factors, such as DNA methylation and chromatin accessibility. As the gene activation potential cannot be predicted by looking at chromatin accessibility or DNA modification alone, methods capable of relating multiple factors are highly desirable. Existing methods for combined chromatin accessibility and DNA modification analysis rely on bisulfite sequencing, which has a number of well known drawbacks. We developed a novel cost-efficient method for simultaneous profiling of DNA methylation and hydroxymethylation within open chromatin loci. Our approach is based on chemo-enzymatic covalent tagging of unmodified (uCG) and hydroxymethylated (5hmC) CG sites along with GC sites in native chromatin, which are then mapped by tag-selective sequencing. Validation of the technology on model DNA systems and mammalian cells demonstrated a great applicability of this method for epigenomic studies. We employed the technology for tracking chromatin dynamics combined with changes of two different cytosine states, unmodified and hydroxymethylated, during differentiation of embryonic stem cells (ESC) which revealed extensive chromatin dynamics and DNA modification changes across gene bodies of development-associated genes at early transition from ESC. Strong DNA demethylation in the ESC-to-neuron differentiation pathway proceeds independently from cell transcriptional programs and highlights the value of separate 5hmC and 5mC analysis in understanding cell fate decisions.

2023-12-01 | GSE231928 | GEO

Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation

Project description:Poly(ADP-ribose) polymerases (PARP1 and PARP2) contribute to DNA base excision repair (BER) and DNA demethylation and has been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.

2023-11-08 | GSE166963 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data