Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenomic profiling of active regulatory elements by enrichment of unmodified CpG dinucleotides

ABSTRACT: In this study we present an enrichment-based and bisulfite-free approach for epigenomic profiling named ‘Active-Seq’ (Azide Click Tagging for In Vitro Epigenomic sequencing) that achieves genome-wide profiling of DNA, by enriching for non-modified CpG sites using a mutated methyltransferase enzyme. Active-Seq is a fast epigenetic profiling platform with a simple and streamlined workflow, performed in tandem with sequencing library preparation. The enzymatic chemistry is non-damaging toward the DNA which is critical for working with low concentration DNA input and will facilitate the future development of multiomics assays.

ORGANISM(S): Homo sapiens

PROVIDER: GSE266366 | GEO | 2025/05/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenomic profiling of active regulatory elements by enrichment of unmodified CpG dinucleotides

Project description:Epigenomic profiling of active regulatory elements by enrichment of unmodified CpG dinucleotides

| PRJNA1106835 | ENA

Selective chemical tracking of Dnmt1 catalytic activity in live cells

Project description:Enzymatic methylation of cytosine to 5-methylcytosine in DNA is a fundamental epigenetic mechanism involved in mammalian development and disease. DNA methylation is brought about by collective action of three AdoMet-dependent DNA methyltransferases (DNMTs), whose catalytic interactions and temporal interplay are poorly understood. We used structure-guided engineering of the Dnmt1 methyltransferase to enable catalytic transfer of azide tags onto DNA from a synthetic cofactor analog, Ado-6-azide, in vitro . We then CRISPR-edited the Dnmt1 locus in mouse embryonic stem cells to install the engineered codon, which, following pulse- internalization of the Ado-6-azide cofactor by electroporation, permitted selective azide-tagging of Dnmt1-specific genomic targets in cellula . The deposited covalent tags were exploited as ‘click’ handles for reading adjoining sequences and precise genomic mapping of the methylation sites. The proposed approach, Dnmt-TOP-seq, enables high-resolution temporal tracking of the Dnmt1 catalysis in mammalian cells paving the way to selective studies of other methylation pathways in eukaryotic systems.

2022-02-04 | GSE182445 | GEO

Impact of azide metabolic glycoengineering and bioorthogonal click chemistry cell-cell tethering in adipose tissue-derived mesenchymal stromal cells

Project description:We report RNA sequencing data from adipose tissue-derived mesenchymal stromal cells (hASCs) functionalized via metabolic glycoengineering with pendant azide sialosides. Beyond the impact of this cell surface engineering on transcriptome, we explore the expression profiles of azide-hASCs covalently tethered to an interfacial glycosaminoglycan via bioorthogonal click chemistry and yielding a 3D multicellular construct. We find global gene expression changes in response to metabolic glycoengineering in 2D cell culture conditions as well as those arising from cell-to-cell tethering into 3D environments.

2024-04-15 | GSE231507 | GEO

Low-cost high-resolution chromatin profiling with CUT&Tag

Project description:We recently introduced CUT&Tag, an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei, and then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds DNA sequencing adapters (“tagmentation”) for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses exposure artifacts to ensure high-fidelity mapping of the antibody-targeted protein and improves signal-to-noise over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube from cells to amplified libraries, providing low-cost high-resolution genome-wide chromatin maps. By simplifying library preparation, CUT&Tag requires less than a day at the bench from live cells to sequencing-ready barcoded libraries. Because of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for ~$25 per sample, enabling routine genome-wide profiling of chromatin proteins and modifications that requires no special skills or equipment.

2020-07-15 | GSE145187 | GEO

Capture, release, and identification of newly synthesized proteins for improved profiling of functional translatomes

Project description:Proteins undergoing active translation in proliferating K562 cells during a 2-hour time frame were labeled with O-propargyl-puromycin for subsequent click reaction with cleavable Dde biotin-azide. Following capture on streptavidin agarose resin, nascent polypeptides were released from the resin by treatment with 2% hydrazine. The method was used to profile the nascent proteome upon acute inhibition of mTOR with MLN128, an ATP-competitive active-site inhibitor of the mTOR kinase.

2022-07-22 | MSV000089950 | MassIVE

Oxidative Azidylation of Proteins

Project description:We describe a method for directly attaching azide to protein to enable downstream click chemistry. Further, we show that azide binds protein noncovalently in hydrophobic patches, which we can capture and identify using MS. Full details are in the associated paper.

2023-08-23 | PXD035808 | Pride

Nascent Transcriptome of Cycloheximide (CHX)-arrested Xenopus laevis Embryos from 5-7.5 hpf

Project description:To characterize the effect of cell cyle elongation on nascent transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and treated the embryos with 0.2 mg/ml of cycloheximide (CHX) to arrest them in interphase from 5 hpf to 7.5 hpf. Control and CHX-arrested embryos were collected for isolating total RNAs, followed by biotinylation using disulfide biotin azide via click reaction and purification of nascent transcripts using streptavidin beads. Libraries were constructed and sequenced on illumina NextSeq 500.

2022-08-22 | GSE201834 | GEO

NAD+-capped RNAs are preferentially produced from inducible genes in response to growth conditions in E. coli

Project description:Recent findings regarding NAD+-capped RNAs (NAD-RNAs) indicate that prokaryotes and eukaryotes employ non-canonical RNA capping to regulate genes, a previously unrecognized mechanism. Two methods for transcriptome-wide analysis of NAD-RNAs, NAD captureSeq and NAD tagSeq, are based on copper-catalyzed azide-alkyne cycloaddition click chemistry reaction to label NAD-RNAs. However, copper can fragment RNA, interfering with the analyses. Here we report development of NAD tagSeq II, which uses copper-free, strain-promoted azide-alkyne cycloaddition for labeling NAD-RNAs, followed by identification of tagged RNA by direct RNA sequencing. Using this method, we compared NAD-RNA and total transcript profiles of E. coli cells in the exponential and stationary phases and identified hundreds of NAD-RNA species. For some genes, the majority of their transcripts were found as NAD-RNAs. Our study indicates that NAD-RNAs are preferentially produced from inducible genes in response to different growth conditions.

2021-04-21 | GSE153253 | GEO

Activity-based proteomic profiling (ABPP) employing a serine hydrolase-directed probe to identify changes in activity profiles of lipid hydrolase in lung tumors

Project description:Lung tumors, as well as normal tumor-adjacent (NTA) tissue of non-small cell lung cancer (NSCLC) patients, were collected and subjected to labeling with a serine hydrolase-directed activity-based probe (ABP) immediately after excision. Labeling with the serine hydrolase-directed ABP allows for the detection of active lipid hydrolases, which are the focus of our investigation. The labeled proteins (corresponding to active enzymes at time of labeling) were enriched using a biotin-containing linker that was covalently attached using strain-promoted alkyne-azide cycloaddition (click chemistry). Shotgun proteomics of the on-bead digested enriched proteins of ABP-treated and control samples enabled identification of enriched proteins as well as comparison of activity profiles between NTA and tumor samples of NSCLC patients.

2023-11-27 | PXD046934 | Pride

RNA-Seq of A375 cells treated with tetracycline-based crosslinking probes, with and without competition by parent tetracyclines, to show specific binding of the tetracycline analogs Col-3 and doxycycline on rRNA substructures of the human ribosome

Project description:Upon finding that the tetracyclines COL-3 and doxycycline target unique rRNA substructures of the 80S ribosome (E-MTAB-7147), we confirmed these putative ribosomal binding sites by showing that tetracycline-based crosslinking probes are specifically competed from these rRNA structures by their parent drugs. In short, we incorporated dual bioorthogonal handles into tetracycline-based probes, containing both a photoactive diazirine to enable direct probe crosslinking to the human ribosome and an azide handle to allow selective enrichment of crosslinked biomolecules via copper-free ‘click’ chemistry. The COL-3 and doxycycline probes were each incubated with A375 cells, followed by irradiation at 365 nm to induce photolysis of the diazirine moiety and subsequent crosslinking to adjacent ribosomal components. Pulldown and RNA-Seq of the crosslinked RNAs from our experiments were used to identify enrichment of reverse transcription (RT) stops at ribosomal RNA sites caused by local crosslinking of our probes. In these experiments, UV crosslinking was preformed with the COL-3 and doxycycline probe compounds in the presence and absence of free COL-3 and doxycycline (i.e., parent tetracycline molecules lacking the bifunctional diazirine-azide moiety), which were used as competitors to specifically diminish crosslinking to the ribosomal RNA. Crosslinking to ribosomal RNA was determined using RNA-Seq based RT stop enrichment, which was was also compared to inactive tetracycline probes containing a modified bifunctional linker, a non-specific aniline probe, and untreated controls.

2018-08-31 | E-MTAB-7161 | biostudies-arrayexpress

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