Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing

ABSTRACT: 5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on the oxidative DNA demethylation pathway and is implicated in regulation of embryogenesis, neurological processes and cancerogenesis. Profiling of this relatively scarce genomic modification in clinical samples requires cost-effective high resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single nucleotide resolution, named hmTOP-seq, which is based on direct sequence readout primed at covalently labeled 5hmC sites from an in situ tethered DNA oligonucleotide. Examination of distinct tethering chemistries suggested a putative model for the targeted non-homologous polymerase priming which permits theoretical evaluation of suitable tethers at the design stage. The robustness and resolution of hmTOP-seq was validated on a small model genome and mouse embryonic stem cells, which allowed construction of single nucleotide 5hmCG maps that reflect subtle differences in strand-specific CG hydroxymethylation. Collectively, hmTOP-seq expands the toolbox of valuable techniques for cost-effective identification of epigenetic changes and new disease biomarkers.

ORGANISM(S): Mus musculus

PROVIDER: GSE140206 | GEO | 2020/04/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion (SCL-exo)

Project description:We report the setup of a new method to map 5-hydroxymethylcytosine (5hmC) genome-wide at CpG resolution. The method combines selective chemical labeling by 5hmC b-glucosyltransferase and exonuclease digestion of the DNA molecules bound to streptavidin beads after biotinylation of the 5-glucosylmethylcytosines. Associated with a straightforward bioinformatic analysis, this new procedure provides a cost-effective and fast method for mapping 5hmC at high resolution.

2016-03-04 | GSE70635 | GEO

DeepH&M: Simultaneous determination of single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods

Project description:Increased appreciation of 5-hydroxymethylation (5hmC) as a stable epigenetic mark, which defines cell identity and disease progress, has engendered a need for cost-effective, but high-resolution 5hmC mapping technology. Current enrichment-based technologies provide cheap, but low-resolution and relative enrichment of 5hmC levels while single base-resolution methods can be prohibitively expensive to scale up to large experiments. To address this problem, we developed a deep learning-based method “DeepH&M”, which integrates enrichment and restriction enzyme sequencing methods to simultaneously estimate absolute hydroxymethylation and methylation levels at single CpG resolution. Using 7-week-old mouse cerebellum data for training DeepH&M model, we demonstrated that the 5hmC and 5mC levels predicted by DeepH&M were in high concordance with gold standard data predicted by TAB-seq and WGBS. The DeepH&M model can be applied to 7-week old frontal cortex and 79-week cerebellum revealing the robust generalizability of this method to other tissues from various biological time points.

2020-09-10 | GSE140125 | GEO

A Sensitive Approach to Map Genome-wide 5-Hydroxymethylcytosine and 5-Formylcytosine at Single-base Resolution

Project description:Mapping genome-wide 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) at single-base resolution is important to understand their biological functions. We present a cost-efficient mapping method that combines 5hmC-specific restriction enzyme PvuRts1I with a 5hmC enrichment method. The sensitive method enables detection of low abundant 5hmC sites, providing a more complete 5hmC landscape than available bisulfite-based methods. This method generated the first genome-wide 5fC map at single-base resolution. Parallel analyses revealed that 5hmC and 5fC existed with lower abundance and more dynamically in non-CpG context than in CpG context. In the genic region, distribution of 5hmCpG and 5fCpG differed from 5hmCH and 5fCH (H=A, T, C). 5hmC and 5fC were distributed distinctly at regulatory protein-DNA binding sites, depleted in permissive transcription factor binding sites, and enriched at active and poised enhancers. This sensitive bisulfite-conversion free method can be applied to biological samples with limited starting material or low abundance of cytosine modifications. Sensitive mapping of genome-wide 5-hydroxymethylcytosine and 5-formylcytosine in mouse embryonic stem cell at single-base resolution by combining 5-hydroxymethylcytosine specific restriction enzyme PvuRts1I and 5-hydroxymethylcytosine enrichment method (selective chemical labeling or SEAL)

2014-12-22 | E-GEOD-64186 | biostudies-arrayexpress

Jump-seq: Capture and amplify 5hmC Sites Whole Genome-Wide

Project description:We developed an efficient and precise method, which we name as Jump-seq, to capture and amplify 5hmC signal whole genome-wide, bridge the gap between base resolution (TAB-seq) and economic cost (hmC-seal).

2019-03-07 | GSE127906 | GEO

A Sensitive Approach to Map Genome-wide 5-Hydroxymethylcytosine and 5-Formylcytosine at Single-base Resolution

2014-12-22 | GSE64186 | GEO

Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution.

2014-12-12 | GSE60225 | GEO

JBP1-seq: a fast and efficient method for genome-wide profiling of 5hmC

Project description:We developed a novel approach, J-binding protein 1 sequencing (JBP1-seq), that combines the benefits of an improved recombinant JBP1 protein, Nextera-based library construction, and nextgeneration sequencing (NGS) for genome-wide profiling of 5-hydroxymethylcytosine (5hmC). Compared with the original JBP1, this new recombinant JBP1 was biotinylatedin vivo and conjugated to magnetic beads via biotin-streptavidin interactions. These modifications allowed a more efficient and consistent pull-down of β-glucosyl-5-hydroxymethylcytosine (β-glu-5hmC), and sequence-ready libraries can be generated within 4.5 hours from DNA inputs as low as 50 ng. 5hmC enrichment of human brain DNA using the new JBP1 resulted in over 25,000 peaks called, which is significantly higher than the 4,003 peaks enriched using the old JBP1. Comparison of the technical duplicates and validations with other platforms indicated the results are reproducible and reliable. Thus, JBP1-seq provides a fast, efficient, cost-effective method for accurate 5hmC genome-wide profiling. An improvement of JBP1-Seq

2014-11-26 | E-GEOD-61193 | biostudies-arrayexpress

Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection

Project description:Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection

| PRJNA623426 | ENA

Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution.

Project description:5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use cost-prohibitive DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community. Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals. Implementing this approach, termed TAB-array, we assessed DNA methylation dynamics in the differentiation of human pluripotent stem cells into cardiovascular and neural progenitors. With the ability to discriminate 5mC and 5hmC, we found a much larger number of dynamically methylated genomic regions implicated in the development of these lineages than we could detect by 5mC analysis alone. The increased resolution and accuracy afforded by this approach provides a powerful means to investigate the distinct contributions of 5mC and 5hmC in human development and disease. We generated illumina 450k DNA methylation data for a total of 9 sample groups with two biological replicates for each group. Data for 4/9 groups were generated from glucosylated and bisulfite converted DNA, from human induced plurupotent stem cells (hIPSCs), differentiated cardiovascular progenitors (CVPs), differentiated neural progenitors (NPCs), and fibroblasts. Data for the next 4/9 groups were generated from glucosylated, TET-oxidized and bisulfite converted DNA, from and included replicates of hIPSCs, CVPs, NPCs, and fibroblasts. Data for the last group was generated from standard bisulfite converted DNA (not glucosylated) from fibroblasts.

2014-12-12 | E-GEOD-60225 | biostudies-arrayexpress

Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics [Stereo-Seq]

Project description:Spatial transcriptomics workflows using barcoded capture arrays are commonly used for resolving gene expression in tissues. However, existing techniques are either limited by capture array density or are cost prohibitive for large scale atlasing. We present Nova-ST, a dense nano-patterned spatial transcriptomics technique derived from randomly barcoded Illumina sequencing flow cells. Nova-ST enables customized, low cost, flexible, and high-resolution spatial profiling of large tissue sections. Benchmarking on mouse brain sections demonstrates significantly higher sensitivity compared to existing methods, at reduced cost.

2024-02-22 | GSE256319 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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