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Series GSE116016 Query DataSets for GSE116016
Status Public on Oct 08, 2018
Title Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.
Overall design Whole-genome ACE-seq analysis of WT or Tet1-3 KO mouse embryonic stem cells as well as adult mouse cortical excitatory neurons
Contributor(s) Schutsky EK, Wu H, Kohli RM
Citation(s) 30295673
NIH grant(s)
Grant ID Grant title Affiliation Name
DP2 HL142044 Charting oxygen-sensing gene regulatory network in cardiomyocytes through single-cell analysis and epigenome editing UNIVERSITY OF PENNSYLVANIA Hao Wu
R00 HG007982 Genomic and functional analysis of active DNA demethylation in mammalian cells UNIVERSITY OF PENNSYLVANIA Hao Wu
Submission date Jun 19, 2018
Last update date Mar 25, 2019
Contact name Hao Wu
Phone 215-573-9360
Organization name University of Pennsylvania
Department Genetics
Lab Hao Wu
Street address 415 Curie Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (6)
GSM3207181 WT-mESC-rep1
GSM3207182 WT-mESC-rep2
GSM3207183 TetTKO-mESC-rep1
BioProject PRJNA476795
SRA SRP150875

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE116016_ACE-Seq_TetTKO.ESC.mm9_CG.txt.gz 255.0 Mb (ftp)(http) TXT
GSE116016_ACE-Seq_WT.ESC.mm9_CG.txt.gz 263.5 Mb (ftp)(http) TXT
GSE116016_ACE-Seq_WT.Neuron.mm9_CG.txt.gz 297.1 Mb (ftp)(http) TXT
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