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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 10, 2017 |
| Title |
Erasure of Tet-oxidized 5-methylcytosine by a SRAP nuclease |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Enzymatic oxidation of 5-methylcytosine (5mC) in DNA by the Tet (Ten-eleven translocation) family of dioxygenases reprograms genome function during pre-implantation development and in primordial germ cells. Tet-oxidized derivatives of 5mC such as 5-hydroxymethylcytosine (5hmC) act as transient intermediates in DNA demethylation or serve as stable epigenetic marks, yet how these alternate fates are specified at individual CpGs is not understood. Here, we report that the Sos-response associated peptidase (SRAP) domain-containing protein Srap1, the mammalian orthologue of an ancient protein superfamily operonically associated with the DNA damage response in bacteria and bacteriophage, binds directly and selectively to Tet-oxidized forms of 5mC in DNA and catalyses turnover of these bases to unmodified cytosine by an autopeptidase cleavage-coupled endonuclease. Biallelic inactivation of Srap1 in mouse embryonic stem (ES) cells results in the global accumulation of Tet-oxidized 5mC derivatives, with ectopic 5hmC in promoters of highly expressed genes, across gene bodies and within enhancer elements. Srap1 deficiency causes partially penetrant lethality in late blastocysts prior to uterine implantation, while surviving midgestation embryos exhibit aberrant patterns of DNA methylation associated with altered gene expression, including hypermethylation in regions closely linked to ectopic 5hmC detected earlier in development. Thus, highly specific removal of 5hmC and its oxidized derivatives by Srap1 sustains genome-wide DNA methylation homeostasis. These findings establish a function for a previously unknown structural class of DNA base modification-specific eraser enzymes that combine the catalytic properties of an autopeptidase with endonuclease activation, and position Srap1 as a key determinant of 5mC demethylation trajectories during mammalian embryonic development.
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| Overall design |
Analysis of Srap1 distribution by ChIP-seq and 5mC/5hmC/5fC/5caC distribution by DIP-seq in wild-type and Srap1 knockout (KO) mouse ES cells. RNA-seq profiling in wild-type and Srap1 KO mouse ES cells. RRBS analysis of E9.5 wild-type and Srap1 KO embryos.
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| Contributor(s) |
Kweon S, Zhu B, Chen Y, Aravind L, Xu S, Feldman DE |
| Citation(s) |
29020633 |
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| Submission date |
May 08, 2016 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Douglas Edmund Feldman |
| E-mail(s) |
defeldma@usc.edu
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| Organization name |
USC Keck School of Medicine
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| Department |
Pathology
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| Lab |
HMR 212
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| Street address |
2011 Zonal Avenue
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (31)
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| Relations |
| BioProject |
PRJNA320954 |
| SRA |
SRP074594 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81222_RAW.tar |
924.2 Mb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BIGWIG, TXT, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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