|
| Status |
Public on Aug 29, 2024 |
| Title |
5-formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming |
| Organism |
Xenopus tropicalis |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Other
Expression profiling by high throughput sequencing
|
| Summary |
5-methylcytosine (5mC) is an established epigenetic mark in vertebrate genomic DNA, but whether its oxidation intermediates formed during TET-mediated DNA demethylation possess an instructive role of their own that is also physiologically relevant remains unresolved. Here, we reveal a 5-formylcytosine (5fC) nuclear chromocenter, which transiently forms during zygotic genome activation (ZGA) in Xenopus and mouse embryos. We identify this chromocenter as the perinucleolar compartment, a structure associated with RNA Pol III transcription. In Xenopus embryos, 5fC is highly enriched on Pol III target genes activated at ZGA, notably at oocyte-type tandem arrayed tRNA genes. By manipulating Tet and Tdg enzymes, we show that 5fC is required as a regulatory mark to promote Pol III recruitment as well as tRNA expression. Concordantly, 5fC modification of a tRNA transgene enhances its expression in vivo. The results establish 5fC as an activating epigenetic mark during zygotic reprogramming of Pol III gene expression.
|
| |
|
| Overall design |
This SuperSeries is composed of the SubSeries listed below.
|
| |
|
| Citation(s) |
39214079 |
| |
| Submission date |
Mar 02, 2023 |
| Last update date |
Sep 01, 2024 |
| Contact name |
Emil Karaulanov |
| Organization name |
Institute of Molecular Biology
|
| Lab |
Bioinformatics Core Facility
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platforms (2) |
| GPL21875 |
Illumina HiSeq 2500 (Xenopus tropicalis) |
| GPL24884 |
Illumina NextSeq 500 (Xenopus tropicalis) |
|
| Samples (32)
|
|
| This SuperSeries is composed of the following SubSeries: |
| GSE226463 |
Pol III chromatin immunoprecipitation-sequencing (ChIP-seq) of Xenopus tropicalis blastula embryos |
| GSE226465 |
DNA immunoprecipitation sequencing (DIP-seq) of Xenopus tropicalis blastula embryos using 5mC, 5hmC, 5fC and 5caC antibodies |
| GSE226466 |
RNA-seq expression profiling of Xenopus tropicalis blastula embryos upon Tet2 and Tet3 knockdown |
|
| Relations |
| BioProject |
PRJNA940392 |
Less...
More...