Transcriptomics,Multiomics

Dataset Information

3

Gene expression profiles of uhrf1 mutant zebrafish


ABSTRACT: UHRF1 (Ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication, is essential for maintaining DNA methylation patterns during cell division and is suggested to direct additional repressive epigenetic marks. Uhrf1 mutation in zebrafish results in multiple embryonic defects including failed hepatic outgrowth, but the epigenetic basis of these phenotypes is not known. We find that DNA methylation is the only epigenetic mark that is depleted in uhrf1 mutants and make the surprising finding that despite the reduced organ size in uhrf1 mutants, genes regulating DNA replication and S-phase progression were highly upregulated. Further, there is a striking increase in BrdU incorporation in uhrf1 mutant cells, and they retained BrdU labeling over several days, indicating they are arrested in S-phase. Moreover, some of the label retaining nuclei co-localized with TUNEL positive nuclei, suggesting that arrested cells are responsible for apoptosis. Importantly, dnmt1 mutation phenocopies the S-phase arrest and hepatic outgrowth defects in uhrf1 mutants and Dnmt1 knock-down enhances the uhrf1 hepatic phenotype. Together, these data indicate that DNA hypomethylation is sufficient to generate the uhrf1 mutant phenotype by promoting an S-phase arrest. We thus propose that cell cycle arrest is a mechanism to restrict propagation of epigenetically deranged cells during embryogenesis. Genome-wide expression profiling was performed on 2 uhrf1 mutant and 2 wildtype zebrafish larvae (120 hours post fertilization) by using Zebrafish Genome Array (Affymetrix) according to manufacturer's instruction.

OTHER RELATED OMICS DATASETS IN: PRJNA239358

ORGANISM(S): Danio rerio  

SUBMITTER: Yujin Hoshida   Vinitha Jacob  Yelena Chernyavskaya  Xintong Chen  Poh Seng S Tan  Kirsten C Sadler 

PROVIDER: E-GEOD-55339 | ArrayExpress | 2015-02-09

SECONDARY ACCESSION(S): GSE55339PRJNA239358

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-55339.idf.txt Idf
E-GEOD-55339.processed.1.zip Processed
E-GEOD-55339.raw.1.zip Raw
E-GEOD-55339.sdrf.txt Txt
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Publications

DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos.

Jacob Vinitha V   Chernyavskaya Yelena Y   Chen Xintong X   Tan Poh Seng PS   Kent Brandon B   Hoshida Yujin Y   Sadler Kirsten C KC  

Development (Cambridge, England) 20150106 3


UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication and is essential for maintaining DNA methylation. uhrf1 mutant zebrafish have global DNA hypomethylation and display embryonic defects, including a small liver, and they die as larvae. We make the surprising finding that, despite their reduced organ size, uhrf1 mutants express high levels of genes controlling S-phase and have many more cells undergoing DNA replication, as mea  ...[more]

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