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Series GSE94148 Query DataSets for GSE94148
Status Public on Mar 14, 2018
Title A novel RNA m6A modulator Zc3h13 plays an anchor role in facilitating nuclear RNA methylation and mouse embryonic stem cell self-renewal
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary N6-methyladenosine (m6A) is an abundant modification in eukaryotic mRNA, regulating mRNA dynamics by influencing mRNA stability, splicing, export and translation. Recent studies discovered m6A methyltransferases (?writer?), demethylases (?eraser?) and binding proteins (?reader?), which modulate m6A methylation. However, the precise m6A regulating machinery still remains incompletely understood. Here we demonstrate that ZC3H13, a zinc finger protein, plays an essential role in modulating m6A methylation on polyadenylated RNA in the nucleus. ZC3H13 exists in an evolutionary-conserved macromolecular complex containing WTAP, Virilizer and Hakai. We confirm the interaction among those proteins and demonstrate that knockdown of Zc3h13 in mouse embryonic stem cell (mESC) significantly decreases global m6A level on mRNA, mainly at 3? untranslated regions (3? UTR). Interestingly, fractionation assays show that upon Zc3h13 knockdown a great majority of WTAP, Virilizer and Hakai translocate to the cytoplasm and the nuclear presence of the methyltransferase Mettl3 and Mettl14 also decrease significantly. In contrast, knockdown of WTAP, Virilizer or Hakai does not change the nuclear localization of Zc3h13. This suggests that Zc3h13 is required for nuclear localization of the Zc3h13-WTAP-Virilizer-Hakai complex, which is important for RNA m6A methylation. Finally, Zc3h13 depletion, as does WTAP, Virilizer or Hakai, impairs self-renewal and triggers mESC differentiation. Taken together, our findings demonstrate that Zc3h13 plays an essential role in anchoring WTAP, Virilizer and Hakai in the nucleus to facilitate m6A methylation and to regulate mESC self-renewal.
Overall design We examined N6-methyladenosine and mRNA profiles in scr and shZc3H13 mouse embryonic stem cells.
MeRIP-seq were performed to examine N6-methyladenosine (m6A) on the transcrits in the cytoplasmic and nuclear fractions of control and Zc3h13 kd mESCs.
RNA-seq were conducted to examine the gene expression profiles of Zc3h13 kd and control mESCs. 3, RIP-seq were carried out to identify Zc3h13 protein binding RNAs in mESCs.
Contributor(s) Ruitu L, Jianbo D, Jing W, Yang S
Citation(s) 29547716
Submission date Jan 27, 2017
Last update date Mar 21, 2019
Contact name Ruitu Lyu
Organization name Institutes of Biomedical Sciences Fudan University
Lab Epigenetics lab
Street address 138 Yixueyuan Road Xuhui District
City Shanghai
ZIP/Postal code 200030
Country China
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (34)
GSM2471049 Sample_WT_m6A_rep1
GSM2471050 Sample_WT_m6A_rep2
GSM2471051 Sample_scr_m6A_Input_rep1
BioProject PRJNA371494
SRA SRP098937

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Supplementary file Size Download File type/resource
GSE94148_RAW.tar 2.8 Gb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA

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