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SRX6602404: GSM3983046: IgG-rep2-RIP; Homo sapiens; RIP-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 45M spots, 13.5G bases, 5.1Gb downloads

Submitted by: NCBI (GEO)
Study: Genome-wide identification of transcripts associated with KIAA1429 by RIP-seq
show Abstracthide Abstract
N6-methyladenosine (m6A) modification, as the most abundant internal methylation of eukaryotic RNA transcripts, is critically implicated in RNA processing, decay, transport and translation. Here we showed that KIAA1429, the largest known component in the m6A methyltransferase complex, was considerably upregulated in hepatocellular carcinoma (HCC) tissues. High expression of KIAA1429 was significantly associated with the malignant clinical features and the poor prognosis of HCC patients. Silencing KIAA1429 suppressed the cell proliferation and metastasis in vitro and in vivo. Integrated MeRIP-seq, RIP-seq and RNA-seq data identified GATA3 as the direct downstream target of KIAA1429-mediated m6A modification. KIAA1429 knockdown markedly impaired the m6A levels of GATA3 mRNA and increased the expression of GATA3. Mechanistically, KIAA1429 induced the m6A methylation on 3' UTR of GATA3 pre-mRNA, leading to the separation of RNA-binding protein HuR and the degradation of GATA3 pre-mRNA, which was followed by the downregulation of GATA3. Strikingly, a long noncoding RNA (lncRNA) GATA3-AS, transcribed from the antisense strand of GATA3 gene, functioned as a cis-acting element for the preferential interaction of KIAA1429 with GATA3 pre-mRNA. Accordingly, we found that the tumor growth and metastasis driven by KIAA1429 or GATA3-AS were mediated by GATA3. Patients with low KIAA1429 and high GATA3 expressions showed greatly better poor overall survival and disease-free survival. In conclusion, our study proposed a complex KIAA1429-GATA3 regulatory model based on m6A modification and provided insights into the epi-transcriptomic dysregulation in hepatocarcinogenesis and metastasis. Overall design: To identify mRNA species bound by KIAA1429, we performed the RIP-seq to immunoprecipitate endogenous mRNAs associated with the KIAA1429 and sequenced the retrieved RNA.
Sample: IgG-rep2-RIP
SAMN12384686 • SRS5167465 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 4000
Strategy: RIP-Seq
Source: TRANSCRIPTOMIC
Selection: other
Layout: PAIRED
Construction protocol: Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.
Experiment attributes:
GEO Accession: GSM3983046
Links:
Runs: 1 run, 45M spots, 13.5G bases, 5.1Gb
Run# of Spots# of BasesSizePublished
SRR984778145,004,82913.5G5.1Gb2019-07-28

ID:
8708836

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