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Homo sapiens

ABSTRACT: Exploring the occupancy and interaction with FXR2, STAT1/3 and H3K4me3 at genomic level of FXR1 in H358 and AGS cell line by ChIP-seq

PROVIDER: PRJNA316816 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3312500.fastq.gz	Fastqsanger.gz
	SRR3312501.fastq.gz	Fastqsanger.gz
	SRR3312502.fastq.gz	Fastqsanger.gz
	SRR3312503.fastq.gz	Fastqsanger.gz
	SRR3312499.fastq.gz	Fastqsanger.gz

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Exploring the occupancy and interaction with FXR2, STAT1/3 and H3K4me3 at genomic level of FXR1 in H358 and AGS cell line by ChIP-seq

Project description:The chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) was conducted in the human cancer cell lines H358 and AGS using FXR1, FXR2, STAT1/3 and H3K4me3 specific antibodies on the platform Illumina HiSeq 2000. ChIP-seq data quality was analyzed using FastQC. Target protein binding genomic regions (called ChIP-seq peaks) were identified by Model-based Analysis of ChIP-Seq (MACS) algorithm using the default p-value cutoff of 1e-5.

2017-09-01 | GSE79707 | GEO

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Project description:Exploring the gene expression profile upon FXR1 knockdown in H358 cells using RNA-seq

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Exploring the gene expression profile upon FXR1 knockdown in H358 cells using RNA-seq

Project description:We performed the RNA-seq in control samples and FXR1 knockdown samples, and compared the gene expression profiles to explore the effect of FXR1 knockdown on gene expression. The study was performed in H358 cells. Doxycycline inducible shRNA3 (sh3) was used to knockdown FXR1. Control shRNA (ctrl) samples were used to get rid of the effect of Doxycycline treatment. Both the Doxycycline treament for 3 days (D3) and 5 days (D5) samples were collected. Each sample has three repeats (rep 1, rep 2, and rep 3). The mRNA profiles were generated by deep sequencing using Illumina.Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using STAR v2.5.3 with parameters --bamRemoveDuplicatesType UniqueIdentical --outSAMmultNmax 1. Raw reads and Reads Per Kilobase per Megabase of library size (RPKM) were calculated using HOMER (PMID: 20513432). Differential gene expression was analyzed using R package DESeq2 using the raw reads.

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Genome-wide map of SET1A occupancy in mouse ES cells

Project description:To identify SET1A genome-wide occupancy and further unveil its role in transcriptional regulation in mouse ES cells, we carried out chromatin immunoprecipitation followed by high sequencing (ChIP-seq).We established a stable ES cell line expressing 2X Flag tagged SET1A and performed ChIP with anti-Flag M2 beads, followed by deep sequencing. We found that the SET1A peaks show an outstanding enrichment in promoter region. Importantly, these SET1A binding loci revealed a clear co-localization with OCT4, and high H3K4me3 level, which is consistent with its interaction with OCT4 and intrinsic H3K4 methylase activity.

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Project description:The RBP, FXR1, is overexpressed in many epithelial tumors containing a canonical RGG box domain. FXR1 controls post-transcriptional gene regulation through changes in mRNA turnover and translation of target genes. Here we show that arginine methyltransferase PRMT5- mediated specific arginine methylation of FXR1 increases its stability in cancer cells. FXR1-dependent gene signatures show decreased expression and instability of G4-rich sequences containing mRNAs such as CDKN1A, PLK2, TCN2, and TRAF4. Furthermore, structural features of FXR1 and G4-RNA interactions provide novel insights into the critical arginine amino acids of FXR1 essential for G4-RNA-binding and turnover activity. In addition, analysis of the eCLIP data provides various RNA targets and the G-rich sequence motifs of FXR1 in head and neck cancer cell line. Thus, our results indicate that PRMT5-mediated methylation of FXR1 binding with G4-RNAs favors mRNA stability and turnover, contributing to cancer cell growth and proliferation.

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