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Genome-wide identification of protein binding sites on RNAs in mammalian cells [PBS-R]

ABSTRACT: Genome-wide identification of protein binding sites on RNAs in mammalian cells [PBS-R]

PROVIDER: PRJNA499055 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8128835_1.fastq.gz	Fastqsanger.gz
	SRR8128835_2.fastq.gz	Fastqsanger.gz
	SRR8128836_1.fastq.gz	Fastqsanger.gz
	SRR8128836_2.fastq.gz	Fastqsanger.gz
	SRR8128837.fastq.gz	Fastqsanger.gz

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Genome-wide identification of protein binding sites on RNAs in mammalian cells [PBS-R]

Project description:We develop a novel method, called protein binding sites on RNA (PBS-R) to identify genome-wide protein binding sites on RNAs without using antibodies. Double click strategy is used for the PBS-R assay. Proteins and RNAs are UV-crosslinked in vivo first, then the proteins are crosslinked to the magnetic beads. The protein binding RNA elements are captured, reverse transcribed and sequenced.

2018-11-10 | GSE121919 | GEO

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Genome-wide identification of protein binding sites in mammalian cells.

Project description:We report the application of genome-wide protein binding sites capture (GWPBS-Cap) technology for high-throughput profiling of protein binding sites in mammalian cells. By obtaining over 37 billion bases of sequence from NaCl washed chromatin DNA in each group, we got an unprecedented view into genome-wide binding patterns of many DNA binding proteins of Hela cells. We find that active promoters contain more PBSs with lower NaCl tolerance and our technology provides a genome-wide landscape of DNA-protein interactions.

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Project description:To identify ZNF506 genome-wide target sites, we performed ChIP-seq assay and found that ZNF506 binding sites enriched at PBS-Pro-containing ERV subfamilies (ERVPs) and further motif calling analysis showed that ZNF506 binds to PBS-Pro sequences, promoting formation of H3K9me3 modifications at binding regions. And ChIP-seq assay also indicated that the distinction of H3K9me3 signals closed to ZNF506 peak regions between ZNF506 overexpressing (OE) HEK293T cells and ZNF506 Knockout (KO) HEK293T cells was correlated with the different recruitment of corepressor KAP1. The ChIP-seq experiments using GFP antibodies and H3K9me3 antibodies on ZNF506-GFP OE HEK293T cell lines, and ZNF417-GFP OE HEK293T cell lines were used as controls for H3K9me3 ChIP. Also, the ChIP-seq experiments were performed using H3K9me3 antibodies and KAP1 antibodies on ZNF506 KO HEK293T cells and ZNF506 OE HEK293T cells.

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Project description:Detection of RNA–DNA binding sites in long noncoding RNAs

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Project description:We report the application of next generation sequencing for high-throughput profiling of Yin Yang 2 (YY2) binding sites in mammalian Trophectoderm Stem cells. Sequencing of chromatin obtained in chromatin-immunoprecipitation (ChIP) assays carried out with αYY2 serum yielded over ten million sequence reads. Peak finding allowed us allowed us to identify a limited number of chromatin targets for YY2. Putative binding sites were validated in regular ChIP assays and gene expression of a few genes nearby was altered in the absence of Yy2. This study provides a framework to understand the role of YY2 in diverse mammalian cell populations.

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ChIP-seq on ZNF506 overexpression HEK293T to verify ZNF506 binding capacity at PBS-Pro sites.

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