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Chrom-seq Identifies RNAs at Chromatin Marks [ChIP-Seq]

ABSTRACT: Chrom-seq Identifies RNAs at Chromatin Marks [ChIP-Seq]

PROVIDER: PRJNA1062751 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27471945_1.fastq.gz	Fastqsanger.gz
	SRR27471945_2.fastq.gz	Fastqsanger.gz
	SRR27471946_1.fastq.gz	Fastqsanger.gz
	SRR27471946_2.fastq.gz	Fastqsanger.gz
	SRR27471947_1.fastq.gz	Fastqsanger.gz

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Chrom-seq Identifies RNAs at Chromatin Marks [Chrom-seq]

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Project description:Chromatin marks are associated with transcriptional regulatory activities. Here, We developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin-mark reader with APEX2 which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1 and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3 and H3K4me3, respectively. Chrom-seq provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in different epigenetic events.

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Chrom-seq identifies RNAs at chromatin marks.

Project description:Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events.

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Chrom-seq Identifies RNAs at Chromatin Marks

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-07-31 | GSE252810 | GEO

ChromID identifies the protein interactome at chromatin marks

Project description:ChromID identifies the protein interactome at chromatin marks

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Chrom-Lasso：A lasso regression-based model to detect functional chromatin interactions using Hi-C data

Project description:We present Chrom-Lasso, an algorithm to identify chromatin interactions from Hi-C data, which performs better in identifying functional chromatin interactions that regulates gene expression when comparing with other methods. To futher assess its performance in investigating biological questions and its ability to deal with noisy data, we use an in vitro mouse CD8+ T cell activation model to generate Hi-C data and RNA-seq data at 4 status(Tn, Teff1, Teff2, Tex) during the process of activation, and we sort T cells at different status by gating criteria as follows: Tn(CD8+, CD44-, CD62L+, at day0), Teff1(CD8+, PD-1+, TIM-3-, at day2), Teff2(CD8+, PD-1+, TIM-3-, at day5), and Tex(CD8+, PD-1+, TIM-3+, at day5), for each status, we prepare 1 Hi-C library following the in situ Hi-C prorocol, and we also prepare 3 RNA-seq libraries from 3 times of parallel experiments. Since functional interactions influence the downstream gene expression level, so the relevance between interactions detected by Chrom-Lasso and gene expression would be powerful evidence proving the capability of Chrom-Lasso in detecting functional interactions.

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