Experiment summary for ENCSR857MYS

Description: Description from ENCODE: "PSU mouse E14Tg2a.4 H3K9me3 ChIP-seq of H3K9me3"

Title from the GEO: "Histone ChIP-seq from E14TG2a.4 (ENCSR857MYS)"

Sequencing data from Mus musculus 129 E14TG2a.4 cell lines and their isogenic replicates targeting H3K9me3 is available to download and view. The interactive tools display connections between sequenced data.

Further information on the datasets can be found in the study:
"In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation."

Supporting documents describe general, pipeline and growth protocols.

Subject of Study

Mus musculus

Subject(s)

Chromatin Immunoprecipitation Sequencing

Mice

Access via ENCODE
ChIP-Seq Data Files
Accession #: ENCSR857MYS

Access via GEO
ChIP-Seq Data Files
Accession #: GSE136526
Access Restrictions: Free to All
Access Instructions: The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

To view files from an experiment, select the 'File details' tab in the Files section of the Experiment summary page. Links to download individual files are available beside each file accession listed in the file section of each experiment page, as well as on each file's individual page. The 'Association graph' tab is an experiment's initial display. The files are shown as a pipeline framework developed by ENCODE using Reference Genomes from NCBI or UCSC. Sequencing output peaks can be viewed in the 'Genome browser' tab, which allows for searching for gene names or coordinates. To view the Genome browser in greater detail, select the "File details' tab and click the blue visualize box in the top right.
DOI: 10.17989/ENCSR857MYS
Associated Publications: Ren W, Fan H, Grimm S, et al. Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation. Proceedings of the National Academy of Sciences of the United States of America. 2020; 117(31):18439-18447.

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.

ENCODE Project Consortium, Moore JE, Purcaro MJ, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020;583(7818):699-710.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2000
High throughput gene sequencing system
Software Used: USCS Genome Browser
The UCSC Genome Browser is a web-based tool serving as a multi-powered microscope that allows researchers to view all 23 chromosomes of the human genome at any scale from a full chromosome down to an individual nucleotide. The browser integrates the work of countless scientists in laboratories worldwide, including work generated at UCSC, in an interactive, graphical display. The Browser also affords access to the genomes of more than one hundred other organisms.
Dataset Format(s): FASTQ, BED, BIGWIG, NARROWPEAK, BAM
Data Tool(s): ChIP Seq
Dataset Size: 4.16GB(FASTQ), 8.2GB (BAM), 22.15MB (narrowPeak), 4.7GB (BIGWIG)

Data Catalog Record Updated: 2021-10-26