Description

Chemical modifications (e.g., methylation and acetylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This track displays genome-wide enrichment levels of the H3K4me3 histone mark, as determined by ENCODE ChIP-seq data across all phases of the project. H3K4me3 refers to the tri-methylation of lysine 4 on the H3 histone protein and is associated with active or poised promoters. The data are processed following the ENCODE Histone ChIP-seq pipeline. Additional histone marks and other chromatin-associated ChIP-seq datasets are available at the ENCODE portal.

For each organ, this track provides up to two subtracks averaging H3K4me3 signal:

• Tissue and Primary Cell averages only the tissue and primary cell experiments.
• All Biosamples averages every experiment for that organ, including the tissue/primary cell ones plus any from cell lines, in vitro differentiated cells, or organoids.

Whether one or two subtracks appear for an organ depends on which kinds of biosamples have been assayed:

• Tissue/primary cell only. There are no cell line, in vitro differentiated cell, or organoid experiments to include, so the two averages would be computed from the same data and produce identical numbers. Only the Tissue and Primary Cell subtrack is shown.
• Cell line, in vitro differentiated cell, or organoid experiments only. There are no tissue or primary cell experiments to average, so only the All Biosamples subtrack is shown. In this case it represents those experiments.
• Both kinds of biosamples available. The two averages give different numbers because one covers only the tissue and primary cell experiments while the other includes everything together. Both subtracks are shown.

Available Organs and Tissues

Display Conventions and Configuration

By default, this track uses a transparent overlay to visualize data from multiple organs or tissues within the same vertical space. For each organ or tissue, signals from all associated experiments were averaged to generate the displayed track. Each organ or tissue is assigned a distinct color following the ENCODE color mapping convention, selected to be light and saturated to maintain clarity when overlaid. Initially, each layered track displays an overlay of five representative organs: blood, brain, kidney, liver, and muscle. Clicking on the track opens a details page where you can view and select organs or tissues.

Data Access

The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored in bigWig files that can be downloaded from our download server. The data may also be explored interactively using our REST API. The original data files are also available from the ENCODE portal.

These files may also be locally explored using our tool bigWigToWig, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain data confined to a given range, e.g.,

bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://hgdownload.soe.ucsc.edu/gbdb/mm10/encode4/regulation/organAve/adiposeH3K4me3.bw stdout

Credits

Data were generated by the ENCODE Consortium. We thank the production labs for generating the data: Drs. Barbara Wold (Caltech), Bing Ren (UCSD), Michael Snyder (Stanford), and Ross Hardison (PennState). The data were further processed for visualization through a collaborative effort between the Weng lab and the Moore lab at UMass Chan Medical School (funded by NIH grant HG012343). Integration and visualization were developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were part of the ENCODE Data Analysis Center.

References

ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. PMID: 32728249; PMC: PMC7410828

Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y et al. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. Nature. 2026 January 7. PMID: 39763870; PMC: PMC11703161