![[PLACEHOLDER: Announcement banner showing the ENCODE4 cCREs and ENCODE4 Regulation container in a browser view]](/images/encode4ReleaseNews.png)
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Smaller software changes are not announced here. A summary of the three-weekly release changes can be found here. For the full list of our daily code changes head to our GitHub page. Lastly, see our credits page for acknowledgments of the data we host.
+ + ++We are excited to announce our major release of the ENCODE4 data collection on the +UCSC Genome Browser for both the human (hg38/GRCh38) and mouse (mm10/GRCm38) +assemblies. This release consists of two major components: the + +ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) container, +and the new + +ENCODE4 Regulation container, both described in + +Moore et al., Nature 2026. +
+ ++Together, these tracks represent the final ENCODE Phase 4 data release integrated +into the browser and cover chromatin accessibility, histone modification and CTCF +ChIP-seq, transcription factor binding, and transcription across thousands of +individual biosamples. As part of this release, the ENCODE4 cCREs and ENCODE4 +Regulation tracks are now the default regulation tracks shown on hg38 and mm10, +replacing the previous ENCODE3 cCREs and ENCODE3 Regulation tracks. The ENCODE3 +tracks remain available for archival use. +
+ +
++The ENCODE Registry of candidate Cis-Regulatory Elements integrates chromatin +accessibility and ChIP-seq signals across thousands of biosamples into a +biosample-agnostic annotation of the regulatory landscape. Human and mouse are +now both up-to-date at ENCODE4: +
++Both human and mouse cCREs are colored by their putative functional assignment: +
+ +![[PLACEHOLDER: cCRE classification color legend / example browser view]](/images/encode4cCREs.png)
+| Color | ++ | UCSC label | +ENCODE classification | +Classification criteria | +
|---|---|---|---|---|
| red | +promoter | +promoter-like signature | +within 200 bp of TSS, high chromatin accessibility and H3K4me3 | |
| orange | +proximal enhancer | +TSS-proximal enhancer-like signature | +high chromatin accessibility and H3K27ac, within 2 kb of TSS; if within 200 bp of TSS, must have low H3K4me3 | |
| yellow | +distal enhancer | +TSS-distal enhancer-like signature | +high chromatin accessibility and H3K27ac, >2 kb from TSS | |
| pink | +CA-H3K4me3 | +chromatin accessibility + H3K4me3 | +high chromatin accessibility and H3K4me3, low H3K27ac, not within 200 bp of TSS | |
| blue | +CA-CTCF | +chromatin accessibility + CTCF | +high chromatin accessibility and CTCF, low H3K4me3 and H3K27ac | |
| dark purple | +CA-TF | +chromatin accessibility + transcription factor | +high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor | |
| green | +CA | +chromatin accessibility | +high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF | |
| light purple | +TF | +transcription factor | +low chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor |
+The new + +ENCODE4 Regulation (hg38) and + +ENCODE4 Regulation (mm10) +containers bring the underlying ENCODE4 experimental data directly into the +browser. Each container combines organ-averaged summary tracks with searchable, +faceted views of thousands of individual experiments across both peak and signal +data types. The following subtracks are available: +
+ +Organ-averaged summary tracks (Layered): transparent overlays of +signal averaged across biosamples from the same organ or tissue. Each track uses +consistent per-organ colors so the same organ is comparable across assays: +
+Transcription factor peak track (hg38):
+Individual-experiment tracks (Indiv.): searchable, faceted +composites providing access to the underlying data behind the summary tracks. +Each experiment is shown as a Signal (bigWig) subtrack and, where available, a +Peak (bigBed) subtrack: +
+![[PLACEHOLDER: browser view of a locus showing the ENCODE4 Regulation layered tracks plus one or two Indiv. composites with peaks visible]](/images/encode4Regulation.png)
++For details, please see the individual track description pages, as well as +Moore et al. + +An Expanded Registry of Candidate cis-Regulatory Elements for Studying +Transcriptional Regulation. Nature. 2026 January 7. +PMID: 39763870; +PMC: PMC11703161. +
+ ++This dataset was produced by the ENCODE Data Analysis Center +(Weng lab at +UMass Chan Medical School). Major kudos to Mingshi Gao, Jill Moore, and Zhiping Weng for creating and +improving the expansive track hubs for ENCODE4 and for iterating with us to +bring them to the browser as native tracks. We also thank the ENCODE Consortium, the ENCODE production +laboratories, and the ENCODE Data Coordination Center for generating and +processing the underlying experiments, and Gerardo Perez, Brian Raney, Max +Haeussler, and Lou Nassar for building and reviewing these tracks. +
+The UCSC Genome Browser consists of software and genome annotation data and changes are released differently. Some annotation tracks are updated automatically every day or few weeks, but most are curated manually, released when they are ready, announced on this page and our announcement email list. The software changes, however, are released in chunks, every three weeks, as software "releases". These are announced on the genome-mirror email list, and only the most important ones on the page that you are reading here. We increase the version number of the software for every release. You can always find the current version of the Genome Browser software on the Genome Browser Configuration Page.