c7a78bd7342f93f63acaf6759ca7077b9caaa64c gperez2 Wed Jul 22 22:05:43 2026 -0700 Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 708f5509089..d0ee164fdec 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -78,219 +78,154 @@ 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.

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[PLACEHOLDER: Announcement banner showing the ENCODE4 cCREs and ENCODE4 Regulation container in a browser view]

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ENCODE4 cCREs and ENCODE4 Regulation tracks at the HBB locus

The ENCODE4 Registry of cCREs, Core Collection, and H3K27ac +(Layered) Regulation tracks at the HBB locus on hg38.

ENCODE4 cCREs (hg38 and mm10)

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:

-ENCODE4 cCREs (hg38): -2,348,854 cCREs identified and classified using data from all phases of the -ENCODE Project (Phases 1–4). Originally announced in January 2026.
-ENCODE4 cCREs (mm10): -926,843 mouse cCREs derived using the same ENCODE4 integrative analysis pipeline -across mouse ENCODE biosamples.
-ENCODE4 Core Collection (hg38) and - -(mm10): +
ENCODE4 cCREs +hg38 and +mm10: +2,348,854 human and 926,843 mouse cCREs identified and classified using the +ENCODE4 integrative analysis pipeline across ENCODE biosamples. Human cCREs +were originally announced in January 2026.
ENCODE4 Core Collection +hg38 and +mm10: Biosample-specific cCREs alongside underlying epigenomic signals for the ENCODE4 Core Collection: 170 human and 18 mouse biosamples that were comprehensively profiled with all four core assays (DNase-seq, H3K4me3 ChIP-seq, H3K27ac ChIP-seq, and CTCF ChIP-seq).

-Both human and mouse cCREs are colored by their putative functional assignment: +Both human and mouse cCREs are colored by their putative functional assignment. See the +description page for the full classification scheme.

[PLACEHOLDER: cCRE classification color legend / example browser view]

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	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

ENCODE4 Regulation container (hg38 and mm10)

-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, +The new ENCODE4 Regulation container for +hg38 and +mm10 +brings the underlying ENCODE4 experimental data directly into the +browser. The 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:

-H3K27ac (Layered) and - -mm10 — histone modification associated with active enhancers and +
H3K27ac (Layered) hg38 and +mm10: histone modification associated with active enhancers and promoters, shown as the default track.
-DNase (Layered) / - -mm10 — open chromatin identified by DNase I hypersensitivity.
-ATAC (Layered) / - -mm10 — open chromatin identified by Tn5 transposase insertion.
-H3K4me3 (Layered) / - -mm10 — histone modification associated with active and poised +
DNase (Layered) hg38 and +mm10: open chromatin identified by DNase I hypersensitivity.
ATAC (Layered) hg38 and +mm10: open chromatin identified by Tn5 transposase insertion.
H3K4me3 (Layered) hg38 and +mm10: histone modification associated with active and poised promoters.
-CTCF (Layered) / - -mm10 — CTCF binding, marking insulators and chromatin loop +
CTCF (Layered) hg38 and +mm10: CTCF binding, marking insulators and chromatin loop anchors.
-Transcription (Layered) / - -mm10 — strand-specific total RNA-seq signal, averaged by organ.
Transcription (Layered) hg38 and +mm10: strand-specific total RNA-seq signal, averaged by organ.

Transcription factor peak track (hg38):

-TF rPeaks: -Representative peak clusters for 911 transcription factors across 1,152 -biosamples, derived from the ENCODE4 TF ChIP-seq collection. The HGNC symbol of -each factor is displayed alongside the peak. Overlapping cognate TF motifs from -FactorBook are shown -as a decorator, with linkouts to the corresponding -SCREEN and FactorBook -pages.

Transcription factor peak track +hg38: +TF rPeaks, representative peak clusters for 912 DNA-associated proteins across 1,152 +biosamples, derived from the ENCODE4 TF ChIP-seq collection, with linkouts to +SCREEN and +FactorBook.

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:

-DNase/ATAC/Histone/CTCF (Indiv.): +
DNase/ATAC/Histone/CTCF (Indiv.) +hg38: 6,353 subtracks (3,199 signal + 3,154 peak) covering DNase-seq, ATAC-seq, and ChIP-seq for H3K4me3, H3K27ac, and CTCF. Filterable by assay, organ, biosample -type, life stage, and data type. -
mm10 equivalent: -1,178 subtracks.

mm10 equivalent:

-TF ChIP-seq (Indiv.): +
TF ChIP-seq (Indiv.) +hg38: 4,964 subtracks (2,462 signal + 2,502 peak) for ChIP-seq of individual transcription factors, DNA-associated proteins, RNA polymerase, and chromatin -regulators. The experimental basis for the TF rPeaks track above. -
mm10 equivalent: -334 subtracks.

mm10 equivalent:

-RNA-seq (Indiv.): -1,046 strand-specific total RNA-seq signal subtracks from individual biosamples. -
mm10 equivalent: -1,054 subtracks.
RNA-seq (Indiv.) +hg38: +1,046 strand-specific total RNA-seq signal subtracks from individual biosamples. mm10 equivalent: +1,054 subtracks.

[PLACEHOLDER: browser view of a locus showing the ENCODE4 Regulation layered tracks plus one or two Indiv. composites with peaks visible]

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ENCODE4 Regulation Layered tracks and an Indiv. composite with peaks at the HBB locus

DNase and H3K27ac (Layered) tracks, plus K562 signal and peak +tracks from the DNase/ATAC/Histone/CTCF (Indiv.) faceted composite, at the HBB locus +on hg38.

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 +UMass Chan Medical School). Thanks 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 +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.

Jul. 16, 2026 Long-read Structural Variants tracks for human (hg38 and hs1)

We are excited to announce a new Long-read Structural Variants container track on the human assemblies GRCh38/hg38 and T2T-CHM13/hs1. The container track brings together structural variant (SV) callsets from 14 long-read sequencing studies worldwide into a single place where you can compare large genomic