3f7562cabb5334750a34f8c0ee1681528cb6c84b lrnassar Wed Jul 8 17:14:41 2026 -0700 News post for the ENCODE4 cCREs and ENCODE4 Regulation tracks (hg38 and mm10). refs #37845 Announces the full ENCODE4 cCREs and ENCODE4 Regulation release, and notes that these tracks are now the default regulation tracks on hg38 and mm10, replacing the ENCODE3 cCREs and Regulation tracks (which remain available for archival use). Also reiterates the hg38 cCREs data originally announced in January 2026 for completeness of this combined release. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html old mode 100755 new mode 100644 index 85b44b9edd4..150749ff564 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,251 @@ <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2026 archived news ============= --> <a name="2026"></a> + +<a name="071526"></a> +<h2>Jul. 15, 2026 ENCODE4 cCREs and ENCODE4 Regulation tracks released for human (hg38) and mouse (mm10)</h2> +<p> +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 +<a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cCREs&position=default" target="_blank"> +<b>ENCODE Registry of cCREs</b></a> (candidate Cis-Regulatory Elements) container, +and the new +<a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4&position=default" target="_blank"> +<b>ENCODE4 Regulation</b></a> container, both described in +<a href="https://www.nature.com/articles/s41586-025-09909-9" target="_blank"> +Moore <em>et al</em>., <em>Nature</em> 2026</a>. +</p> + +<p> +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. +</p> + +<div class="text-center" style="margin-top: 1.5em;"> +<a href="https://genome.ucsc.edu/s/Lou/HBBexample" target="_blank"> +<img alt="[PLACEHOLDER: Announcement banner showing the ENCODE4 cCREs and ENCODE4 Regulation container in a browser view]" src="/images/encode4ReleaseNews.png" width='75%'></a> +</div> + +<h3>ENCODE4 cCREs (hg38 and mm10)</h3> +<p> +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: +</p> +<ul> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cCREregistry&position=default" target="_blank"> +ENCODE4 cCREs (hg38)</a>:</b> +2,348,854 cCREs identified and classified using data from all phases of the +ENCODE Project (Phases 1–4). Originally announced in <a href="#011526">January 2026</a>.</li> +<li><b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=cCREregistry&position=default" target="_blank"> +ENCODE4 cCREs (mm10)</a>:</b> +926,843 mouse cCREs derived using the same ENCODE4 integrative analysis pipeline +across mouse ENCODE biosamples.</li> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=coreCcres&position=default" target="_blank"> +ENCODE4 Core Collection (hg38)</a></b> and +<b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=coreCcres&position=default" target="_blank"> +(mm10)</a>:</b> +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).</li> +</ul> + +<p> +Both human and mouse cCREs are colored by their putative functional assignment: +</p> + +<div class="text-center"> +<img alt="[PLACEHOLDER: cCRE classification color legend / example browser view]" src="/images/encode4cCREs.png" width='35%'> +</div> + +<table cellpadding='2' align='center'> + <tr> + <th style="border-bottom: 2px solid;">Color</th> + <th style="border-bottom: 2px solid;"></th> + <th style="border-bottom: 2px solid;">UCSC label</th> + <th style="border-bottom: 2px solid;">ENCODE classification</th> + <th style="border-bottom: 2px solid;">Classification criteria</th> + </tr> +<tr><td style='background-color: #FF0000;'> </td><td>red</td> + <td>promoter</td> + <td>promoter-like signature</td> + <td>within 200 bp of TSS, high chromatin accessibility and H3K4me3</td></tr> +<tr><td style='background-color: #FFA700;'> </td><td>orange</td> + <td>proximal enhancer</td> + <td>TSS-proximal enhancer-like signature</td> + <td>high chromatin accessibility and H3K27ac, within 2 kb of TSS; if within 200 bp of TSS, must have low H3K4me3</td></tr> +<tr><td style='background-color: #FFCD00;'> </td><td>yellow</td> + <td>distal enhancer</td> + <td>TSS-distal enhancer-like signature</td> + <td>high chromatin accessibility and H3K27ac, >2 kb from TSS</td></tr> +<tr><td style='background-color: #FFAAAA;'> </td><td>pink</td> + <td>CA-H3K4me3</td> + <td>chromatin accessibility + H3K4me3</td> + <td>high chromatin accessibility and H3K4me3, low H3K27ac, not within 200 bp of TSS</td></tr> +<tr><td style='background-color: #00B0F0;'> </td><td>blue</td> + <td>CA-CTCF</td> + <td>chromatin accessibility + CTCF</td> + <td>high chromatin accessibility and CTCF, low H3K4me3 and H3K27ac</td></tr> +<tr><td style='background-color: #800080;'> </td><td>dark purple</td> + <td>CA-TF</td> + <td>chromatin accessibility + transcription factor</td> + <td>high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor</td></tr> +<tr><td style='background-color: #06B050;'> </td><td>green</td> + <td>CA</td> + <td>chromatin accessibility</td> + <td>high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF</td></tr> +<tr><td style='background-color: #CC99FF;'> </td><td>light purple</td> + <td>TF</td> + <td>transcription factor</td> + <td>low chromatin accessibility, low H3K4me3, H3K27ac, and CTCF, bound by transcription factor</td></tr> +</table> + +<h3>ENCODE4 Regulation container (hg38 and mm10)</h3> +<p> +The new +<a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4&position=default" target="_blank"> +ENCODE4 Regulation (hg38)</a> and +<a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4Reg&position=default" target="_blank"> +ENCODE4 Regulation (mm10)</a> +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: +</p> + +<p><b>Organ-averaged summary tracks (Layered):</b> 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: +</p> +<ul> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4MarkH3k27ac&position=default" target="_blank"> +H3K27ac (Layered)</a></b> and +<b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegMarkH3k27ac&position=default" target="_blank"> +mm10</a></b> — histone modification associated with active enhancers and +promoters, shown as the default track.</li> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4Dnase&position=default" target="_blank"> +DNase (Layered)</a></b> / +<b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegDnase&position=default" target="_blank"> +mm10</a></b> — open chromatin identified by DNase I hypersensitivity.</li> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4Atac&position=default" target="_blank"> +ATAC (Layered)</a></b> / +<b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegAtac&position=default" target="_blank"> +mm10</a></b> — open chromatin identified by Tn5 transposase insertion.</li> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4MarkH3k4me3&position=default" target="_blank"> +H3K4me3 (Layered)</a></b> / +<b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegMarkH3k4me3&position=default" target="_blank"> +mm10</a></b> — histone modification associated with active and poised +promoters.</li> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4MarkCtcf&position=default" target="_blank"> +CTCF (Layered)</a></b> / +<b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegMarkCtcf&position=default" target="_blank"> +mm10</a></b> — CTCF binding, marking insulators and chromatin loop +anchors.</li> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4Txn&position=default" target="_blank"> +Transcription (Layered)</a></b> / +<b><a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegTxn&position=default" target="_blank"> +mm10</a></b> — strand-specific total RNA-seq signal, averaged by organ.</li> +</ul> + +<p><b>Transcription factor peak track (hg38)</b>:</p> +<ul> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4TfPeaks&position=default" target="_blank"> +TF rPeaks</a>:</b> +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 +<a href="https://www.factorbook.org/" target="_blank">FactorBook</a> are shown +as a decorator, with linkouts to the corresponding +<a href="https://screen.wenglab.org/" target="_blank">SCREEN</a> and FactorBook +pages.</li> +</ul> + +<p><b>Individual-experiment tracks (Indiv.):</b> 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: +</p> +<ul> +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4Epigenetics&position=default" target="_blank"> +DNase/ATAC/Histone/CTCF (Indiv.)</a></b>: +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. +<br><b>mm10 equivalent:</b> +<a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegEpigenetics&position=default" target="_blank">1,178 subtracks</a>.</li> + +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4TfChip&position=default" target="_blank"> +TF ChIP-seq (Indiv.)</a></b>: +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. +<br><b>mm10 equivalent:</b> +<a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegTfChip&position=default" target="_blank">334 subtracks</a>.</li> + +<li><b><a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4RnaSeq&position=default" target="_blank"> +RNA-seq (Indiv.)</a></b>: +1,046 strand-specific total RNA-seq signal subtracks from individual biosamples. +<br><b>mm10 equivalent:</b> +<a href="/cgi-bin/hgTrackUi?db=mm10&c=chr7&g=encode4RegRnaSeq&position=default" target="_blank">1,054 subtracks</a>.</li> +</ul> + +<div class="text-center"> +<img alt="[PLACEHOLDER: browser view of a locus showing the ENCODE4 Regulation layered tracks plus one or two Indiv. composites with peaks visible]" src="/images/encode4Regulation.png" width='75%'> +</div> + +<p> +For details, please see the individual track description pages, as well as +Moore <em>et al</em>. +<a href="https://www.nature.com/articles/s41586-025-09909-9" target="_blank"> +An Expanded Registry of Candidate cis-Regulatory Elements for Studying +Transcriptional Regulation</a>. <em>Nature</em>. 2026 January 7. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39763870" target="_blank">39763870</a>; +PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11703161/" target="_blank">PMC11703161</a>. +</p> + +<p> +This dataset was produced by the ENCODE Data Analysis Center +(<a href="https://www.umassmed.edu/zlab/" target="_blank">Weng lab</a> 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. +</p> + <a name="070726"></a> <h2>Jul. 7, 2026 UCSC Genome Browser reaches version 500</h2> <p> 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 <a href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce">our announcement email list</a>. The software changes, however, are released in chunks, every three weeks, as software "releases". These are announced on the <a href="https://groups.google.com/a/soe.ucsc.edu/g/genome-mirror">genome-mirror email list</a>, 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 <a href="../../cgi-bin/hgTracks?hgTracksConfigPage=Configure"> Genome Browser Configuration Page</a>.