+This track displays the ENCODE Registry of candidate cis-Regulatory Elements (cCREs) +in the human genome from ENCODE 4. A total of 2,348,854 elements identified and classified by the +ENCODE Data Analysis Center according to biochemical signatures. Most cCREs are anchored on +DNase hypersensitive sites further annotated with histone modifications (H3K4me3 and H3K27ac) +or CTCF binding measured by ChIP-seq experiments. In this latest version of the Registry (V4), +the representative DNase hypersensitive sites (rDHSs) were supplemented +with 86,748 representative transcription factor ChIP-seq peaks (TF +rPeaks)—peaks that represent binding sites for at least five TFs. The Registry of cCREs is +one of the core components of the integrative level of the ENCODE Encyclopedia of DNA Elements.
+ +Additional exploration of the cCREs and underlying raw ENCODE signal data can be done with the +Core Collection track. The data is also available on the SCREEN (Search Candidate cis-Regulatory +Elements) web tool, designed specifically for the Registry, accessible by item mouseovers and linkouts from the +track details page.
+ ++Each cCRE is displayed as a colored box by type, which reflects its putative functional assignment +based on biochemical signatures and genomic context:
+
+
+Mousing over the data will display the accession ID, the assigned cCRE class type, and the Max-Z scores +for the various underlying biosignals (DNase, H3K4me3, H3K27ac, CTCF). A track filter is also available +to selectively show items based on their cCRE class type.
+ ++Candidate cis-regulatory elements (cCREs) were first anchored on nucleosome-sized DNase +hypersensitive sites (rDHSs) identified from DNase-seq data. These rDHSs were then annotated +using ChIP-seq data for histone modifications—H3K4me3 and H3K27ac, marking promoters and +enhancers, respectively—and CTCF, marking insulators. To supplement rDHS-anchored cCRE +definitions, transcription factor ChIP-seq peaks were incorporated, enabling identification +of cCREs even in regions of low chromatin accessibility. Although not used for anchoring, +ATAC-seq data were used to assess chromatin accessibility in biosamples lacking DNase-seq.
+ ++Classification of cCRE's was performed based on the following criteria:
++The ENCODE accession numbers of the constituent datasets at the ENCODE Portal are available from the cCRE details page.
+
+The data in this track can be interactively explored with the Table Browser or the Data Integrator. The data can be accessed from
+scripts through our a
+For automated download and analysis, this annotation is stored in a bigBed file
+that can be downloaded from our download server.
+The file for this track is called cCREregistry.bb. Individual regions or the whole genome
+annotation can be obtained using our tool bigBedToBed 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 only features within a given range, e.g.
+bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4/ccre/cCREregistry.bb -chrom=chr21 -start=0 -end=100000000 stdout
+Data were generated by the ENCODE Consortium. 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. We thank the ENCODE production labs +for generating the data.
+ ++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. +bioRxiv. 2024 Dec 26;. +PMID: 39763870; PMC: PMC11703161 +