This track displays mouse genomic intervals that were predicted to be cis-regulatory elements (cCREs) and have been tested experimentally for enhancer activity. The methods for predicting the cCRE have included a Regulatory Potential score based on machine learning of genomic DNA sequence alignments (Taylor et al. 2006, Wang et al. 2006), peaks of occupancy by GATA1 based on ChIP-chip data (Cheng et al. 2008, Zhang et al. 2009), and peaks of occupancy by TAL1 based on ChIP-seq data (Dogan et al. 2015). The coverage of the genome by this track is not comprehensive, but rather it has rich information for a subset of genomic loci that have been studied experimentally.
The genomic intervals tested for enhancer activity are shown as rectangles colored by the result of the assay, with red indicating the activity exceeded the threshold for calling an enhancer, orange indicating that the activity was close to the threshold, and blue for not showing enhancer activity in the assay. In pack mode, the tested intervals are shown as rectangles with the name of the element. Some of these names reflect the information used in the prediction, e.g. GHPx means "GATA1 hit positive number x" from the GATA1 ChIP-chip data (Cheng et al. 2009) and "MACS_peak_1494" indicates that the interval was called by the program MACS as a peak of TAL1 occupancy based on ChIP-seq data along with the number of the peak. In dense mode, only the colored rectangles are shown.
The enhancer assays using reporter gene constructs from the Hardison lab used transient transfections of plasmid constructs into K562 cells (Wang et al. 2006, Cheng et al. 2008, Zhang et al. 2009, Dogan et al. 2015) or directed integration into a site close the Tal1 gene in MEL cells (Wang et al. 2006).
Nergiz Dogan and Ross Hardison compiled the data. Belinda Giardine generated the track and developed the track hub.
Cheng Y, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC. Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res. 2008 Dec;18(12):1896-905. doi: 10.1101/gr.083089.108. Epub 2008 Sep 25. PMID: 18818370; PMCID: PMC2593580.
Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin. 2015 Apr 23;8:16. doi: 10.1186/s13072-015-0009-5. PMID: 25984238; PMCID: PMC4432502.
Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC. Experimental validation of predicted mammalian erythroid cis- regulatory modules. Genome Res. 2006 Dec;16(12):1480-92. doi: 10.1101/gr.5353806. Epub 2006 Oct 12. PMID: 17038566; PMCID: PMC1665632.
Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC. Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Res. 2009 Nov;37(21):7024-38. doi: 10.1093/nar/gkp747. PMID: 19767611; PMCID: PMC2790884.
These data are available for use without restrictions.
Ross Hardison rch8@psu.edu