This track displays mouse genomic intervals that have been reported in the literature as erythroid regulatory elements (REs), which are also called cis-regulatory elements (CREs). This list has been compiled and updated since it was first used in Zhang et al. (2009). It contains all the elements tested and found to be positive in enhancer reporter assays in the Hardison lab (see the companion Tested enhancers track) plus many additional elements gleaned from the literature. The table of REs along with coordinates and literature citations have been provided as Supplemental Information in publications such as Xiang et al. (2020 and 2024). 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 intensively studied experimentally.
In pack mode, the REs are shown as purple rectangles with the name of the element, in a format like GeneName_ElementNumber. In dense mode, only the purple 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). Other REs gleaned from the literature used a wide range of methods, including transgenic mice assays, transfections, and directed mutagenesis.
Ying Zhang, 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.
Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res. 2020 Mar;30(3):472-484. PMID: 32132109; PMCID: PMC7111515.
Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024 Aug 20;34(7):1089-1105. PMID: 38951027; PMCID: PMC11368181.
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