Description

Functional Assays
This super track groups tracks displaying results from experimental assays of cis-regulatory element function in mouse hematopoietic cells, compiled as part of the VISION project (ValIdated Systematic IntegratiON of hematopoietic epigenomes).

This super track contains the following tracks:

Tested enhancers

Mouse genomic intervals predicted to be cis-regulatory elements that were tested experimentally for enhancer activity using reporter gene constructs. Predictions were based on Regulatory Potential scores from machine learning of genomic DNA sequence alignments, peaks of GATA1 occupancy from ChIP-chip data, and peaks of TAL1 occupancy from ChIP-seq data. Elements are colored by assay result: red for enhancers, orange for threshold activity, and blue for no enhancer activity.

Annotated erythroid regulatory elements

Known erythroid regulatory elements (REs) compiled from the literature, including elements verified by transgenic mouse assays, transfections, and directed mutagenesis. This curated set has been maintained and updated since Zhang et al. (2009).

Credits

Ying Zhang, Nergiz Dogan, and Ross Hardison compiled the functional data. Belinda Giardine generated the tracks displayed and developed the track hub.

References

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.

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.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu