Description

Candidate cis-regulatory elements (cCREs)
This super track groups tracks related to candidate cis-regulatory elements (cCREs) identified in mouse blood cell types as part of the VISION project (ValIdated Systematic IntegratiON of hematopoietic epigenomes). The cCREs were defined as DNA intervals with a high signal for chromatin accessibility (ATAC-seq) in any blood cell type, as determined by peak calling using the IDEAS method in the IS mode (Xiang et al. 2020 and 2024).

This super track contains the following composite tracks:

cCREs

A compilation of all cCREs discovered in mouse blood cell types from the joint human-mouse IDEAS segmentation with 25 states, annotated with evolutionary categories (conserved in both sequence and inferred function, conserved in sequence only, or nonconserved) and joint metacluster (JmC) assignments that group cCREs with similar activity profiles across blood cell types in human and mouse.

cCREs with state

The cCREs colored by the dominant epigenetic state found in each cCRE in each cell type, as determined by the joint human-mouse IDEAS segmentation with 25 epigenetic states.

Methods

The cCREs were identified using IDEAS in the IS mode for peak calling on chromatin accessibility data (Xiang et al. 2021 and 2024). The epigenetic signals used as input were normalized across cell types using the S3V2 version of S3norm (Xiang et al. 2020). Evolutionary categories were assigned by evaluating sequence conservation and conservation of inferred function between human and mouse using the liftOver tool (Xiang et al. 2024). Joint metaclusters were determined by clustering cCREs based on epigenetic state Regulatory Potential (esRP) scores across blood cell types shared by human and mouse.

Credits

The data normalization, peak calls using IDEAS in the IS mode, and generation of the joint metaclusters were done by Guanjue Xiang. Xi He assigned cCREs to the evolutionary categories. The data downloads, re-mapping and processing, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine.

References

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, Keller CA, Giardine B, An L, Li Q, Zhang Y, Hardison RC. S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data. Nucleic Acids Res. 2020 May 7;48(8):e43. doi:10.1093/nar/gkaa105. PMID: 32086521; PMCID: PMC7192629.

Xiang G, Giardine BM, Mahony S, Zhang Y, Hardison RC. S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. Bioinformatics. 2021 Sep 29;37(18):3011-3013. doi:10.1093/bioinformatics/btab148. PMID: 33681991; PMCID: PMC8479670.

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.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu