CTCF: an R/bioconductor data package of human and mouse CTCF binding sites

Author:

Dozmorov Mikhail G12ORCID,Mu Wancen3ORCID,Davis Eric S4ORCID,Lee Stuart56ORCID,Triche Timothy J789ORCID,Phanstiel Douglas H410111213ORCID,Love Michael I314ORCID

Affiliation:

1. Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298, USA

2. Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284, USA

3. Department of Biostatistics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, USA

4. Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA

5. Department of Econometrics and Business Statistics, Monash University , Clayton, NC 3168, Australia

6. Molecular Medicine Division, Walter and Eliza Hall Institute , Parkville, VIC 3052, Australia

7. Center for Epigenetics, Van Andel Research Institute , Grand Rapids, MI 49503, USA

8. Department of Pediatrics, College of Human Medicine, Michigan State University , East Lansing, MI 48824, USA

9. Department of Translational Genomics, Keck School of Medicine, University of Southern California , Los Angeles, CA 90033, USA

10. Thurston Arthritis Research Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA

11. Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA

12. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA

13. Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA

14. Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27514, USA

Abstract

Abstract Summary CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome’s 3D structure and function. The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and predicted CTCF binding sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE. We recommend filtering strategies for CTCF binding motifs and demonstrate that liftOver is a viable alternative to convert CTCF coordinates between assemblies. Our comprehensive data resource and usage recommendations can serve to harmonize and strengthen the reproducibility of genomic studies utilizing CTCF binding data. Availability and implementation https://bioconductor.org/packages/CTCF. Companion website: https://dozmorovlab.github.io/CTCF/; Code to reproduce the analyses: https://github.com/dozmorovlab/CTCF.dev. Supplementary information Supplementary data are available at Bioinformatics Advances online.

Funder

National Institute of Child Health and Human Development

Publisher

Oxford University Press (OUP)

Subject

Cell Biology,Developmental Biology,Embryology,Anatomy

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