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

Mikhail G Dozmorov; Wancen Mu; Eric S Davis; Stuart Lee; Timothy J Triche Jr; Douglas H Phanstiel; Michael I Love

doi:10.1093/bioadv/vbac097

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

Bioinform Adv. 2022 Dec 16;2(1):vbac097. doi: 10.1093/bioadv/vbac097. eCollection 2022.

Authors

Mikhail G Dozmorov^{1

2}, Wancen Mu³, Eric S Davis⁴, Stuart Lee^{5

6}, Timothy J Triche Jr^{7

8

9}, Douglas H Phanstiel^{4

10

11

12

13}, Michael I Love^{3

14}

Affiliations

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

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.