The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF

• Published in: The Journal of biological chemistry Vol. 294; no. 37; pp. 13580 - 13592
• Main Authors: Ciccone, David N., Namiki, Yuka, Chen, Changfeng, Morshead, Katrina B., Wood, Andrew L., Johnston, Colette M., Morris, John W., Wang, Yanqun, Sadreyev, Ruslan, Corcoran, Anne E., Matthews, Adam G.W., Oettinger, Marjorie A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 13.09.2019; American Society for Biochemistry and Molecular Biology
• Subjects: adaptive immunity; Adaptive Immunity - genetics; Animals; antigen receptor; Binding Sites; CCCTC-Binding Factor - genetics; CCCTC-Binding Factor - metabolism; CCTC-binding factor (CTCF); cellular immune response; chromatin; Chromatin - genetics; Chromatin - metabolism; chromatin immunoprecipitation (ChIP); chromatin regulation; DNA and Chromosomes; DNA binding; DNA recombination; DNA-Binding Proteins - genetics; Gene Rearrangement; Humans; Immunoglobulin Heavy Chains - genetics; Immunoglobulin Heavy Chains - metabolism; Immunoglobulin Variable Region; K562 Cells; Mice; Mice, Knockout; NIH 3T3 Cells; Nucleotide Motifs; Regulatory Sequences, Nucleic Acid; Repressor Proteins - metabolism; V(D)J; cellular immune response; chromatin regulation; antigen receptor; CCTC-binding factor (CTCF); DNA recombination; chromatin; V(D)J; adaptive immunity; DNA binding; chromatin immunoprecipitation (ChIP)
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.RA118.007348

Antigen receptor assembly in lymphocytes involves stringently-regulated coordination of specific DNA rearrangement events across several large chromosomal domains. Previous studies indicate that transcription factors such as paired box 5 (PAX5), Yin Yang 1 (YY1), and CCCTC-binding factor (CTCF) play a role in regulating the accessibility of the antigen receptor loci to the V(D)J recombinase, which is required for these rearrangements. To gain clues about the role of CTCF binding at the murine immunoglobulin heavy chain (IgH) locus, we utilized a computational approach that identified 144 putative CTCF-binding sites within this locus. We found that these CTCF sites share a consensus motif distinct from other CTCF sites in the mouse genome. Additionally, we could divide these CTCF sites into three categories: intergenic sites remote from any coding element, upstream sites present within 8 kb of the VH-leader exon, and recombination signal sequence (RSS)-associated sites characteristically located at a fixed distance (∼18 bp) downstream of the RSS. We noted that the intergenic and upstream sites are located in the distal portion of the VH locus, whereas the RSS-associated sites are located in the DH-proximal region. Computational analysis indicated that the prevalence of CTCF-binding sites at the IgH locus is evolutionarily conserved. In all species analyzed, these sites exhibit a striking strand-orientation bias, with >98% of the murine sites being present in one orientation with respect to VH gene transcription. Electrophoretic mobility shift and enhancer-blocking assays and ChIP–chip analysis confirmed CTCF binding to these sites both in vitro and in vivo.