TY - JOUR
T1 - ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation
AU - Thompson, Joyce J.
AU - Kaur, Rupinder
AU - Sosa, Carlos P.
AU - Lee, Jeong Heon
AU - Kashiwagi, Katsunobu
AU - Zhou, Dan
AU - Robertson, Keith D.
N1 - Funding Information:
We are grateful to the University of Minnesota Genomics Core for running the RNA-seq and IlluminaMethylation BeadChip EPIC arrays, and the Mayo Clinic Medical Genomic Facility for deep sequencing of ChIP samples. We thank Yuichi Machida for the FLAG-lentiviral vectors and Reeja Maskey for advice on lentiviral experiments. We also thank Bonnie Alver and Ryan Hlady for advice on bioinformatics analyses, and Martin Fernandez-Zapico and Stephanie Safgren for advice on luciferase assays. National Institutes of Health [CA114229 to KDR]; Mayo Clinic Center for Individualized Medicine Epigenomics Program. Funding for open access charge: National Institutes of Health.
Funding Information:
Three of the BTB-family members function as established readers of DNA methylation and coordinate with histone modifying enzymes to bring about changes in transcription. In this study, our data do not support a role for ZBTB24 as a 5mC reader, although we did observe genome-wide loss of DNA methylation resulting from ZBTB24 depletion. Our finding that ZBTB24 co-immunoprecipitates with DNMT3B led us to ask whether ZBTB24 coordinates with DNMT3B in some way to maintain DNA methylation. We indeed observed co-binding of ZBTB24 and DNMT3B at a subset of genes involved in general cellular maintenance; loss of function of either of the factors deregulated gene body methylation suggestive of a coordinated role between the two factors. The mechanism by which the two proteins coordinate to achieve this function remains unknown, however, we hypothesize that promoter-bound ZBTB24 recruits DNMT3B to gene bodies of their target loci and thus acts as a loading factor. This hypothesis is supported by our observation of reduced DNMT3B occupancy resulting from ZBTB24 depletion, within bodies of genes bound by ZBTB24 and DNMT3B (Supplementary Figure S6L). DNA sequences can form loops bringing promoters, enhancers, and downstream exons in close proximity in three-dimensional space (66). CTCF, in addition to mediating long-range chromosomal interactions, also mediates promoter-exon interactions that direct splicing (67). Defects in splicing have been reported in ICF1 patients with DNMT3B mutations and in Dnmt3b-/- mES cells. Therefore, an alternative mechanism that ZBTB24 and DNMT3B may coordinate their activities is through regulation of interactions within transcription units to modulate expression, intra-domain communication, or alternative mRNA splicing.
Publisher Copyright:
© The Author(s) 2018.
PY - 2018/11/2
Y1 - 2018/11/2
N2 - The interplay between transcription factors and epigenetic writers like the DNA methyltransferases (DNMTs), and the role of this interplay in gene expression, is being increasingly appreciated. ZBTB24, a poorly characterized zinc-finger protein, or the de novo methyltransferase DNMT3B, when mutated, cause Immunodeficiency, Centromere Instability, and Facial anomalies (ICF) syndrome, suggesting an underlying mechanistic link. Chromatin immunoprecipitation coupled with loss-of-function approaches in model systems revealed common loci bound by ZBTB24 and DNMT3B, where they function to regulate gene body methylation. Genes coordinately regulated by ZBTB24 and DNMT3B are enriched for molecular mechanisms essential for cellular homeostasis, highlighting the importance of the ZBTB24-DNMT3B interplay in maintaining epigenetic patterns required for normal cellular function. We identify a ZBTB24 DNA binding motif, which is contained within the promoters of most of its transcriptional targets, including CDCA7, AXIN2, and OSTC. Direct binding of ZBTB24 at the promoters of these genes targets them for transcriptional activation. ZBTB24 binding at the promoters of RNF169 and CAMKMT, however, targets them for transcriptional repression. The involvement of ZBTB24 targets in diverse cellular programs, including the VDR/RXR and interferon regulatory pathways, suggest that ZBTB24’s role as a transcriptional regulator is not restricted to immune cells.
AB - The interplay between transcription factors and epigenetic writers like the DNA methyltransferases (DNMTs), and the role of this interplay in gene expression, is being increasingly appreciated. ZBTB24, a poorly characterized zinc-finger protein, or the de novo methyltransferase DNMT3B, when mutated, cause Immunodeficiency, Centromere Instability, and Facial anomalies (ICF) syndrome, suggesting an underlying mechanistic link. Chromatin immunoprecipitation coupled with loss-of-function approaches in model systems revealed common loci bound by ZBTB24 and DNMT3B, where they function to regulate gene body methylation. Genes coordinately regulated by ZBTB24 and DNMT3B are enriched for molecular mechanisms essential for cellular homeostasis, highlighting the importance of the ZBTB24-DNMT3B interplay in maintaining epigenetic patterns required for normal cellular function. We identify a ZBTB24 DNA binding motif, which is contained within the promoters of most of its transcriptional targets, including CDCA7, AXIN2, and OSTC. Direct binding of ZBTB24 at the promoters of these genes targets them for transcriptional activation. ZBTB24 binding at the promoters of RNF169 and CAMKMT, however, targets them for transcriptional repression. The involvement of ZBTB24 targets in diverse cellular programs, including the VDR/RXR and interferon regulatory pathways, suggest that ZBTB24’s role as a transcriptional regulator is not restricted to immune cells.
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U2 - 10.1093/nar/gky682
DO - 10.1093/nar/gky682
M3 - Article
C2 - 30085123
AN - SCOPUS:85056256717
SN - 0305-1048
VL - 46
SP - 10034
EP - 10051
JO - Nucleic acids research
JF - Nucleic acids research
IS - 19
ER -