ZBTB33 (Kaiso) methylated binding sites are associated with primed heterochromatin

Abstract

Background: ZBTB33, also known as Kaiso, is a member of the zinc finger and BTB/POZ family. In contrast to many transcription factors, ZBTB33 has the ability to bind both a sequence-specific consensus and methylated DNA. Although these dual binding preferences enable ZBTB33 to function as an active as well as repressive regulator of gene expression, little is known about the underlining molecular mechanisms. Results: In this study, we aimed to investigate the role of ZBTB33 as a methylated DNA binding factor. We took advantage of the latest releases of the ENCODE sequencing datasets, including ZBTB33 ChIPseq, whole genome bisulfite sequencing (WGBS), histone mark ChIP-seq and sequencing assays determining the chromatin states, to characterize the chromatin landscapes surrounding methylated ZBTB33 binding sites. Interestingly, our integrative analyses demonstrated that the majority of methylated ZBTB33 binding sites were located within condensed chromatin, which are inaccessible to DNase I and Tn5 transposase. Moreover, these sites were carrying a newly revealed histone post-translational modification signature, with significant enrichment of mono-methylation at lysine 4 of histone 3 (H3K4me1) and a complete absence of other active or expected repressive histone marks. Conclusions: Overall, our analyses revealed that ZBTB33 has the unique ability to bind methylated DNA across heterochromatin in a transition state, suggesting a potential role for ZBTB33 in heterochromatin priming. KeywordsKaiso, DNA methylation, H3K4me1, primed heterochromatin 3 Background ZBTB33, also known as Kaiso, is a member of the zinc finger and BTB/POZ family. Similar to DNA (cytosine-5)-methyltransferase 1 (DNMT1) depletion, ZBTB33 knockdown phenotypes in Xenopus embryos include precocious activation of gene expression, apoptosis and developmental arrest [1].Likewise, ZBTB33 depletion in the K562 cell line inhibits granulocyte differentiation and promotes cell proliferation [2]. In mammals, though, ZBTB33-knockout mice lack any significant phenotypes [3,4]; the depletion of ZBTB33 leads to intestinal tumorigenesis resistance [3], splenomegaly [4], increased locomotion and reduced volume of the lateral ventricles [5].Like other BTB/POZ proteins, ZBTB33 forms a homodimer or heterodimer via its highly conserved BTB/POZ domains [6,7]. In contrast to many transcription factors, ZBTB33 has the ability to bind both a sequence-specific consensus and methylated DNA [8,9], which allows ZBTB33 to act as an activator or repressor of gene expression. In many types of cancer cells, ZBTB33 methyl-CpG-dependent binding events in the proximal promoters of essential tumor suppressor genes, such as Cyclin-dependent kinase inhibitor 2a (Cdk2a), Hypermethylated in cancer 1 (H1c1) and O-6-methylguanine-DNA methyltransferase (Mgmt) [10], are associated with repressive regulation, suggesting a crucial role in tumorigenesis. Further, ZBTB33 binding activity within the methylated promoter of E-cadherin is associated with E-cadherin silencing and an increase in canc...

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