PT  - JOURNAL ARTICLE
AU  - Quy Xiao Xuan Lin
AU  - Khadija Rebbani
AU  - Sudhakar Jha
AU  - Touati Benoukraf
TI  - ZBTB33 (Kaiso) methylated binding sites are associated with primed heterochromatin
AID  - 10.1101/585653
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 585653
4099  - http://biorxiv.org/content/early/2019/03/24/585653.short
4100  - http://biorxiv.org/content/early/2019/03/24/585653.full
AB  - 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 ChIP- seq, 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.WGBSwhole genome bisulfite sequencing5-aza-dC5-aza-2’-deoxycytidineRRBSreduced representation bisulfite sequencingGOgene ontologyGREATthe genomic regions enrichment of annotation toolFAIRE-seqformaldehyde-assisted isolation of regulatory element sequencingDNase-seqDNase I hypersensitive site sequencingATAC-seqassay for transposase-accessible chromatin sequencingIDRirreproducible discovery ratePSWMposition-specific weight matrix