Dataset Information

Kaiso engages with non-canonical binding motifs to regulate DNA damage responses in breast cancer

ABSTRACT: In breast cancer, nuclear localization of Kaiso (ZBTB33), a bimodal DNA binding factor, is a hallmark of high grade ductal-type carcinomas, especially in estrogen receptor negative disease. Regulation of gene expression by Kaiso is orchestrated via its engagement to distinct Kaiso binding sequence (KBS) motifs that either be canonical (cKBS; TCCTGCNA) or CG-containing palindromic KBS (CG-KBS; TCTCGCGAGA), depending on context. While clinical connection of Kaiso to breast cancer exists, it remains unclear how Kaiso controls bi-modal canonical versus noncanonical transcriptional modulation. Here, we have combined Kaiso-specific chromatin immunoprecipitation (ChIP) and Kaiso-Dam methyltransferase identification (Dam-ID) approaches to map genomic Kaiso binding sites in breast cancer cells. We find that Kaiso mostly occupies the non-canonical CG-KBS sites in transcriptionally active and hypo-methylated (H3K4me3 and H3K27Ac enriched) promoter regions. Noncanonical CG-KBS targets are actively transcribed and linked to fast biological processes such as metabolism, cell cycle regulation and DNA damage repair. Functionally, we show that Kaiso expression is essential to prevent DNA damage in breast cancer cells. Loss of Kaiso leads to reduced levels of DNA damage response gene expression. Treatment with the chemotherapeutic agent cisplatin leads to overt accumulation of DNA damage in cells devoid of Kaiso. Our data thus favor a model in which Kaiso promotes fast transcriptional activation of key cellular processes in cancer cells through binding of its non-canonical consensus site.

ORGANISM(S): Mus musculus

PROVIDER: GSE309273 | GEO | 2026/09/01

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. The second contained 180,000 features with each CG containing 8-mer present three times. The first design was better for identification of binding motifs, while the second was better for quantification. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. This methodology can be used to identify new methylated DNA sequences preferentially bound by TF, which may be functional in vivo. To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. The second contained 180,000 features with each CG containing 8-mer present three times. The first design was better for identification of binding motifs, while the second was better for quantification. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. This methodology can be used to identify new methylated DNA sequences preferentially bound by TF, which may be functional in vivo. Protein binding microarray (PBM) experiments were performed for a set of 8 mouse B-ZIP homodimers and one hetrodimer transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded and methylated or unmethylated 44K Agilent microarrays, containing a DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

Dataset Information

Kaiso engages with non-canonical binding motifs to regulate DNA damage responses in breast cancer

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets