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Updated: Jun 4, 2025
Comparing Metastatic Clear Cell Renal Cell Carcinoma Model Established in Mouse Kidney and on Chicken Chorioallantoic Membrane
Published on: February 8, 2020
Dissecting the Kaiso binding profile in clear renal cancer cells
Alexey Starshin1, Pavel Abramov1, Yaroslava Lobanova1
1Federal Research Centre, Fundamentals of Biotechnology», Russian Academy of Sciences, 119071, Moscow, Russia.
Background:
There has been a notable increase in interest in the transcriptional regulator Kaiso, which has been linked to the regulation of clonal hematopoiesis, myelodysplastic syndrome, and tumorigenesis. Nevertheless, there are no consistent data on the binding sites of Kaiso in vivo in the genome. Previous ChIP-seq analyses for Kaiso contradicted the accumulated data of Kaiso binding sites obtained in vitro. Here, we studied this discrepancy by characterizing the distribution profile of Kaiso binding sites in Caki-1 cells using Kaiso-deficient cells as a negative control, and compared its pattern on chromatin with that in lymphoblastoid cell lines.
Results:
We employed Caki-1 kidney carcinoma cells and their derivative, which lacks the Kaiso gene, as a model system to identify the genomic targets of Kaiso. The principal binding motifs for Kaiso are CGCG and CTGCNAT, with 60% of all binding sites containing both sequences. The significance of methyl-DNA binding activity was confirmed through examination of the genomic distribution of the E535A mutant variant of Kaiso, which cannot bind methylated DNA in vitro but is able to interact with CTGCNA sequences. Our findings indicate that Kaiso is present at CpG islands with a preference for methylated ones. We identified Kaiso target genes whose methylation and transcription are dependent on its expression. Furthermore, Kaiso binding sites are enriched at CpG islands, with partial methylation at the 5' and/or 3' boundaries. We discovered CpG islands exhibiting wave-like methylation patterns, with Kaiso detected in the majority of these areas. Similar data were obtained in other cell lines.
Conclusion:
The present study delineates the genomic distribution of Kaiso in cancer cells, confirming its role as a factor with a complex mode of DNA binding and a strong association with CpG islands, particularly with methylated and eroded CpG islands, revealing a new potential Kaiso target gene-SQSTM1, involved in differentiation of acute myeloid leukemia cells. Furthermore, we discovered the existence of a new class of CpG islands characterized by wave-like DNA methylation.
Insights
Kaiso, a transcriptional regulator, binds to methylated CpG islands in cancer cells, influencing gene expression and revealing novel methylation patterns. This research clarifies Kaiso
Area of Science:
- Molecular Biology
- Epigenetics
- Cancer Research
Background:
- Kaiso is a transcriptional regulator implicated in clonal hematopoiesis, myelodysplastic syndrome, and tumorigenesis.
- Previous studies showed discrepancies between in vitro and in vivo Kaiso binding site data.
- The genomic distribution of Kaiso binding sites requires clarification.
Purpose of the Study:
- To characterize the genomic distribution of Kaiso binding sites in cancer cells.
- To resolve discrepancies in Kaiso binding site data between in vitro and in vivo studies.
- To identify novel Kaiso target genes and understand its role in DNA methylation.
Main Methods:
- Utilized Kaiso-deficient Caki-1 kidney carcinoma cells and their wild-type counterparts.
- Employed ChIP-seq to map Kaiso binding sites on chromatin.
- Analyzed Kaiso binding motifs and DNA methylation status at binding sites.
Main Results:
- Identified CGCG and CTGCNAT as principal Kaiso binding motifs.
- Kaiso preferentially binds to methylated CpG islands, including those with wave-like methylation patterns.
- Discovered Kaiso target genes whose methylation and transcription are dependent on Kaiso expression, including SQSTM1.
Conclusions:
- Kaiso exhibits complex DNA binding, strongly associating with methylated and eroded CpG islands.
- Revealed a novel class of CpG islands characterized by wave-like DNA methylation.
- Identified SQSTM1 as a potential new Kaiso target gene involved in acute myeloid leukemia cell differentiation.
