Starshin Alexey, Abramov Pavel, Lobanova Yaroslava, Sharko Fedor, Filonova Galina, Kaluzhny Dmitry, Kaplun Daria, Deyev Igor, Mazur Alexander, Prokhortchou Egor, Zhenilo Svetlana
Federal Research Centre, Fundamentals of Biotechnology», Russian Academy of Sciences, 119071, Moscow, Russia.
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia.
Epigenetics Chromatin. 2024 Dec 19;17(1):38. doi: 10.1186/s13072-024-00565-3.
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.
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.
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.
转录调节因子Kaiso引发的关注显著增加，它与克隆性造血、骨髓增生异常综合征及肿瘤发生的调控相关。然而，关于Kaiso在体内基因组中的结合位点，尚无一致的数据。先前针对Kaiso的染色质免疫沉淀测序（ChIP-seq）分析与体外获得的Kaiso结合位点累积数据相矛盾。在此，我们以缺乏Kaiso的细胞作为阴性对照，通过表征Caki-1细胞中Kaiso结合位点的分布概况来研究这一差异，并将其在染色质上的模式与淋巴母细胞系中的模式进行比较。
我们采用Caki-1肾癌细胞及其缺乏Kaiso基因的衍生物作为模型系统，以鉴定Kaiso的基因组靶点。Kaiso的主要结合基序是CGCG和CTGCNAT，所有结合位点中有60%包含这两个序列。通过检测Kaiso的E535A突变体变体的基因组分布，证实了甲基化DNA结合活性的重要性，该突变体在体外不能结合甲基化DNA，但能够与CTGCNA序列相互作用。我们的研究结果表明，Kaiso存在于CpG岛，且更倾向于甲基化的CpG岛。我们鉴定出其甲基化和转录依赖于其表达的Kaiso靶基因。此外，Kaiso结合位点在CpG岛富集，在5'和/或3'边界存在部分甲基化。我们发现了呈现波浪状甲基化模式的CpG岛，在这些区域的大多数中检测到Kaiso。在其他细胞系中也获得了类似的数据。
本研究描绘了Kaiso在癌细胞中的基因组分布，证实了其作为一种具有复杂DNA结合模式且与CpG岛，特别是与甲基化和侵蚀的CpG岛密切相关的因子的作用，揭示了一个新的潜在Kaiso靶基因——SQSTM1，其参与急性髓系白血病细胞的分化。此外，我们发现了一类以波浪状DNA甲基化为特征的新型CpG岛的存在。
