YY1 and Lig3 collaboratively regulate ecDNA biogenesis (CUT&Tag)
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ABSTRACT:
PROVIDER: PRJNA1211587 | ENA |
REPOSITORIES: ENA
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Project description:Extrachromosomal DNA (ecDNA) is an important carrier for the amplification of proto-oncogenes. It can not only drive cancer progression by increasing the copy number of oncogenes but also influence the transcriptional regulation of oncogenes by increasing chromatin accessibility and regulating chromatin interactions. Currently, the generation of ecDNA is rather complex and the exact mechanism remains unclear. This study aims to investigate the molecular mechanism underlying the generation of ecDNA in order to identify the targets for ecDNA-targeted drug therapies. We analyzed the chromatin landscape in COLO320-DM and COLO320-HSR cells through CUT&Tag. The results of CUT&Tag for Lig3, the open chromatin marker H3K27ac, and the promoter marker H3K4me3 showed that Lig3 was specifically enriched in the MYC ecDNA amplification regions and bound to a large number of open chromatin regions and promoter regions, indicating that Lig3 may be related to the formation of ecDNA and stably bind to ecDNA, thereby maintaining the integrity of the genes carried by ecDNA. Furthermore, we found that there were a large number of merge peaks between Lig3 and YY1 across the whole genome, which were abundantly occupied at the MYC ecDNA amplification sites. Meanwhile, we observed that in COLO320-DM cells (where oncogenes are amplified in the form of ecDNA), there was a significant enrichment of YY1 in the MYC amplification regions, while in COLO320-HSR cells (where oncogenes are amplified on the homogeneously staining regions, HSR), the peaks of YY1 were significantly decreased. Our data suggest that YY1 is essential for the generation of ecDNA. It forms a complex with Lig3 to jointly regulate the formation of ecDNA, and this complex can be detected as it resides on ecDNA for a relatively long period of time. This may also be related to the stability of ecDNA and its involvement in genomic regulation.
2025-07-25 | GSE287200 | GEO
Project description:YY1 is a widely expressed transcriptional regulatory factor that is overexpressed in various cancer types, promoting the expression of numerous oncogenes and contributing to cancer progression. It has been identified as a significant biomarker of cancer, correlating with poor prognosis in cancer patients. Moreover, YY1 is an essential regulator of DNA looping, preferentially occupying enhancers and promoters. YY1-mediated enhancer-promoter loops participate in various cancer-related biological functions by regulating gene expression. The circular nature of ecDNA suggests that its formation involves a DNA looping process. Notably, in tumor cells, YY1-mediated DNA looping is closely associated with the activation of multiple oncogenes and immunosuppressive genes, resembling the types of genes carried by ecDNA. Therefore, we investigated the link between DNA looping mediated by YY1 and ecDNA generation. We conducted YY1 HiCUT in COLO320-DM/HSR cells. We found that in COLO320-DM cells, a large number of YY1-mediated loops were located in the MYC amplification region, while only 1% of these loops were observed in the same region in COLO320-HSR cells. The result indicates YY1 mediates DNA looping through dimerization in cells has potential correlation with ecDNA biogenesis.
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Project description:To map the chromatin binding sites for SMC1 in OE19 cells, we performed CUT&TAG.
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Project description:To map the chromatin binding sites for various factors in OE19 cells, we performed CUT&TAG.
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Project description:YY1-mediated DNA looping promotes the generation of ecDNA (HiCUT)
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Project description:We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.
2024-09-06 | GSE249799 | GEO