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Studies in recent years have shown that extrachromosomal circular DNA (ecDNA) can promote the amplification of oncogenes, drive tumor evolution, and has genetic heterogeneity, which plays a key role in the occurrence of cancer [1,2,3,4]

Current research mainly uses copy number variation (such as Amplicon Architect) [5] and identifying ecDNA junction sites (such as Circle-Map and CIRC_finder) [6,7] to identify ecDNA from sequencing data

When using traditional ATAC-Seq and Chip-Seq methods for ecDNA research, DNA must be interrupted and short-sequence sequenced.

Based on the above, Dr.

01.

In this study, m6A MTase methyltransferase was used to process genomic DNA to obtain m6A DNA methylation modifications in open regions of chromatin at the single-molecule level (Figure 1A)

Figure 2 M6A methylation probability distribution of treated and untreated samples

Figure 3 Chromatin accessibility of highly expressed genes around the transcription start site

Figure 4 The distribution of CCDA-seq signal and DNase-seq chromatin accessibility signal on the genome

Figure 5 Length distribution of ONT reads

Figure 6 Methylation rate density distribution in ecDNA and linear DNA

Figure 7 The average methylation rate of gene regions on ecDNA and linear DNA

Figure 8 The signal value distribution of ecDNA and linear DNA upstream and downstream of transcription start site and transcription termination site

Figure 9 Complete ecDNA

Figure 10 Gene ontology analysis of ecDNA-related genes

CCDA-seq provides the chromatin state of several thousand bases in single molecule resolution.

Next, the co-accessibility mode of ecDNA and linear genomic DNA was studied by evaluating the correlation of nucleosome positioning.

Figure 11 Chromatin signal distribution at the single-molecule level of linear DNA and ecDNA

Figure 12 Overview of chromatin co-accessibility between linear DNA and ecDNA (chr16:46407201-46410201)

02.

In general, using CCDA-seq, we observed the diversity of ecDNA in the open chromatin region, localized the distribution of nucleosomes on a length scale of several thousand bases, and quantified the distribution of distal regulatory elements at single-molecule resolution.
The correlation of chromatin states reveals the different chromatin states of single-molecule linear DNA and ecDNA
.
CCDA-seq helps to understand the regulation of ecDNA epigenome more comprehensively, and provides insights into the unique mechanism of ecDNA regulation
.

Literature link:
https://epigeneticsandchromatin.
biomedcentral.
com/articles/10.
1186/s13072-021-00416-5

references

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Circular ecDNA promotes accessible chromatin and high oncogene expression.
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Kumar P, Kiran S, Saha S, Su Z, Paulsen T, Chatrath A, et al.
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8.
Lee I, Razaghi R, Gilpatrick T, Molnar M, Gershman A, Sadowski N, et al.
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