Detection and characterization of jagged ends of double-stranded DNA in plasma

Abstract

Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to the emerging field of cell-free DNA fragmentomics. However, one aspect of plasma DNA fragmentomics as to whether double-stranded plasma molecules might carry single-stranded ends, termed a jagged end in this study, remains underexplored. We have developed two approaches for investigating the presence of jagged ends in a plasma DNA pool. These approaches utilized DNA end repair to introduce differential methylation signals between the original sequence and the jagged ends, depending on whether unmethylated or methylated cytosines were used in the DNA end-repair procedure. The majority of plasma DNA molecules (87.8%) were found to bear jagged ends. The jaggedness varied according to plasma DNA fragment sizes and appeared to be in association with nucleosomal patterns. In the plasma of pregnant women, the jaggedness of fetal DNA molecules was higher than that of the maternal counterparts. The jaggedness of plasma DNA correlated with the fetal DNA fraction. Similarly, in the plasma of cancer patients, tumor-derived DNA molecules in patients with hepatocellular carcinoma showed an elevated jaggedness compared with nontumoral DNA. In mouse models, knocking out of the Dnase1 gene reduced jaggedness, whereas knocking out of the Dnase1l3 gene enhanced jaggedness. Hence, plasma DNA jagged ends represent an intrinsic property of plasma DNA and provide a link between nuclease activities and the fragmentation of plasma DNA.

Fetal mitochondrial DNA in maternal plasma in surrogate pregnancies: Detection and topology

“…For example, one may focus on enriching the linear mtDNA molecules. Our research group is currently studying many other fragmentation features of cell‐free fetal DNA 2,26,27 . Some of these features are more pronounced among the fetal nuclear DNA than the maternal nuclear DNA.…”

“…Our research group is currently studying many other fragmentation features of cell-free fetal DNA. 2,26,27 Some of these features are more pronounced among the fetal nuclear DNA than the maternal nuclear DNA. If such additional features are identified for placental mtDNA, even more specific assays could be devel-…”

Genetic-epigenetic tissue mapping for plasma DNA: applications in prenatal testing, transplantation and oncology

“…There has been increasing interests in the tissue composition circulating cell-free DNA. Methods based on analysis of DNA methylation (Gai et al, 2018; Lehmann-Werman et al, 2016; Sun et al, 2015), nucleosome footprint (Snyder et al, 2016; Sun et al, 2019), sequence motifs, end coordinates and jaggedness (Chan et al, 2016; Jiang et al, 2018; Jiang, Sun, et al, 2020; Jiang, Xie, et al, 2020) have been developed. However, existing methods only allow the deconvolution of all the DNA as a single entity.…”

“…To overcome this, recent efforts have been made to measure the composition of DNA using epigenetic approaches. These approaches include methylation deconvolution (Moss et al, 2018; Sun et al, 2015), mapping nucleosomal patterns (Snyder et al, 2016; Sun et al, 2019), analysis of end DNA motifs, end positions and jaggedness (Chan et al, 2016; Jiang et al, 2018; Jiang, Sun, et al, 2020; Jiang, Xie, et al, 2020), and the profiling of RNA transcripts (Koh et al, 2014; Tsui et al, 2014). In these methods, the features of interest, e.g.…”

Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology

“…To overcome this, recent efforts have been made to measure the composition of DNA using epigenetic approaches. These approaches include methylation deconvolution ( Moss et al, 2018 ; Sun et al, 2015 ), mapping nucleosomal patterns ( Snyder et al, 2016 ; Sun et al, 2019 ), analysis of end DNA motifs, end positions and jaggedness ( Chan et al, 2016 ; Jiang et al, 2018 ; Jiang et al, 2020b ; Jiang et al, 2020a ), and the profiling of RNA transcripts ( Koh et al, 2014 ; Tsui et al, 2014 ). In these methods, the features of interest, for example, methylation patterns, of the plasma DNA were profiled and compared with those of the candidate tissues.…”