Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA

Abstract

SignificanceCirculating DNA in plasma has many diagnostic applications, including noninvasive prenatal testing and cancer liquid biopsy. Plasma DNA consists of short fragments of DNA. However, there is little information about mechanisms that are involved in the fragmentation of plasma DNA. We showed that mice in which Dnase1l3 had been deleted showed aberrations in the fragmentation of plasma DNA. We also observed a change in the ranked frequencies of end motifs of plasma DNA caused by the Dnase1l3 deletion. In Dnase1l3−/− mice pregnant with Dnase1l3+/− fetuses, we observed a partial reversal of the plasma DNA aberrations. This study has thus linked the fields of nuclease biology and circulating nucleic acids and has opened up avenues for future research.

The Biology of Cell-free DNA Fragmentation and the Roles of DNASE1, DNASE1L3, and DFFB

“…Furthermore, previous work using plasma DNA sequenced using the Pacific Bioscience Single Molecule, Real-Time (SMRT) system indicated that fragments in the 600 to 2,000 bp range accounted for less than 4.8% of the cf.DNA population. 9 Paired-end reads sharing the same start and end genomic coordinates were deemed PCR duplicates and were discarded from downstream analysis. Table S1 summarizes the number of nonduplicate fragments obtained for each condition.…”

“…This clear preference for C-ends in all sizes of circulating cf.DNA fragments, as seen in Figure 3, suggests the presence of a nuclease that prefers to cleave 5 0 to a C. Previously, we had demonstrated that cf.DNA from WT mice had a high frequency of fragments ending in CCNN motifs (i.e., motifs consisting of two consecutive cytosines, followed by two nucleotides of any type) and that this preference for CCNN motifs in cf.DNA fragment ends was reduced in Dnase1l3-deficient mice. 9 Because C-end fragments are comprised of CCNN end motifs, we hypothesized that the nuclease responsible for the C-end preference might also be DNASE1L3.…”

“…[4][5][6][7][8] Previously, we have demonstrated that the DNASE1L3 nuclease contributes to the size profile of cf.DNA in plasma. 9 In this study, we aimed to investigate the respective roles of DNASE1, DNASE1L3, and DNA fragmentation factor subunit beta (DFFB, also known as caspase-activated DNase) in cf.DNA fragmentation. We compared the cf.DNA profiles between mice deficient in each type of nuclease and their wildtype (WT) counterparts.…”

Identification and characterization of extrachromosomal circular DNA in maternal plasma

“…eccDNA | cell-free DNA | noninvasive prenatal testing | plasma DNA topologics T he fragmentation patterns of cell-free DNA (cfDNA) in human plasma is an area of intense research interest (1)(2)(3)(4). Recent studies on the size distributions (1), end locations (5), and end motifs (3) revealed that these fragmentation patterns in cfDNA bore relationships with their tissues of origin.…”

“…eccDNA | cell-free DNA | noninvasive prenatal testing | plasma DNA topologics T he fragmentation patterns of cell-free DNA (cfDNA) in human plasma is an area of intense research interest (1)(2)(3)(4). Recent studies on the size distributions (1), end locations (5), and end motifs (3) revealed that these fragmentation patterns in cfDNA bore relationships with their tissues of origin. In pregnancy, fetal-derived plasma DNA (mainly of placental origin) were observed to be linear fragments of DNA that were shorter than the maternal-derived (mainly of hematopoietic origin) DNA (1,5,6).…”