RT Journal
A1 Han, Diana S.C.
A1 Ni, Meng
A1 Chan, Rebecca W.Y.
A1 Wong, Danny K.L.
A1 Hiraki, Linda T.
A1 Volpi, Stefano
A1 Jiang, Peiyong
A1 Lui, Kathy O.
A1 Chan, K.C. Allen
A1 Chiu, Rossa W.K.
A1 Lo, Y.M. Dennis
T1 Nuclease deficiencies alter plasma cell-free DNA methylation profiles
JF Genome Research 
JO Genome Research 
YR 2021 
FD November 01 
VO 31 
IS 11 
SP 2008 
OP 2021 
DO 10.1101/gr.275426.121 
UL http://genome.cshlp.org/content/31/11/2008.abstract 
AB The effects of DNASE1L3 or DNASE1 deficiency on cell-free DNA (cfDNA) methylation were explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wild-type cfDNA, cfDNA in DNASE1L3-deficient mice was significantly hypomethylated, while cfDNA in DNASE1-deficient mice was hypermethylated. The cfDNA hypomethylation in DNASE1L3-deficient mice was due to increased fragmentation and representation from open chromatin regions (OCRs) and CpG islands (CGIs). These findings were absent in DNASE1-deficient mice, demonstrating the preference of DNASE1 to cleave in hypomethylated OCRs and CGIs. We also observed a substantial decrease of fragment ends at methylated CpGs in the absence of DNASE1L3, thereby demonstrating that DNASE1L3 prefers to cleave at methylated CpGs. Furthermore, we found that methylation levels of cfDNA varied by fragment size in a periodic pattern, with cfDNA of specific sizes being more hypomethylated and enriched for OCRs and CGIs. These findings were confirmed in DNASE1L3-deficient human cfDNA. Thus, we have found that nuclease-mediated cfDNA fragmentation markedly affects cfDNA methylation level on a genome-wide scale. This work provides a foundational understanding of the relationship between methylation, nuclease biology, and cfDNA fragmentation.