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Nuclease deficiencies alter plasma cell-free DNA methylation profiles
Diana S C Han1,2, Meng Ni1,2, Rebecca W Y Chan1,2
1Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
Abstract:
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.
Insights
Cell-free DNA (cfDNA) methylation is significantly impacted by DNASE1L3 and DNASE1 nucleases. DNASE1L3 deficiency causes hypomethylation, while DNASE1 deficiency leads to hypermethylation in cfDNA.
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- Cell-free DNA (cfDNA) methylation patterns are crucial biomarkers.
- The role of specific nucleases, DNASE1-like 3 (DNASE1L3) and DNASE1, in shaping cfDNA methylation is not fully understood.
Purpose of the Study:
- To investigate how DNASE1L3 and DNASE1 deficiencies affect cfDNA methylation profiles.
- To elucidate the mechanisms by which these nucleases influence cfDNA fragmentation and methylation.
Main Methods:
- Analysis of cfDNA methylation in plasma from DNASE1L3-deficient and DNASE1-deficient mice.
- Comparison with cfDNA from DNASE1L3-deficient human subjects.
- Assessment of cfDNA fragmentation patterns and representation from open chromatin regions (OCRs) and CpG islands (CGIs).
Main Results:
- DNASE1L3 deficiency resulted in significantly hypomethylated cfDNA due to increased fragmentation from open chromatin regions and CpG islands.
- DNASE1 deficiency led to hypermethylated cfDNA, with DNASE1 showing a preference for cleaving hypomethylated regions.
- DNASE1L3 demonstrated a preference for cleaving methylated CpGs, and cfDNA methylation varied periodically with fragment size.
Conclusions:
- Nuclease activity, particularly DNASE1L3 and DNASE1, profoundly influences genome-wide cfDNA methylation levels.
- Understanding nuclease-mediated cfDNA fragmentation is fundamental to interpreting epigenetic information in cfDNA.
- This study establishes a foundational link between DNA methylation, nuclease biology, and cfDNA fragmentation patterns.
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