Functional and Epigenomic Consequences of DNMT1 Variants in Inherited Neurological Disorders

Area of Science:

• Genetics and Epigenetics
• Neuroscience
• Molecular Biology

Background:

• DNA methyltransferase 1 (DNMT1) variants are associated with complex neurodegenerative disorders.
• The functional and epigenomic consequences of specific DNMT1 variants are not well understood.

Purpose of the Study:

• To investigate the functional and epigenomic effects of DNMT1 variants identified in patients with neurodegenerative syndromes.
• To characterize the impact of these variants on DNMT1 protein function, cellular localization, and genome-wide DNA methylation patterns.

Main Methods:

• Identified DNMT1 variants in eight patients via gene-panel or whole-exome sequencing.
• Assessed functional effects using site-directed mutagenesis and cell expression studies.
• Performed genome-wide methylation profiling using Nanopore sequencing for direct 5-methylcytosine (5mC) quantification.

Main Results:

• DNMT1 variants in the RFTS domain impaired protein expression, enzymatic activity, and caused cytosolic aggregation.
• C-terminal catalytic domain variants showed reduced protein expression with milder functional impact.
• p.Y511H variant carriers exhibited reduced global 5mC levels and distinct methylomic profiles, with significant heterogeneity observed.

Conclusions:

• DNMT1 variants exhibit domain-dependent functional consequences affecting protein expression and enzymatic activity.
• Nanopore sequencing revealed variant-specific and heterogeneous epigenomic alterations, including global and regional DNA hypomethylation.
• This study provides crucial insights into the molecular mechanisms underlying DNMT1-associated neurodegenerative syndromes.