Yifan Liu

Structural basis of DNA N6-adenine methylation in eukaryotes

This study determines the structural basis of DNA N6-adenine methylation by modeling the AMT1 complex and validating its function through mutagenesis.

SMAC: identifying DNA N6-methyladenine (6mA) at the single-molecule level using SMRT CCS data

SMAC detects DNA N6-methyladenine at the single-molecule level using SMRT CCS data, improving accuracy over existing methods.

Dual modes of DNA N6-methyladenine maintenance by distinct methyltransferase complexes

The paper identifies two distinct methyltransferase complexes that coordinate to maintain DNA N6-methyladenine (6mA) through different mechanisms during replication and transcription.

Revealing long-range heterogeneous organization of nucleoproteins with N6-methyladenine footprinting

The paper develops a novel 6mA-calling pipeline for SMRT sequencing data, improving accuracy and efficiency, and applies it to map nucleosome positioning and transcription factor occupancy at single-molecule resolution.

Semi-conservative transmission of DNA N6-adenine methylation in a unicellular eukaryote

The paper demonstrates that DNA N6-adenine methylation (6mA) is transmitted semi-conservatively in Tetrahymena thermophila, with AMT1-dependent maintenance and AMT1-independent de novo methylation mechanisms.

Distinct nucleosome distribution patterns in two structurally and functionally differentiated nuclei of a unicellular eukaryote

The paper compares nucleosome distribution patterns between two nuclei in Tetrahymena thermophila, finding distinct positioning in the active MAC and delocalized patterns in the silent MIC.