Heather J Lee

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

The paper examines DNA methylation dynamics in marsupial embryos, finding global demethylation in the trophectoderm but not the embryonic lineage, suggesting 5mC erasure in extraembryonic tissue is ancestral in therian mammals.

Acute testicular hyperthermia leads to a rapid loss of global piRNA levels and a consequent increase in transcript abundance, including LINE1 activity within heat-sensitive male germ cells.

This study shows testicular hyperthermia rapidly reduces piRNA levels and increases LINE1 activity in male germ cells, leading to DNA damage and potential infertility.

Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation

This study shows maternal SMCHD1 is essential for imprinted Xist expression and X chromosome inactivation in mouse embryos and placenta.

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells

The paper introduces scTEM-seq to profile DNA methylation and transcriptomes in single cells, finding DNA methylation heterogeneity linked to gene expression and transposable element activity in AML cells.

Smchd1 is a maternal effect gene required for autosomal imprinting

This study identifies Smchd1 as a maternal effect gene that regulates imprinted expression of 16 genes by translating polycomb-mediated histone methylation marks into a heritable chromatin state.

Genome-scale oscillations in DNA methylation during exit from pluripotency

The paper shows that during exit from pluripotency, coexpression of DNMT3s and TETs drives genome-scale DNA methylation oscillations, with amplitude dependent on CpG density, observed both in vitro and in vivo.

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

This paper introduces scNMT-seq, a method for joint profiling of chromatin accessibility, DNA methylation, and transcription in single cells, and validates it in differentiating mouse embryonic stem cells.

Accurate prediction of single-cell DNA methylation states using deep learning

This paper introduces DeepCpG, a deep learning method to predict single-cell DNA methylation states from sequence and incomplete profiles, showing improved accuracy over existing methods.

Tracking the embryonic stem cell transition from ground state pluripotency

The paper tracks the transition of mouse embryonic stem cells from ground state pluripotency to a formative phase, showing acute exit from naive status and transcriptome changes similar to early post-implantation epiblast.