Anne C. Ferguson‐Smith

The paper investigates the role of IAP retrotransposons in regulating placental gene expression and transcriptional diversity in mice.

The paper investigates regulatory mechanisms of maternal imprinting at the Dlk1-Dio3 domain, showing that loss of expression is more detrimental than gain and identifying active regulatory factors on the unmethylated maternal chromosome.

This study identifies ZFP57 as a regulator of postnatal growth and lifelong health by influencing mammary gland function and lactation, with effects on offspring metabolic syndrome.

The paper analyzes young KRAB-zinc finger gene clusters in mice, showing ERVs drive genetic heterogeneity through recombination and duplication mechanisms.

The paper provides an allelic expression map of the mouse mammary gland across 10 developmental stages, identifying imprinted genes and their cell-type-specific expression patterns.

The paper presents T2T mouse genomes for C57BL/6J and CAST/EiJ, revealing structural diversity in telomeres, centromeres, and key loci like PAR and KZFPs.

The paper develops methods to model transcription factor binding in modified DNA by expanding the DNA alphabet and adapting existing tools to handle custom alphabets, identifying modification-sensitive motifs and validating them with experimental data.

The paper analyzes RNA-seq data to assess the validity of weak parental-origin expression biases, finding many are artifacts and highlighting the need for better tools and validation.

The paper measures mitotic DNA methylation inheritance at single CpG sites and finds that intermediate methylation is imprecise due to DNMT1 activity, challenging the stability of DNA methylation as an epigenetic mark.

The paper shows that defective folate metabolism leads to germline epigenetic instability and identifies Hira transcript expression as a biomarker for maternal phenotypic inheritance.

The paper identifies a spontaneously formed retrotransposon variant in mice that exhibits distinct epigenetic marks and is associated with metabolic and gene expression changes.

The paper investigates the relationship between subnuclear localization and gene expression at the imprinted Dlk1-Dio3 locus, finding that transcriptional activity, not repression or parental origin, determines localization.

The paper identifies and characterizes variably methylated retrotransposons in mice, showing their potential for long-range regulation and inter-individual transcriptional variability.

The paper shows that maternal high-fat diet induces epigenetic changes in mice that affect two generations, with altered Dlk1 expression and DNA methylation.

This study shows that high dropout rates in scRNA-seq hinder alternative splicing analysis, while low isoform quantification errors in mice reduce this obstacle.

The paper investigates ZFP57's role in epigenetic regulation, showing it maintains DNA methylation and repressive marks at imprinted regions but is not essential for silencing transposable elements.

The paper benchmarks isoform quantification tools on simulated single-cell RNA-seq data, finding good performance on SMARTer and SMART-seq2 but poor on Drop-seq, and highlights biological insights from real data.

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.

The paper investigates cis and trans mechanisms influencing transcription factor binding and gene expression evolution in mice by analyzing allele-specific occupancy in crosses of two inbred strains.