Zachary D. Smith

Epigenetic regulators partition the genome by evolutionary and developmental constraint

The paper uses single-cell RNA sequencing to analyze mutant phenotypes of epigenetic regulators in mouse embryos, revealing how these regulators partition the genome based on developmental and evolutionary constraints.

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Extracting interpretable single-cell metabolic states with graph-guided representation learning

The paper introduces MeRN, a graph-guided variational autoencoder for learning single-cell metabolic states from transcriptomes, and identifies metabolic drivers in various biological contexts.

Folate deficiency disrupts key metabolic transitions within the developing neural ectoderm

This study uses a deep-learning model to analyze scRNA-seq data and identifies how folate deficiency disrupts metabolic transitions in developing mouse neural ectoderm, leading to morphological defects.

Lamin A/C directs nucleosome-scale chromatin remodeling to define early lineage segregation in mammals

The paper investigates how Lamin A/C influences chromatin structure during early mammalian lineage segregation, showing its role in maintaining trophectoderm identity.

A second wave of Notch signaling diversifies the intestinal secretory lineage

The paper identifies a rare secretory cell type in the intestine, CHEs, and shows that a second wave of Notch signaling is required for their specification.

DOT1L bridges transcription and heterochromatin formation at pericentromeres

This study shows that DOT1L is essential for transcription of pericentromeric repeats and maintains genome stability by bridging transcription and heterochromatin formation.

Diverse mechanisms for epigenetic imprinting in mammals

This study investigates epigenetic mechanisms in mammals, revealing distinct roles of DNA methylation and Polycomb group repressors in autosomal imprinting and identifying unique pathways in the extraembryonic ectoderm.

In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation

This study shows that Firre and Dxz4 deletions in mice affect autosomal gene regulation without impacting XCI.

Molecular recording of mammalian embryogenesis

The paper develops a molecular recorder to track lineage and define a mouse cell fate map using scRNA-seq, revealing transcriptional convergence of endodermal cells and estimating progenitor cell numbers.