Sébastien A. Smallwood

The paper develops a linear model to predict chromatin dynamics based on transcription factor binding in C. elegans, identifying key regulators that schedule gene expression rhythms.

The paper systematically mutagenizes human bZIP domains and uses deep mutational scanning to quantify interactions, revealing complex genetic architecture and enabling synthetic bZIP design.

The paper creates a comprehensive atlas of transcription factor interactions in S. pombe using experimental methods and introduces a web tool for exploring the data.

This study shows that paternal DNA methylation affects nucleosome retention in sperm and H3K4 methylation deposition in early embryos.

This study shows that KDM2A and KDM2B prevent aberrant DNA methylation in mouse oocytes, which is critical for early embryonic development.

The paper uses single-cell RNA sequencing in Hydra to show that morphallactic regeneration involves progressive cell fate specification, similar to epimorphic regeneration.

This study develops a model to culture human intestinal organoids and identifies two stem cell states crucial for regeneration and lineage balance.

The paper quantifies how enhancer-promoter interactions influence transcription through nonlinear relationships and reveals mechanisms of transcriptional control via chromosome structure.

The paper uses live-cell imaging to show that chromosomal contacts within TADs are dynamic and stabilized by CTCF and cohesin.

This study identifies ZBTB2 as a btb-domain transcription factor that recruits chromatin remodelers and a histone chaperone during exit from pluripotency, revealing shared and unique functions of the btb-TF family.

This study identifies Hdac3 and Dax1 as repressors that restrict mESCs from transdifferentiating into extraembryonic endoderm by silencing Gata6 enhancers, while Nr5a2 and Esrrb promote this conversion.

The paper shows Wnt3 expression reflects tissue stretching during Hydra regeneration and can drive regeneration without mechanical input.

The paper uses single cell triple-omics analysis to reveal how epigenetic changes drive germ layer specification in mouse embryos, showing distinct epigenetic priming and remodeling in different lineages.

The paper introduces damC, a method to measure chromatin structure in vivo without crosslinking or ligation, confirming TADs and CTCF loops and showing chromatin rigidity below 5 kilobases.

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.