Peter J. Rugg‐Gunn

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency

The paper investigates the chromosomal contacts of poised enhancers during the transition from naive to primed human pluripotency, revealing their dynamics and functional significance.

XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans

This study shows that XIST is required for XCI in human extraembryonic cells, which is essential for their survival and development.

TrAEL-seq captures DNA replication dynamics in mammalian cells

TrAEL-seq is a method for profiling DNA replication dynamics in mammalian cells without requiring synchronization or drugs, showing replication fork speed and initiation zone effects.

Dbx2, an aging-related homeobox gene, inhibits the proliferation of adult neural progenitors

This study identifies Dbx2 as a gene that inhibits adult neural progenitor proliferation and is downregulated in the aged SVZ niche.

NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naive pluripotent stem cells

The paper shows NANOGP1, a duplicate of NANOG, has partial functional conservation in human naive pluripotent stem cells, contributing to pluripotency but not maintaining undifferentiated status.

Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells

This study shows that satellite repeat transcripts in mouse ESCs drive heterochromatin condensates, which are crucial for chromosome stability and nuclear organization.

Genome-wide analysis of DNA replication and DNA double strand breaks by TrAEL-seq

This paper introduces TrAEL-seq, a method to detect DNA replication fork stalling and double strand breaks with high resolution, and demonstrates its application in yeast and mammalian cells.

Network analysis of promoter interactions reveals the hierarchical differences in genome organisation between human pluripotent states

The paper analyzes promoter interactions in human pluripotent states to reveal hierarchical differences in genome organization using a network-graph approach.

Mechanistic diversification of XIST regulatory network in mammals

The paper investigates the mechanistic differences in XIST regulatory networks between humans and mice, showing that JPX regulates XIST expression through distinct mechanisms in each species.

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

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.

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.