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The paper trains a deep-learning model to predict nucleosome occupancy from DNA sequence in mouse embryonic stem cells and identifies short DNA motifs that organize nucleosome arrays.

The paper identifies transposable element insertions that repurpose immune endonucleases to cause hybrid embryo death in mice, contributing to reproductive isolation.

This study identifies MYC and MAX as critical for post-mitotic genome reactivation in pluripotent mouse embryonic stem cells, showing MAX's role in bookmarking and MYC recruitment.

This study maps positive DNA supercoiling across interphase and mitosis, revealing its role in transcriptional control and genome architecture.

This study investigates how GATA6, a pioneer transcription factor, drives Primitive Endoderm differentiation by remodeling chromatin and interacting with other TFs.

This study identifies PI3K/AKT signaling as an upstream regulator that enables ICM formation and specifies both epiblast and primitive endoderm lineages in mouse embryos.

This study shows Nr5a2 is essential for morula development in mice, as its absence causes embryonic arrest, lineage specification issues, and genome instability.

The paper investigates mitotic chromosome architecture across species and cell types, finding species-specific loop sizes but no cell type differences, and links loop size to chromosome arm compaction.

The paper shows that redundancy among nuclear receptor bookmarking factors ensures robust reactivation of pluripotency genes after mitosis.

The paper identifies H3K9me3 at the Nanog locus as a repressive mark that marks differentiation commitment and enables primitive endoderm fate acquisition in ES cells.

The paper identifies a genetic circuitry where OCT4 activates an antisense lncRNA that represses Suv39h1, linking H3K9 methylation levels to pluripotency in mouse ES cells.

The paper shows that CTCF mitotic bookmarking enables rapid post-mitotic gene reactivation in ES cells, with some genes being sensitive to CTCF depletion.

This study shows that Esrrb and Nr5a2 are essential for maintaining naive pluripotency in mouse ESCs by regulating the pluripotency network and preventing differentiation.

The paper shows that CTCF and Esrrb maintain nucleosome positioning at gene regulatory regions during DNA replication and mitosis in mouse ES cells.

This study shows how Nanog uses different mechanisms to enhance embryonic stem cell self-renewal by rewiring pluripotency networks and blocking differentiation through histone modification.

The paper investigates how transcription factors maintain gene regulatory information during mitosis by comparing fixation methods and analyzing nucleosome organization.