Elphège Pierre Nora

Antibody background in ChIP-seq skews estimates of cohesin positioning by CTCF barriers

The paper develops a framework to correct cohesin positioning measurements in ChIP-seq by accounting for antibody background, revealing its impact on cohesin positioning estimates.

Cohesin bridging as a physical principle of enhancer-promoter communication

This study proposes that cohesin bridging, not spatial proximity, mediates enhancer-promoter communication and develops a model to validate this mechanism through engineered cell systems.

The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control

This study shows that cohesin loading at enhancers does not significantly contribute to genome folding or long-range transcriptional control, as inhibiting cohesin recruitment near enhancers reduces target promoter transcription.

Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption

The paper shows that the extrusion rate of cohesin is tunable by cofactor dosage and buffers chromosome structure against genetic disruption.

Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation

The paper investigates how CTCF mutations affect chromatin accessibility, cohesin binding, and gene regulation through multivariate modeling and mutant perturbations.

The single-molecule accessibility landscape of newly replicated mammalian chromatin

This study introduces RASAM, a method to analyze nascent chromatin structure, finding that newly replicated chromatin is hyperaccessible and has unique organization features.

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

This study shows that cohesin is not always necessary for enhancer function, as some enhancers can act independently through synergy or insulators.

Inversion of a topological domain leads to restricted changes in its gene expression and affects inter-domain communication

The paper inverts a topological domain and shows it causes limited gene expression changes but affects inter-domain communication, particularly in Xist expression.

Live-cell imaging and physical modeling reveal control of chromosome folding dynamics by cohesin and CTCF

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

CTCF is a Barrier for Totipotent-like Reprogramming

This study identifies CTCF as a barrier to 2C-like reprogramming in ESCs, showing its role in maintaining chromatin structure and that its depletion promotes totipotent-like state conversion.

WAPL maintains dynamic cohesin to preserve lineage specific distal gene regulation

This study shows WAPL maintains dynamic cohesin at lineage-specific regulatory regions in mouse embryonic stem cells, which is essential for gene expression and pluripotency.

Molecular basis of CTCF binding polarity in genome folding

The paper investigates how CTCF binding polarity influences chromatin loop formation by showing that CTCF positions cohesin but does not control its binding dynamics.

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

The paper investigates the distinct and combined roles of CTCF and CTCFL in chromosome organization and transcription by analyzing their binding sites and functional domains.

CTCF confers local nucleosome resiliency after DNA replication and during mitosis

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

RNA interactions with CTCF are essential for its proper function

The paper shows that CTCF's RNA-binding ability is crucial for its chromatin association and insulation function.

Identification of cis elements for spatio-temporal control of DNA replication

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization

This study shows CTCF is essential for TAD organization but not for genome compartmentalization, revealing distinct mechanisms for chromatin folding and insulation.