Geoffrey Fudenberg

Oct 12, 2024 | biorxiv.org | Hadi Rahmaninejad |Yao Xiao |Maxime M.C. Tortora |Geoffrey Fudenberg

AbstractIn mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This interplay leads to the enrichment of cohesin at barriers, isolation between neighboring topologically associating domains, and elevated contact frequency between convergent CTCF barriers across the genome.

Aug 24, 2024 | biorxiv.org | Geoffrey Fudenberg |Maxime M.C. Tortora

AbstractLoop extrusion constitutes a universal mechanism of genome organization, whereby structural maintenance of chromosomes (SMC) protein complexes load onto the chromatin fiber and generate DNA loops of increasingly-larger sizes until their eventual release. In mammalian interphase cells, loop extrusion is mediated by the cohesin complex, which is dynamically regulated by the interchange of multiple accessory proteins.

Aug 4, 2024 | biorxiv.org | David Kelley |Geoffrey Fudenberg |Paulina N Smaruj |Fahad Kamulegeya

AbstractInterphase mammalian genomes are folded in 3D with complex locus-specific patterns that impact gene regulation. CTCF (CCCTC-binding factor) is a key architectural protein that binds specific DNA sites, halts cohesin-mediated loop extrusion, and enables long-range chromatin interactions. There are hundreds of thousands of annotated CTCF-binding sites in mammalian genomes; disruptions of some result in distinct phenotypes, while others have no visible effect.