In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this ...

CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor implicated in a wide range of functions, including genome organization, transcription activation, and elongation. To explore the basis for CTCF ...

Nucleosomes form heterogeneous groups in vivo, named clutches. Clutches are smaller and less dense in mouse embryonic stem cells (ESCs) compared to neural progenitor cells (NPCs). Using coarse-grained modeling of the ...

Chromatin fiber organization is essential for gene function in all cell types. Moreover it helps to determine cell fate in embryonic/adult stem cells and in somatic cells undergoing reprogramming to pluripotency. Until now ...

Elucidating the mechanism of somatic cell reprogramming has been hampered by the limitations of iPSC systems to uncover the correctly reprogramming cells. Here, by using the highly efficient heterokaryon system we dissected ...

The chromatin fiber folds into loops, but the mechanisms controlling loop extrusion are still poorly understood. Using super-resolution microscopy, we visualize that loops in intact nuclei are formed by a scaffold of cohesin ...

The relationship between the 4D folding of the genome and its function is an outstanding question in biology. A range of methods that probe the folding of the genome in space and time with unprecedented resolution have ...