ИСТИНА

Development of the so-called C-methods – experimental protocols allowing the study of the 3D organization of the eukaryotic genome – has permitted to make observations resulting in a new concept in molecular genetics. In became evident that the 3D genome organization constitutes a part of epigenetic mechanisms essential for maintaining the identity of differentiated cells. In this respect, the assembly of distant regulatory elements in active chromatin hubs appears to be of primary importance. Here we show that one of the principal assumptions behind the C-methods is not correct. All C-methods are based on the “proximity ligation” which is preferential cross-ligation of interacting DNA fragments that remain joined by protein bridges after solubilization from formaldehyde-fixed nuclei. We show that the proximity ligation in the 3C procedure really occurs within non-lysed nuclei inside a cage formed by cross-linked chromatin fibers. Based on this finding we suggest a new model of an active chromatin hub.