The size of chromatin loops in HeLa cells.

It is widely believed that the chromatin fibre is organized into loops during interphase, with the loop being implicated as an important unit of nuclear function. However, there remains little direct evidence for looping, with estimates of loop size varying widely. This has led to the suggestion that some loops, or even all of them, arise artefactually during isolation as chromatin aggregates so easily. We have now investigated the effect of isolation procedure on loop size using HeLa cells encapsulated in agarose to allow easy manipulation. Loop size in various derivatives (i.e. nuclei, nucleoids, matrices and scaffolds) critically depended on procedure; some (or all) of their loops are artefacts. The loop size in derivatives isolated using the most ‘physiological’ conditions was 86 kb; this remained unchanged throughout the cell cycle. This loop size is probably an average of a range of loops of between 5 and 200 kb.