Trabajo presentado en el EMBO Workshop: DNA topoisomerases and DNA topology, celebrado en Les Diablerets (Suiza), del 17 al 21 de septiembre de 2017In contrast to our approximated view of the topology and conformations of naked DNA
molecules in vitro, we can hardly picture the topology and spatial configurations of DNA in
vivo. Chromatin architecture and its enzymatic activities determine how twist and writhe
deformations of DNA are constrained or unconstrained, and how DNA supercoiling energy is
generated, buffered or dissipated at each genomic site. Understanding the topology of
nucleosomal DNA and nucleosomal fibers is therefore a fundamental prerequisite to evaluate
the DNA topology outcomes of more complex chromatin structures. In this regard, we have
revisited the "linking number paradox" of nucleosomal DNA, which states that the 1.7 lefthanded turns of DNA around a histone octamer results in the apparent stabilization of only one
negative DNA supercoil (∆Lk ≈ -1). In order to assess how nucleosomal fibers are packaged in
vivo, we have also conducted a first analysis of the probability of DNA knot formation in
eukaryotic chromatin. We found that steady state fractions of trefoils and more complex knot
species are maintained by topoisomerase II activity. We uncovered also that the knotting
probability of intracellular DNA does not scale proportionally to chromatin length. On the
basis of our experimental observations, we inferred novel traits of the nucleosomal DNA
topology and the chromatin architecture in vivo.N