Polymorphic 30-nm Chromatin Fiber and Linking Number Paradox. Evidence for the Occurrence of Two Distinct Topoisomers

Abstract

We discuss various models of spatial organization of the 30-nm fiber that remains enigmatic despite 40 years of intensive studies. Using computer simulations, we found two topologically different families of the fiber conformations distinguished by the linker length, L: the fibers with L = {10n} and {10n+5} bp have DNA linking numbers per nucleosome DLk » -1.5 and -1.0, respectively. The fibers with DLk » -1.5 were observed earlier, while the topoisomer with DLk » -1.0 is novel. These predictions were confirmed for circular nucleosome arrays with precisely positioned nucleosomes. We suggest that topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. In particular, the {10n+5} DNA linkers are likely to produce transcriptionally competent chromatin structures. This hypothesis is consistent with available data for several eukaryotes, from yeast to human. We also analyzed two recent studies of chromatin fibers -on the nucleosome crosslinking in vitro, and on radioprobing DNA folding in human cells. In both cases, we show that the novel topoisomer with DLk » -1.0 has to be taken into account to interpret experimental data. This is yet another evidence for occurrence of two distinct fiber topoisomers. Potentially, our findings may reflect a general tendency of chromosomal domains with different levels of transcription to retain topologically different higher-order structures.

Topological polymorphism of nucleosome fibers and folding of chromatin

“…2 C ). Overall, the FLD profile calculated for a mixture of T1 and T2 topoisomers ( 78 ) is in qualitative agreement with the experimental data ( Fig. 3 , A – C ).…”

“…It is therefore unlikely that RICC-seq data can be interpreted based solely on the crystal structures of chromatin fibers, and some alternative fiber conformations should be taken into account. We suggested that the novel T1 topoisomer described above could be such an alternative ( 78 ).

Figure 3 Comparison of the experimental RICC-seq data with theoretical predictions.

…”

Book of Abstracts. Albany 2019: The 20th Conversation

“…We suggest that topological polymorphism of chromatin fibers may play a role in the process of transcription, i. e., the {10n þ 5} DNA linkers are likely to produce transcriptionally competent chromatin structures. This hypothesis is consistent with available data for several eukaryotes, from yeast to mouse (Norouzi, Katebi, Cui, & Zhurkin, 2015;Norouzi and Zhurkin, 2018). Here, we analyzed the data from a recent genome-wide radio-probing study of DNA folding in human cells.…”

“…We show that the novel topoisomer with Lk % -1.0 has to be taken into account to interpret the experimental data, especially for the transcriptionally active regions (Figure 1). This is yet another evidence for occurrence of two distinct fiber topoisomers (Norouzi and Zhurkin, 2018). Potentially, our findings may reflect a general tendency of chromosomal domains with different levels of transcription to retain topologically distinct higherorder fiber conformations, T1 and T2.…”

“…Figure1(Left) Comparison of the experimental RICC-seq data(Risca et al, 2017) with theoretical predictions(Norouzi and Zhurkin, 2018). The experimental genome-wide Fragment Length Distribution (FLD) profiles calculated for the transcriptionally active (H3K27ac, top red curve) and repressed (H3K9me3, top blue curve) regions in human genome correspond to the topoisomer T1 (bottom red curve) and T2 (bottom blue curve), respectively.…”