New research reveals unexpected function for basic DNA-based processes during chromosome folding
Depletion of the cohesin loader Scc2 in G2/M phase disrupts chromosome loop formation. (A) Normalized Hi-C contact maps (2-kb binning) showing cis interactions along the arm of chromosome XIV (150 to 450 kb from left telomere) in G2/M-arrested WT cells or in cells after depletion of Scc2 and Wpl1 (Scc2-AID, Wpl1-AID) in G2/M arrest. Highlights as in Fig. 1B), with an additional light green arrow showing a loop anchor only detected after Wpl1 depletion. (B) Normalized Hi-C ratio maps (without binning) comparing chromosome cis interactions in G2/M-arrested WT cells with those detected in cells depleted of Scc2 and Wpl1 (Scc2-AID, Wpl1-AID), along the same chromosomal regions as depicted in (A). (C) Contact probability plots as function of genomic distance displaying interactions in G2/M-arrested WT cells, or after depletion of Scc2 and Wpl1 (Scc2-AID, Wpl1-AID) in G2/M arrest. (D) Number of loops anchored at cohesin sites in G2/M-arrested WT cells, or after depletion of Scc2 and Wpl1 (Scc2-AID, Wpl1-AID) in G2/M arrest. (E) Quantification of cis and trans interactions in G2/M-arrested WT cells, or after depletion of Scc2 and Wpl1 (Scc2-AID, Wpl1-AID) in G2/M arrest. (D) and (E) display results from two biological repeats, and statistical significance is indicated with P values from binominal tests. Credit: Science Advances (2022). DOI: 10.1126/sciadv.abn7063

The function and organization of chromosomes in the cell nucleus are communicated by two ways. It has been shown that the organization of chromosomal DNA into loops regulates the function of genes. A new interplay known to be important in avoiding diseases was revealed by the new results.

The three-dimensional organization of chromosomes in the cell nucleus is governed by mechanisms that read genes. They limit the progress of the cohesin by folding it into loops. Understanding the function of a healthy cell can be difficult. In a medical perspective, folding is important for several cellular processes that protect chromosomes against disease-promoting aberrations.

"Our findings of this two-way communication opens new perspectives of chromosome organization and the role of cohesin in genome function and stability," says Professor Camilla Bjrkegren, who is one of the authors of the publication.

The study was done using yeast as a model and using Hi-C analysis to look at the interaction between the chromosomes. The basic principles of chromosome organization and function are the same in both yeast and humans.

The structure of the helix will be included in the analysis as preliminary results show that structural alterations in the double helix are related to the reading and copying mechanisms. They suggest that the basis for the 3D-organization can be found in the spiral structure of the DNA.

More information: Kristian Jeppsson et al, Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks, Science Advances (2022). DOI: 10.1126/sciadv.abn7063 Journal information: Science Advances