Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

Meiosis: dances between homologs

D Zickler, N Kleckner - Annual Review of Genetics, 2023 - annualreviews.org
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation
and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled …

Pairtools: from sequencing data to chromosome contacts

Open2C, N Abdennur, G Fudenberg… - PLOS Computational …, 2024 - journals.plos.org
The field of 3D genome organization produces large amounts of sequencing data from Hi-C
and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive …

Cooltools: Enabling high-resolution Hi-C analysis in Python

Open2C, N Abdennur, S Abraham… - PLOS Computational …, 2024 - journals.plos.org
Chromosome conformation capture (3C) technologies reveal the incredible complexity of
genome organization. Maps of increasing size, depth, and resolution are now used to probe …

[HTML][HTML] Mitotic chromosomes

JR Paulson, DF Hudson, F Cisneros-Soberanis… - Seminars in cell & …, 2021 - Elsevier
Our understanding of the structure and function of mitotic chromosomes has come a long
way since these iconic objects were first recognized more than 140 years ago, though many …

Conformation of sister chromatids in the replicated human genome

M Mitter, C Gasser, Z Takacs, CCH Langer, W Tang… - Nature, 2020 - nature.com
The three-dimensional organization of the genome supports regulated gene expression,
recombination, DNA repair, and chromosome segregation during mitosis. Chromosome …

Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae

A Dumont, N Mendiboure, J Savocco, L Anani… - Molecular Cell, 2024 - cell.com
Homology search is a central step of DNA double-strand break (DSB) repair by homologous
recombination (HR). How it operates in cells remains elusive. We developed a Hi-C-based …

Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome

B Conin, I Billault-Chaumartin, H El Sayyed… - Nucleic acids …, 2022 - academic.oup.com
In bacteria, chromosome segregation occurs progressively from the origin to terminus within
minutes of replication of each locus. Between replication and segregation, sister loci are …

Chromatin-centric insights into DNA replication

Y Liu, Z Zhangding, X Liu, J Hu - Trends in Genetics, 2025 - cell.com
DNA replication ensures the precise transmission of genetic information from parent to
daughter cells. In eukaryotes, this process involves the replication of every base pair within a …

Influence of active loop extrusion on the statistics of triple contacts in the model of interphase chromosomes

SA Belan, DE Starkov - JETP Letters, 2022 - Springer
The statistics of triple contacts between the regions of an interphase chromosome in the
presence of an active loop extrusion mechanism is theoretically studied. When modeling …