We analyze multiplexed fluorescence in situ hybridization (m-FISH) data for human and mouse cell lines. The m-FISH technique uses fluorescently-labeled single-stranded probes which hybridize to specific chromosomal regions, thereby allowing the measurement of the spatial positions of up to tagged sites for several thousands of interphase chromosomes. Our analysis focuses on a wide range of different cell lines and two distinct organisms and provides a unified picture of chromatin structure for scales ranging from 5 kb (kilobases) up to 2 Mb (megabases), thus covering a genomic region of almost three orders of magnitude. Confirming recent analysis [Remini et al., Phys. Rev. E 109, 024408 (2024)], we show that there are two characteristic arrangements of chromatin referred to as phase α (crumpled globule) and phase β (looped domain) and discuss the physical properties of these phases. We show that a simple heterogeneous random walk model captures the main behavior observed in experiments and brings considerable insights into chromosomal structure.
Skip Nav Destination
,
,
,
Article navigation
7 February 2025
Research Article|
February 04 2025
Inferring interphase chromosomal structure from multiplexed fluorescence in situ hybridization data: A unified picture from human and mouse cells Available to Purchase
Special Collection:
Chromatin Structure and Dynamics: Recent Advancements
Loucif Remini
;
Loucif Remini
(Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Validation, Writing – original draft, Writing – review & editing)
1
Laboratoire Charles Coulomb (L2C), Univ Montpellier, CNRS
, Montpellier, France
Search for other works by this author on:
Midas Segers
;
Midas Segers
(Investigation, Methodology, Writing – original draft)
2
Soft Matter and Biophysics, KU Leuven
, Celestijnenlaan 200D, 3001 Leuven, Belgium
Search for other works by this author on:
Andrea Parmeggiani
;
Andrea Parmeggiani
(Investigation, Project administration, Writing – original draft, Writing – review & editing)
1
Laboratoire Charles Coulomb (L2C), Univ Montpellier, CNRS
, Montpellier, France
Search for other works by this author on:
Enrico Carlon
Enrico Carlon
a)
(Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Validation, Writing – original draft, Writing – review & editing)
2
Soft Matter and Biophysics, KU Leuven
, Celestijnenlaan 200D, 3001 Leuven, Belgium
a)Author to whom correspondence should be addressed: [email protected]
Search for other works by this author on:
Loucif Remini
1
Midas Segers
2
Andrea Parmeggiani
1
Enrico Carlon
2,a)
1
Laboratoire Charles Coulomb (L2C), Univ Montpellier, CNRS
, Montpellier, France
2
Soft Matter and Biophysics, KU Leuven
, Celestijnenlaan 200D, 3001 Leuven, Belgium
a)Author to whom correspondence should be addressed: [email protected]
J. Chem. Phys. 162, 054110 (2025)
Article history
Received:
August 30 2024
Accepted:
January 16 2025
Citation
Loucif Remini, Midas Segers, Andrea Parmeggiani, Enrico Carlon; Inferring interphase chromosomal structure from multiplexed fluorescence in situ hybridization data: A unified picture from human and mouse cells. J. Chem. Phys. 7 February 2025; 162 (5): 054110. https://doi.org/10.1063/5.0236067
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
112
Views
Citing articles via
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
CREST—A program for the exploration of low-energy molecular chemical space
Philipp Pracht, Stefan Grimme, et al.
GPAW: An open Python package for electronic structure calculations
Jens Jørgen Mortensen, Ask Hjorth Larsen, et al.
Related Content
Viscoelasticity of model interphase chromosomes
J. Chem. Phys. (December 2014)
Combination of fluorescence in situ hybridization and scanning force microscopy for the ultrastructural characterization of defined chromatin regions
J. Vac. Sci. Technol. B (March 1996)
The synergy between compartmentalization and motorization in chromatin architecture
J. Chem. Phys. (March 2025)
Topological interactions between ring polymers: Implications for chromatin loops
J. Chem. Phys. (January 2010)
Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function
J. Chem. Phys. (February 2025)