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 100 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.

1.
W. A.
Bickmore
, “
The spatial organization of the human genome
,”
Annu. Rev. Genomics Hum. Genet.
14
,
67
84
(
2013
).
2.
J.
Dekker
and
L.
Mirny
, “
The 3D genome as moderator of chromosomal communication
,”
Cell
164
,
1110
1121
(
2016
).
3.
K.
Polovnikov
,
S.
Nechaev
, and
M.
Tamm
, “
Effective Hamiltonian of topologically stabilized polymer states
,”
Soft Matter
14
,
6561
6570
(
2018
).
4.
A.
Lesage
,
V.
Dahirel
,
J.-M.
Victor
, and
M.
Barbi
, “
Polymer coil-globule phase transition is a universal folding principle of Drosophila epigenetic domains
,”
Epigenet. Chromatin
12
,
28
(
2019
).
5.
S. M.
Espinola
,
M.
Götz
,
M.
Bellec
,
O.
Messina
,
J.-B.
Fiche
,
C.
Houbron
,
M.
Dejean
,
I.
Reim
,
A. M.
Cardozo Gizzi
,
M.
Lagha
, and
M.
Nollmann
, “
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development
,”
Nat. Genet.
53
,
477
486
(
2021
).
6.
M.
Conte
,
E.
Irani
,
A. M.
Chiariello
,
A.
Abraham
,
S.
Bianco
,
A.
Esposito
, and
M.
Nicodemi
, “
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
,”
Nat. Commun.
13
,
4070
(
2022
).
7.
S. A.
Belan
and
D. E.
Starkov
, “
Influence of active loop extrusion on the statistics of triple contacts in the model of interphase chromosomes
,”
JETP Lett.
115
,
763
769
(
2022
).
8.
M.
Liefsoens
,
T.
Földes
, and
M.
Barbi
, “
Spectral-based detection of chromatin loops in multiplexed super-resolution FISH data
,”
Nat. Commun.
15
,
7670
(
2024
).
9.
B.
Bintu
,
L. J.
Mateo
,
J.-H.
Su
,
N. A.
Sinnott-Armstrong
,
M.
Parker
,
S.
Kinrot
,
K.
Yamaya
,
A. N.
Boettiger
, and
X.
Zhuang
, “
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
,”
Science
362
,
eaau1783
(
2018
).
10.
L. J.
Mateo
,
S. E.
Murphy
,
A.
Hafner
,
I. S.
Cinquini
,
C. A.
Walker
, and
A. N.
Boettiger
, “
Visualizing DNA folding and RNA in embryos at single-cell resolution
,”
Nature
568
,
49
54
(
2019
).
11.
E.
Lieberman-Aiden
,
N. L.
Van Berkum
,
L.
Williams
,
M.
Imakaev
,
T.
Ragoczy
,
A.
Telling
,
I.
Amit
,
B. R.
Lajoie
,
P. J.
Sabo
,
M. O.
Dorschner
et al, “
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
,”
Science
326
,
289
293
(
2009
).
12.
A. M. C.
Gizzi
,
D. I.
Cattoni
,
J.-B.
Fiche
,
S. M.
Espinola
,
J.
Gurgo
,
O.
Messina
,
C.
Houbron
,
Y.
Ogiyama
,
G. L.
Papadopoulos
,
G.
Cavalli
et al, “
Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms
,”
Mol. Cell
74
,
212
222
(
2019
).
13.
J.
Gurgo
,
J.-C.
Walter
,
J.-B.
Fiche
,
C.
Houbron
,
M.
Schaeffer
,
G.
Cavalli
,
F.
Bantignies
, and
M.
Nollmann
, “
Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila polycomb genes
,”
Cell Rep.
43
,
114167
(
2024
).
14.
L.
Remini
,
M.
Segers
,
J.
Palmeri
,
J.-C.
Walter
,
A.
Parmeggiani
, and
E.
Carlon
, “
Chromatin structure from high resolution microscopy: Scaling laws and microphase separation
,”
Phys. Rev. E
109
,
024408
(
2024
).
15.
A. Y.
Grosberg
,
S. K.
Nechaev
, and
E. I.
Shakhnovich
, “
The role of topological constraints in the kinetics of collapse of macromolecules
,”
J. Phys. Fr.
49
,
2095
2100
(
1988
).
16.
M.
Liu
,
Y.
Lu
,
B.
Yang
,
Y.
Chen
,
J. S.
Radda
,
M.
Hu
,
S. G.
Katz
, and
S.
Wang
, “
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
,”
Nat. Commun.
11
,
2907
(
2020
).
17.
P.-G.
De Gennes
,
Scaling Concepts in Polymer Physics
(
Cornell University Press
,
1979
).
18.
K. E.
Polovnikov
,
H. B.
Brandão
,
S.
Belan
,
B.
Slavov
,
M.
Imakaev
, and
L. A.
Mirny
, “
Crumpled polymer with loops recapitulates key features of chromosome organization
,”
Phys. Rev. X
13
,
041029
(
2023
).
19.
L. A.
Mirny
, “
The fractal globule as a model of chromatin architecture in the cell
,”
Chromosome Res.
19
,
37
51
(
2011
).
20.
S.
Belan
and
V.
Parfenyev
, “
Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable model
,”
J. Chem. Phys.
160
,
124901
(
2024
).
21.
D.
Starkov
and
S.
Belan
, “
Effect of active loop extrusion on the two-contact correlations in the interphase chromosome
,”
J. Chem. Phys.
161
,
074903
(
2024
).
22.
L. A.
Mirny
, “
Chromosome and protein folding: In search for unified principles
,”
Curr. Opin. Struct. Biol.
81
,
102610
(
2023
).
23.
M.
Barbieri
,
M.
Chotalia
,
J.
Fraser
,
L.-M.
Lavitas
,
J.
Dostie
,
A.
Pombo
, and
M.
Nicodemi
, “
Complexity of chromatin folding is captured by the strings and binders switch model
,”
Proc. Natl. Acad. Sci. U. S. A.
109
,
16173
(
2012
).
24.
C. A.
Brackley
,
S.
Taylor
,
A.
Papantonis
,
P. R.
Cook
, and
D.
Marenduzzo
, “
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization
,”
Proc. Natl. Acad. Sci. U. S. A.
110
,
E3605
(
2013
).
25.
D.
Jost
,
P.
Carrivain
,
G.
Cavalli
, and
C.
Vaillant
, “
Modeling epigenome folding: Formation and dynamics of topologically associated chromatin domains
,”
Nucleic Acids Res.
42
,
9553
(
2014
).
26.
E.
Alipour
and
J. F.
Marko
, “
Self-organization of domain structures by DNA-loop-extruding enzymes
,”
Nucleic Acids Res.
40
,
11202
11212
(
2012
).
27.
A.
Goloborodko
,
J. F.
Marko
, and
L. A.
Mirny
, “
Chromosome compaction by active loop extrusion
,”
Biophys. J.
110
,
2162
2168
(
2016
).
28.
V. F.
Scolari
and
M.
Cosentino Lagomarsino
, “
Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid
,”
Soft Matter
11
,
1677
1687
(
2015
).
29.
T. J.
Stevens
,
D.
Lando
,
S.
Basu
,
L. P.
Atkinson
,
Y.
Cao
,
S. F.
Lee
,
M.
Leeb
,
K. J.
Wohlfahrt
,
W.
Boucher
,
A.
O’Shaughnessy-Kirwan
et al, “
3D structures of individual mammalian genomes studied by single-cell Hi-C
,”
Nature
544
,
59
64
(
2017
).
30.
A.
Buckle
,
C. A.
Brackley
,
S.
Boyle
,
D.
Marenduzzo
, and
N.
Gilbert
, “
Polymer simulations of heteromorphic chromatin predict the 3D folding of complex genomic loci
,”
Mol. Cell
72
,
786
797.e11
(
2018
).
31.
E. H.
Finn
,
G.
Pegoraro
,
H. B.
Brandão
,
A.-L.
Valton
,
M. E.
Oomen
,
J.
Dekker
,
L.
Mirny
, and
T.
Misteli
, “
Extensive heterogeneity and intrinsic variation in spatial genome organization
,”
Cell
176
,
1502
1515.e10
(
2019
).
32.
G.
Shi
and
D.
Thirumalai
, “
Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox
,”
Nat. Commun.
10
,
3894
(
2019
).
33.
M.
Conte
,
L.
Fiorillo
,
S.
Bianco
,
A. M.
Chiariello
,
A.
Esposito
, and
M.
Nicodemi
, “
Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation
,”
Nat. Commun.
11
,
3289
(
2020
).
You do not currently have access to this content.