bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Dec. 17, 2023
Abnormalities
in
the
shapes
of
mammalian
cell
nuclei
are
hallmarks
a
variety
diseases,
including
progeria,
muscular
dystrophy,
and
various
cancers.
Experiments
have
shown
that
there
is
causal
relationship
between
chromatin
organization
nuclear
morphology.
Decreases
heterochromatin
levels,
perturbations
to
organization,
increases
euchromatin
levels
all
lead
misshapen
nuclei,
which
exhibit
deformations,
such
as
blebs
ruptures.
However,
polymer
physical
mechanisms
how
governs
shape
integrity
poorly
understood.
To
investigate
euchromatin,
thought
microphase
separate
We
propose
the
Self
Returning
Excluded
Volume
(SR-EV)
model
for
structure
of
chromatin
based
on
stochastic
rules
and
physical
interactions
that
can
capture
observed
behavior
across
imaging
sequencing
measures
organization.
From
nucleosome
to
chromosome
scales,
captures
overall
organization
as
a
corrugated
system,
with
dense
dilute
regions
alternating
in
manner
resembles
mixing
two
disordered
bi-continuous
phases.
This
particular
organizational
topology
is
consequence
multiplicity
processes
ocurring
nuclei,
mimicked
by
proposed
return
rules.
Single
configuration
properties
ensemble
averages
show
robust
agreement
between
theoretical
experimental
results
including
volume
concentration,
contact
probability,
packing
domain
identification
size
characterization,
scaling
behavior.
Model
suggest
there
an
inherent
regardless
cell
character
resistent
external
forcings
such
Rad21
degradation.
We
propose
the
Self
Returning
Excluded
Volume
(SR-EV)
model
for
structure
of
chromatin
based
on
stochastic
rules
and
physical
interactions.
The
SR-EV
return
generate
conformationally-defined
domains
observed
by
single
cell
imaging
techniques.
From
nucleosome
to
chromosome
scales,
captures
overall
organization
as
a
corrugated
system,
with
dense
dilute
regions
alternating
in
manner
that
resembles
mixing
two
disordered
bi-continuous
phases.
This
particular
organizational
topology
is
consequence
multiplicity
interactions
processes
occurring
nuclei,
mimicked
proposed
rules.
Single
configuration
properties
ensemble
averages
show
robust
agreement
between
theoretical
experimental
results
including
volume
concentration,
contact
probability,
packing
domain
identification
size
characterization,
scaling
behavior.
Model
suggest
there
an
inherent
regardless
character
resistant
external
forcing
such
Rad21
degradation.
The Journal of Chemical Physics,
Journal Year:
2024,
Volume and Issue:
161(22)
Published: Dec. 9, 2024
Chromatin
is
partially
structured
through
the
effects
of
biological
motors.
“Swimming
motors”
such
as
RNA
polymerases
and
chromatin
remodelers
are
thought
to
act
differentially
on
active
parts
genome
stored
inactive
part.
By
systematically
expanding
many-body
master
equation
for
chromosomes
driven
by
swimming
motors,
we
show
that
this
nonuniform
aspect
motorization
leads
heterogeneously
folded
conformations,
thereby
contributing
chromosome
compartmentalization.
arXiv (Cornell University),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Jan. 1, 2023
We
propose
the
Self
Returning
Excluded
Volume
(SR-EV)
model
for
structure
of
chromatin
based
on
stochastic
rules
and
physical
interactions
that
is
able
to
capture
observed
behavior
across
imaging
sequencing
measures
organization.
The
SR-EV
takes
return
Random
Walk,
incorporates
excluded
volume
interactions,
chain
connectivity
expands
length
scales
range
from
10
nm
over
1
micron.
computationally
fast
we
created
thousands
configurations
grouped
in
twelve
different
ensembles
according
two
main
parameters
model.
analysis
was
done
a
way
completely
analogous
experimental
treatments
used
determine
concentration,
contact
probability,
packing
domain
identification
size
characterization,
scaling
behavior.
find
robust
agreement
between
theoretical
results.
overall
organization
corrugated,
with
dense
domains
alternating
very
dilute
regions
manner
resembles
mixing
disordered
bi-continuous
phases.
combined
lead
formation
domains.
transition
short
scale
regime
long
occurring
at
genomic
separations
$\sim
4\times
10^4$
base
pairs
or
$\sim$
100
distance.
probability
reflects
this
change
exponent
larger
than
-1
approximately
-1.
pair
correlation
function
reveals
organizes
following
power
law
$D
\in
\{2,3\}$
region
distance
regimes.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Dec. 17, 2023
Abnormalities
in
the
shapes
of
mammalian
cell
nuclei
are
hallmarks
a
variety
diseases,
including
progeria,
muscular
dystrophy,
and
various
cancers.
Experiments
have
shown
that
there
is
causal
relationship
between
chromatin
organization
nuclear
morphology.
Decreases
heterochromatin
levels,
perturbations
to
organization,
increases
euchromatin
levels
all
lead
misshapen
nuclei,
which
exhibit
deformations,
such
as
blebs
ruptures.
However,
polymer
physical
mechanisms
how
governs
shape
integrity
poorly
understood.
To
investigate
euchromatin,
thought
microphase
separate
