bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 17, 2024
Abstract
Nucleosomes
at
actively
transcribed
promoters
have
specific
histone
post-transcriptional
modifications
and
variants.
These
features
are
thought
to
contribute
the
formation
maintenance
of
a
permissive
chromatin
environment.
Recent
reports
drawn
conflicting
conclusions
about
whether
these
depend
on
transcription.
We
used
triptolide
inhibit
transcription
initiation
degrade
RNA
Polymerase
II
interrogated
effect
modifications.
Transcription
was
dispensable
for
de
novo
steady-state
acetylation
start
sites
(TSSs)
enhancers.
However,
steady
state,
blocking
increased
levels
H2AZ
incorporation
active
TSSs.
results
demonstrate
that
deposition
TSSs
is
not
dependent
limits
marks.
How
chromatin
dynamics
relate
to
transcriptional
activity
remains
poorly
understood.
Using
single-molecule
tracking,
coupled
with
machine
learning,
we
show
that
histone
H2B
and
multiple
chromatin-bound
regulators
display
two
distinct
low-mobility
states.
Ligand
activation
results
in
a
marked
increase
the
propensity
of
steroid
receptors
bind
lowest-mobility
state.
Mutational
analysis
revealed
interactions
state
require
an
intact
DNA
binding
domain
oligomerization
domains.
These
states
are
not
spatially
separated
as
previously
believed,
but
individual
bound-TF
molecules
can
dynamically
switch
between
them
on
time
scales
seconds.
Single
different
mobilities
exhibit
dwell
distributions,
suggesting
mobility
TFs
is
intimately
their
dynamics.
Together,
our
identify
unique
appear
represent
common
pathways
for
transcription
mammalian
cells.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Май 16, 2024
Abstract
In
the
nucleus,
biological
processes
are
driven
by
proteins
that
diffuse
through
and
bind
to
a
meshwork
of
nucleic
acid
polymers.
To
better
understand
this
interplay,
we
present
an
imaging
platform
simultaneously
visualize
single
protein
dynamics
together
with
local
chromatin
environment
in
live
cells.
Together
super-resolution
imaging,
new
fluorescent
probes,
biophysical
modeling,
demonstrate
nucleosomes
display
differential
diffusion
packing
arrangements
as
density
increases
whereas
viscoelastic
properties
accessibility
interchromatin
space
remain
constant.
Perturbing
nuclear
functions
impacts
nucleosome
diffusive
manner
is
dependent
both
on
relative
location
within
nucleus.
Our
results
support
model
wherein
transcription
locally
stabilizes
while
allowing
for
free
exchange
proteins.
Additionally,
they
reveal
heterogeneity
arises
from
active
passive
highlight
need
account
different
organizational
principles
when
modeling
environments.
A
string
of
nucleosomes,
where
genomic
DNA
is
wrapped
around
histones,
organized
in
the
cell
as
chromatin,
ranging
from
euchromatin
to
heterochromatin,
with
distinct
genome
functions.
Understanding
physical
differences
between
and
heterochromatin
crucial,
yet
specific
labeling
methods
living
cells
remain
limited.
Here,
we
have
developed
replication-dependent
histone
(Repli-Histo)
mark
nucleosomes
based
on
replication
timing.
Using
this
approach,
investigated
local
nucleosome
motion
four
known
chromatin
classes,
human
mouse
cells.
The
more
euchromatic
(earlier-replicated)
heterochromatic
(later-replicated)
regions
exhibit
greater
lesser
motions,
respectively.
Notably,
profile
each
class
persists
throughout
interphase.
Genome
essentially
replicated
although
timing
perturbed.
Our
findings,
combined
computational
modeling,
suggest
that
earlier-replicated
accessibility,
can
be
a
major
determinant
genome-wide
Current Opinion in Structural Biology,
Год журнала:
2024,
Номер
87, С. 102873 - 102873
Опубликована: Июль 1, 2024
Cell
states
result
from
the
ordered
activation
of
gene
expression
by
transcription
factors.
Transcription
factors
face
opposing
design
constraints:
they
need
to
be
dynamic
trigger
rapid
cell
state
transitions,
but
also
stable
enough
maintain
terminal
identities
indefinitely.
Recent
progress
in
live-cell
single-molecule
microscopy
has
helped
define
biophysical
principles
underlying
this
paradox.
Beyond
factor
activity,
experiments
have
revealed
that
at
nearly
every
level
regulation,
control
emerges
multiple
short-lived
stochastic
interactions,
rather
than
deterministic,
interactions
typical
other
biochemical
pathways.
This
architecture
generates
consistent
outcomes
can
rapidly
choreographed.
Here,
we
highlight
recent
results
demonstrate
how
order
regulation
apparent
molecular-scale
chaos
and
discuss
remaining
conceptual
challenges.
Proceedings of the National Academy of Sciences,
Год журнала:
2024,
Номер
121(42)
Опубликована: Окт. 9, 2024
The
analysis
of
tissues
origin
cell-free
DNA
(cfDNA)
is
research
and
diagnostic
interest.
Many
studies
focused
on
bisulfite
treatment
or
immunoprecipitation
protocols
to
assess
the
cfDNA.
loss
often
occurs
during
such
processes.
Fragmentomics
cfDNA
molecules
has
uncovered
a
wealth
information
related
There
still
much
room
for
development
tools
assessing
contributions
from
various
into
plasma
using
fragmentomic
features.
Hence,
we
developed
an
approach
analyze
relative
different
plasma,
by
identifying
characteristic
fragmentation
patterns
associated
with
selected
histone
modifications.
We
named
this
technique
as
FRAGmentomics-based
Histone
modification
Analysis
(FRAGHA).
Deduced
placenta-specific
H3
lysine
27
acetylation
(H3K27ac)-associated
signal
correlated
well
fetal
fraction
in
maternal
(Pearson’s
r
=
0.96).
deduced
liver-specific
H3K27ac-associated
donor-derived
liver
transplantation
recipients
0.92)
was
significantly
increased
patients
hepatocellular
carcinoma
(HCC)
(
P
<
0.01,
Wilcoxon
rank-sum
test).
Significant
elevations
erythroblasts-specific
colon-specific
signals
were
observed
β-thalassemia
major
colorectal
cancer,
respectively.
Furthermore,
tissue-specific
H3K27ac
regions,
machine
learning
algorithm
enhance
HCC
detection,
area
under
curve
(AUC)
up
0.97.
Finally,
genomic
regions
4
trimethylation
(H3K4me3)
found
exhibit
This
study
shed
light
relationship
between
fragmentomics
modifications,
thus
expanding
armamentarium
liquid
biopsy.
Nucleosomes
at
promoters
of
active
genes
are
marked
by
specific
histone
post-translational
modifications
and
variants.
These
features
thought
to
promote
the
formation
maintenance
an
“open”
chromatin
environment
that
is
suitable
for
transcription.
However,
recent
reports
have
drawn
conflicting
conclusions
about
whether
these
depend
on
To
further
interrogate
this
relationship,
we
inhibited
transcription
initiation
using
triptolide,
which
triggered
degradation
RNA
polymerase
II,
examined
impact
modifications.
Transcription
was
not
required
either
hormone-induced
or
steady-state
start
sites
(TSSs)
enhancers.
Rather,
blocking
increased
levels
acetylation
H2AZ
incorporation
TSSs.
P300
activity
dispensable
effect,
but
inhibition
deacetylases
masked
acetylation.
Together,
our
results
demonstrate
occur
independently
Furthermore,
findings
suggest
process
coordinates
removal
limit
gene
activity.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Март 11, 2025
Abstract
Faithful
epigenetic
inheritance
across
cell
divisions
is
essential
to
maintaining
identity
and
involves
numerous
modifications,
whose
roles
in
establishing
chromatin
architecture
are
less
understood.
Technological
approaches
temporally
order
modifications
throughout
the
cycle
often
face
limitations
sequence
resolution
rely
on
potentially
damaging
mitotic
labeling
or
conversion
steps.
Herein,
we
present
M
ethylation
P
seudotime
A
nalysis
T
hrough
read-level
H
eterogeneity
(MPATH),
a
label-
conversion-free
method
infer
post-replication
DNA
strand
maturity
from
methylation
patterns
single
molecules.
We
use
MPATH
hydroxymethylation
inheritance,
revealing
that
CpGs
within
cis-regulatory
elements
undergo
transitions
between
states
at
sub-cell-cycle
timescales.
When
applied
long
reads
generated
by
NOMe-seq,
uncovered
relationships
nucleosome
occupancy
maturity.
Finally,
extension
of
phased
reveals
allele-specific
trends
pseudotime
distribution
associated
with
X
chromosome
activity.
Our
findings
suggest
when
coupled
multimodal
sequencing
strategies,
could
provide
valuable
insights
into
restoration
dynamics.
Proceedings of the Japan Academy Series B,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
The
organization
and
dynamics
of
chromatin
are
critical
for
genome
functions
such
as
transcription
DNA
replication/repair.
Historically,
was
assumed
to
fold
into
the
30-nm
fiber
progressively
arrange
larger
helical
structures,
described
in
textbook
model.
However,
over
past
15
years,
extensive
evidence
including
our
studies
has
dramatically
transformed
view
from
a
static,
regular
structure
one
that
is
more
variable
dynamic.
In
higher
eukaryotic
cells,
forms
condensed
yet
liquid-like
domains,
which
appear
be
basic
unit
structure,
replacing
fiber.
These
domains
maintain
proper
accessibility,
ensuring
regulation
reaction
processes.
During
mitosis,
these
assemble
form
gel-like
mitotic
chromosomes,
further
constrained
by
condensins
other
factors.
Based
on
available
evidence,
I
discuss
physical
properties
live
emphasizing
its
viscoelastic
nature-balancing
local
fluidity
with
global
stability
support
functions.