BMC Genomics,
Journal Year:
2023,
Volume and Issue:
24(1)
Published: Aug. 28, 2023
Chromatin-associated
phase
separation
proteins
establish
various
biomolecular
condensates
via
liquid-liquid
(LLPS),
which
regulates
vital
biological
processes
spatially
and
temporally.
However,
the
widely
used
methods
to
characterize
are
still
based
on
low-throughput
experiments,
consume
time
could
not
be
explore
protein
LLPS
properties
in
bulk.By
combining
gradient
1,6-hexanediol
(1,6-HD)
elution
quantitative
proteomics,
we
developed
chromatin
enriching
hexanediol
coupled
with
liquid
chromatography-mass
spectrometry
(CHS-MS)
of
different
chromatin-associated
(CAPs).
First,
found
that
CAPs
were
enriched
more
effectively
1,6-HD
treatment
group
than
isotonic
solution
group.
Further
analysis
showed
enrich
prone
LLPS.
Finally,
compared
representative
eluted
by
gradients
2%
had
highest
percentage
IDRs
LCDs,
whereas
10%
opposite
trend.This
study
provides
a
convenient
high-throughput
experimental
method
called
CHS-MS.
This
can
efficiently
extended
systems.
Nucleus,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: May 22, 2023
Transcription
is
the
fundamental
process
of
gene
expression,
which
in
eukaryotes
occurs
within
complex
physicochemical
environment
nucleus.
Decades
research
have
provided
extreme
detail
molecular
and
functional
mechanisms
transcription,
but
spatial
genomic
organization
transcription
remains
mysterious.
Recent
discoveries
show
that
transcriptional
components
can
undergo
phase
separation
create
distinct
compartments
inside
nucleus,
providing
new
models
through
to
view
eukaryotes.
In
this
review,
we
focus
on
condensates
their
separation-like
behaviors.
We
suggest
differentiation
between
physical
descriptions
dynamic
biomolecular
assemblies
required
for
productive
discuss
how
are
central
organizing
three-dimensional
genome
across
temporal
scales.
Finally,
map
approaches
therapeutic
manipulation
ask
what
technical
advances
needed
understand
more
completely.
Experimental & Molecular Medicine,
Journal Year:
2024,
Volume and Issue:
56(4), P. 772 - 787
Published: April 25, 2024
Abstract
Although
often
located
at
a
distance
from
their
target
gene
promoters,
enhancers
are
the
primary
genomic
determinants
of
temporal
and
spatial
transcriptional
specificity
in
metazoans.
Since
discovery
first
enhancer
element
simian
virus
40,
there
has
been
substantial
interest
unraveling
mechanism(s)
by
which
communicate
with
partner
promoters
to
ensure
proper
expression.
These
research
efforts
have
benefited
considerably
application
increasingly
sophisticated
sequencing-
imaging-based
approaches
conjunction
innovative
(epi)genome-editing
technologies;
however,
despite
various
proposed
models,
principles
enhancer–promoter
interaction
still
not
fully
elucidated.
In
this
review,
we
provide
an
overview
recent
progress
eukaryotic
transcription
field
pertaining
specificity.
A
better
understanding
mechanistic
basis
lineage-
context-dependent
engagement,
along
continued
identification
functional
enhancers,
will
key
insights
into
spatiotemporal
control
expression
that
can
reveal
therapeutic
opportunities
for
range
enhancer-related
diseases.
Proceedings of the National Academy of Sciences,
Journal Year:
2022,
Volume and Issue:
119(32)
Published: Aug. 1, 2022
The
eukaryotic
genome
is
partitioned
into
distinct
topological
domains
separated
by
boundary
elements.
Emerging
data
support
the
concept
that
several
well-established
nuclear
compartments
are
ribonucleoprotein
condensates
assembled
through
physical
process
of
phase
separation.
Here,
based
on
our
demonstration
chemical
disruption
condensate
assembly
weakens
insulation
properties
a
specific
subset
(∼20%)
topologically
associated
domain
(TAD)
boundaries,
we
report
disrupted
boundaries
characterized
high
level
transcription
and
striking
spatial
clustering.
These
regions
tend
to
be
spatially
associated,
even
interchromosomally,
segregate
with
speckles,
harbor
“housekeeping”
genes
widely
expressed
in
diverse
cell
types.
observations
reveal
previously
unappreciated
mode
organization
mediated
conserved
elements
harboring
highly
units
transcriptional
condensates.
Nucleus,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: Feb. 23, 2023
The
establishment,
maintenance
and
dynamic
regulation
of
three-dimensional
(3D)
chromatin
structures
provide
an
important
means
for
partitioning
genome
into
functionally
distinctive
domains,
which
helps
to
define
specialized
gene
expression
programs
associated
with
developmental
stages
cell
types.
Increasing
evidence
supports
critical
roles
intrinsically
disordered
regions
(IDRs)
harbored
within
transcription
factors
(TFs)
chromatin-modulatory
proteins
in
inducing
phase
separation,
a
phenomenon
forming
membrane-less
condensates
through
biomolecules.
Such
process
is
also
critically
involved
the
establishment
high-order
looping.
IDR-
separation-driven
3D
(re)organization
often
goes
wrong
disease
such
as
cancer.
This
review
discusses
about
recent
advances
understanding
how
separation
(IDPs)
modulates
looping
expression.
Nucleic Acids Research,
Journal Year:
2023,
Volume and Issue:
51(13), P. 6654 - 6667
Published: June 7, 2023
Target
search
models
of
DNA-binding
proteins
in
cells
typically
consider
mechanisms
that
include
3D
diffusion
and
1D
sliding,
which
can
be
characterized
by
single-molecule
tracking
on
DNA.
However,
the
finding
liquid
droplets
DNA
nuclear
components
cast
doubt
extrapolation
from
behavior
ideal
non-condensed
conditions
to
those
cells.
In
this
study,
we
investigate
target
reconstituted
DNA-condensed
using
fluorescence
microscopy.
To
mimic
condensates,
dextran
PEG
polymers.
droplets,
measured
translational
movement
four
(p53,
Nhp6A,
Fis
Cas9)
p53
mutants
possessing
different
structures,
sizes,
oligomeric
states.
Our
results
demonstrate
presence
fast
slow
mobility
modes
for
proteins.
The
mode
capability
is
correlated
strongly
molecular
size
number
domains
proteins,
but
only
moderately
affinity
single
segments
conditions.
interpreted
as
a
multivalent
interaction
protein
multiple
segments.
Cellular and Molecular Life Sciences,
Journal Year:
2025,
Volume and Issue:
82(1)
Published: Feb. 20, 2025
Liquid–liquid
phase
separation
(LLPS),
driven
by
dynamic,
low-affinity
multivalent
interactions
of
proteins
and
RNA,
results
in
the
formation
macromolecular
condensates
on
chromatin.
These
structures
are
likely
to
provide
high
local
concentrations
effector
factors
responsible
for
various
processes
including
transcriptional
regulation
DNA
repair.
In
particular,
enhancers,
super-enhancers,
promoters
serve
as
platforms
condensate
assembly.
current
paradigm,
enhancer-promoter
(EP)
interaction
could
be
interpreted
a
result
enhancer-
promoter-based
contact/fusion.
There
is
increasing
evidence
that
spatial
juxtaposition
enhancers
provided
loop
extrusion
(LE)
SMC
complexes.
Here,
we
propose
may
act
barriers
LE,
thereby
contributing
nuclear
contacts
between
regulatory
genomic
elements.
Transcription
activation
of
genes
by
estrogen
is
driven
enhancers,
which
are
often
located
within
the
same
Topologically
Associating
Domain
(TAD)
as
non-targeted
promoters.
We
investigated
how
acute
enhancer-driven
affects
neighbouring
non-target
TAD.
Using
single-molecule
RNA
FISH
(smFISH),
we
tracked
transcription
TFF1
(enhancer-targeted)
and
TFF3
(non-targeted)
during
stimulation.
observed
mutually
exclusive
expression
patterns:
peaked
at
1
hour,
while
reached
its
peak
3
hours,
after
’s
had
diminished.
Chromatin
looping
data
indicated
that
enhancer
loops
with
but
not
,
suggesting
upregulation
due
to
direct
enhancer-promoter
interactions.
CRISPR
deletion
1,6-hexanediol
(HD)
exposure
revealed
enhancer:promoter
undergo
Liquid-Liquid
Phase
Separation
(LLPS),
sequesters
transcriptional
machinery
inhibits
expression.
As
signalling
wanes
or
LLPS
disrupted,
declines
increases.
Our
findings
reveal
can
indirectly
influence
genes,
highlighting
a
dynamic
shift
in
gene
progresses.
