bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Март 29, 2023
Abstract
How
enhancers
regulate
their
target
genes
in
the
context
of
3D
chromatin
organization
is
extensively
studied
and
models
which
do
not
require
direct
enhancer-promoter
contact
have
recently
emerged.
Here,
we
use
activation
estrogen
receptor-dependent
a
breast
cancer
cell
line
to
study
communication.
This
allows
high
temporal
resolution
tracking
molecular
events
from
hormone
stimulation
efficient
gene
activation.
We
examine
how
both
spatial
proximity
assayed
by
DNA
fluorescence
situ
hybridization,
frequencies
resulting
fragmentation
ligation
Capture-C,
change
dynamically
during
enhancer-driven
These
orthogonal
methods
produce
seemingly
paradoxical
results:
upon
enhancer
increase
while
decreases.
explore
this
apparent
discrepancy
using
different
receptor
ligands
transcription
inhibitors.
Our
data
demonstrate
that
are
independent
but
influenced
enhancer-bound
protein
complexes
whereas
altered
depends
on
transcription.
results
emphasize
relationship
between
physical
distance
nucleus,
especially
over
short
genomic
distances,
always
simple
one.
Genes & Development,
Год журнала:
2023,
Номер
37(9-10), С. 354 - 376
Опубликована: Май 1, 2023
RNA
granules
are
mesoscale
assemblies
that
form
in
the
absence
of
limiting
membranes.
contain
factors
for
biogenesis
and
turnover
often
assumed
to
represent
specialized
compartments
biochemistry.
Recent
evidence
suggests
assemble
by
phase
separation
subsoluble
ribonucleoprotein
(RNP)
complexes
partially
demix
from
cytoplasm
or
nucleoplasm.
We
explore
possibility
some
nonessential
condensation
by-products
arise
when
RNP
exceed
their
solubility
limit
as
a
consequence
cellular
activity,
stress,
aging.
describe
use
evolutionary
mutational
analyses
single-molecule
techniques
distinguish
functional
"incidental
condensates."
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Ноя. 30, 2023
Expansion
microscopy
(ExM)
is
a
highly
effective
technique
for
super-resolution
fluorescence
that
enables
imaging
of
biological
samples
beyond
the
diffraction
limit
with
conventional
microscopes.
Despite
development
several
enhanced
protocols,
ExM
has
not
yet
demonstrated
ability
to
achieve
precision
nanoscopy
techniques
such
as
Single
Molecule
Localization
Microscopy
(SMLM).
Here,
address
this
limitation,
we
have
developed
an
iterative
ultrastructure
expansion
(iU-ExM)
approach
achieves
SMLM-level
resolution.
With
iU-ExM,
it
now
possible
visualize
molecular
architecture
gold-standard
samples,
eight-fold
symmetry
nuclear
pores
or
organization
conoid
in
Apicomplexa.
its
wide-ranging
applications,
from
isolated
organelles
cells
and
tissue,
iU-ExM
opens
new
avenues
scientists
studying
structures
functions.
Communications Biology,
Год журнала:
2024,
Номер
7(1)
Опубликована: Фев. 16, 2024
Whether
phase-separation
is
involved
in
the
organization
of
transcriptional
machinery
and
if
it
aids
or
inhibits
process
a
matter
intense
debate.
In
this
Mini
Review,
we
will
cover
current
knowledge
regarding
role
condensates
on
gene
expression
regulation.
We
summarize
latest
discoveries
relationship
between
condensate
formation,
genome
organization,
activity,
focusing
strengths
weaknesses
experimental
approaches
used
to
interrogate
these
aspects
transcription
living
cells.
Finally,
discuss
challenges
for
future
research.
Molecular Biology of the Cell,
Год журнала:
2025,
Номер
36(3)
Опубликована: Янв. 29, 2025
Biomolecular
condensation
has
emerged
as
an
important
mechanism
to
control
various
cellular
processes
through
the
formation
of
membraneless
organelles.
Fluorescent
protein
tags
have
been
extensively
used
study
and
properties
condensates
in
vitro
vivo,
but
there
is
evidence
that
may
perturb
proteins.
In
this
study,
we
carefully
assess
effects
on
yeast
DEAD-box
ATPase
Dhh1,
a
central
regulator
processing
bodies
(P-bodies),
which
are
biomolecular
involved
mRNA
metabolism.
We
show
fluorescent
well
polyhistidine
tag
greatly
affect
Dhh1
lead
with
different
dynamic
properties.
Tagging
proteins
vivo
alters
number
P-bodies
upon
glucose
starvation
some
even
constitutive
nonstressed
cells.
These
data
raise
concerns
about
accuracy
tagged
experiments,
highlighting
need
for
caution
when
interpreting
results.
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.
PLoS Genetics,
Год журнала:
2024,
Номер
20(5), С. e1011277 - e1011277
Опубликована: Май 23, 2024
How
enhancers
regulate
their
target
genes
in
the
context
of
3D
chromatin
organization
is
extensively
studied
and
models
which
do
not
require
direct
enhancer-promoter
contact
have
recently
emerged.
Here,
we
use
activation
estrogen
receptor-dependent
a
breast
cancer
cell
line
to
study
communication
at
two
loci.
This
allows
high
temporal
resolution
tracking
molecular
events
from
hormone
stimulation
efficient
gene
activation.
We
examine
how
both
spatial
proximity
assayed
by
DNA
fluorescence
situ
hybridization,
frequencies
resulting
fragmentation
ligation,
change
dynamically
during
enhancer-driven
These
orthogonal
methods
produce
seemingly
paradoxical
results:
upon
enhancer
increase
while
decreases.
explore
this
apparent
discrepancy
using
different
receptor
ligands
transcription
inhibitors.
Our
data
demonstrate
that
are
independent
whereas
altered
depends
on
transcription.
results
emphasize
relationship
between
physical
distance
nucleus,
especially
over
short
genomic
distances,
always
simple
one.
iScience,
Год журнала:
2024,
Номер
27(6), С. 109927 - 109927
Опубликована: Май 7, 2024
YAP/TEAD
signaling
is
essential
for
organismal
development,
cell
proliferation,
and
cancer
progression.
As
a
transcriptional
coactivator,
how
YAP
activates
its
downstream
target
genes
incompletely
understood.
forms
biomolecular
condensates
in
response
to
hyperosmotic
stress,
concentrating
transcription-related
factors
activate
genes.
However,
whether
under
other
signals,
organize
function,
transcription
general
are
unknown.
Here,
we
report
that
endogenous
sub-micron
scale
Hippo
pathway
regulation
actin
cytoskeletal
tension.
stabilized
by
the
factor
TEAD1,
recruit
BRD4,
coactivator
enriched
at
active
enhancers.
Using
single-particle
tracking,
found
slowed
diffusion
within
condensate
boundaries,
possible
mechanism
promoting
search.
These
results
reveal
formation
highly
regulated
process
critical
gene
expression.
