The Journal of Cell Biology,
Год журнала:
2024,
Номер
224(1)
Опубликована: Окт. 14, 2024
Maximizing
cell
survival
under
stress
requires
rapid
and
transient
adjustments
of
RNA
protein
synthesis.
However,
capturing
these
dynamic
changes
at
both
single-cell
level
across
an
organism
has
been
challenging.
Here,
we
developed
a
system
named
MONITTR
(MS2-embedded
mCherry-based
monitoring
transcription)
for
real-time
simultaneous
measurement
nascent
transcripts
endogenous
levels
in
C.
elegans.
Utilizing
this
system,
monitored
the
transcriptional
bursting
fasting-induced
genes
found
that
epidermis
responds
to
fasting
by
modulating
proportion
actively
transcribing
nuclei
kinetics
individual
alleles.
Additionally,
our
findings
revealed
essential
roles
transcription
factors
NHR-49
HLH-30
governing
fasting.
Furthermore,
tracked
dynamics
during
heat-shock
response
ER
unfolded
observed
conditions.
Collectively,
study
provides
foundation
quantitatively
investigating
how
animals
spatiotemporally
modulate
various
physiological
pathological
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 16, 2024
ABSTRACT
Eukaryotic
gene
regulation
relies
on
the
binding
of
sequence-specific
transcription
factors
(TFs).
TFs
bind
chromatin
transiently
yet
occupy
their
target
sites
by
forming
high-local
concentration
microenvironments
(hubs
and
condensates)
that
increase
frequency
binding.
Despite
ubiquity,
such
are
difficult
to
study
in
endogenous
contexts
due
technical
limitations.
Here,
we
use
live
embryo
light-sheet
imaging,
single-molecule
tracking,
genomics
overcome
these
limitations
investigate
how
hubs
localized
genes
drive
TF
occupancy
transcription.
By
examining
mutants
a
hub-forming
TF,
Zelda,
Drosophila
embryos,
find
hub
formation
propensity,
spatial
distributions,
temporal
stabilities
differentially
regulated
DNA
disordered
protein
domains.
We
show
localization
genomic
targets
is
driven
finely-tuned
kinetic
balance
interactions
between
proteins
chromatin,
can
be
redirected
new
when
this
perturbed.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Фев. 14, 2025
CRISPR
activation
(CRISPRa)
is
a
powerful
tool
for
endogenous
gene
activation,
yet
the
mechanisms
underlying
its
optimal
transcriptional
remain
unclear.
By
monitoring
real-time
bursts,
we
find
that
CRISPRa
modulates
both
burst
duration
and
amplitude.
Our
quantitative
imaging
reveals
CRISPR-SunTag
activators,
with
three
tandem
VP64-p65-Rta
(VPR),
form
liquid-like
condensates
exhibit
high
potency.
Although
visible
are
associated
some
RNA
overall
levels
of
phase
separation
do
not
correlate
bursting
or
strength
in
individual
cells.
When
number
SunTag
scaffolds
increased
to
10
more,
solid-like
form,
sequestering
co-activators
such
as
p300
MED1.
These
display
low
dynamicity
liquidity,
resulting
ineffective
activation.
Overall,
our
studies
characterize
various
phase-separated
systems
highlighting
foundational
principles
engineering
CRISPR-based
programmable
synthetic
appropriate
properties
effectively
modulate
expression.
The
elusive.
Here,
authors
show
activators
droplets
boost
expression,
while
creates
sequester
coactivators,
impairing
ABSTRACT
The
precise
regulation
of
the
transcription
genes
is
essential
for
normal
development
and
maintenance
life.
Aberrant
gene
expression
changes
drive
many
human
diseases.
Despite
this,
we
still
do
not
completely
understand
how
controlled
in
living
systems.
Enhancers
are
key
regulatory
elements
that
enable
cells
to
specifically
activate
response
environmental
cues,
or
a
stage
tissue‐specific
manner.
Any
model
enhancer
activity
needs
answer
two
main
questions:
(1)
enhancers
able
identify
act
on
specific
(2)
influence
transcription.
To
address
these
points,
first
outline
some
basic
principles
can
be
established
from
simpler
prokaryotic
systems,
then
discuss
recent
work
aberrant
leukemia.
We
argue
highly
protein–protein
interactions
driver
enhancer‐promoter
proximity,
allowing
enhancer‐bound
factors
directly
RNA
polymerase
Transcription
Factors
(TFs)
are
proteins
crucial
for
regulating
gene
expression.
Effective
regulation
requires
the
TFs
to
rapidly
bind
their
correct
target,
enabling
cell
respond
efficiently
stimuli
such
as
nutrient
availability
or
presence
of
toxins.
However,
search
process
is
hindered
by
slow
diffusive
movement
and
‘false’
targets
-
DNA
segments
that
similar
true
target.
In
eukaryotic
cells,
most
contain
an
Intrinsically
Disordered
Region
(IDR),
which
a
long,
flexible
polymeric
tail
composed
hundreds
amino
acids.
Recent
experimental
findings
indicate
IDR
certain
plays
pivotal
role
in
process.
principles
underlying
IDR’s
remain
unclear.
Here,
we
reveal
key
design
related
TF
binding
affinity
time.
Our
results
demonstrate
significantly
enhances
both
these
aspects.
Furthermore,
our
model
shows
good
agreement
with
results,
propose
further
experiments
validate
model’s
predictions.
Transcription
Factors
(TFs)
are
proteins
crucial
for
regulating
gene
expression.
Effective
regulation
requires
the
TFs
to
rapidly
bind
their
correct
target,
enabling
cell
respond
efficiently
stimuli
such
as
nutrient
availability
or
presence
of
toxins.
However,
search
process
is
hindered
by
slow
diffusive
movement
and
‘false’
targets
-
DNA
segments
that
similar
true
target.
In
eukaryotic
cells,
most
contain
an
Intrinsically
Disordered
Region
(IDR),
which
a
long,
flexible
polymeric
tail
composed
hundreds
amino
acids.
Recent
experimental
findings
indicate
IDR
certain
plays
pivotal
role
in
process.
principles
underlying
IDR’s
remain
unclear.
Here,
we
reveal
key
design
related
TF
binding
affinity
time.
Our
results
demonstrate
significantly
enhances
both
these
aspects.
Furthermore,
our
model
shows
good
agreement
with
results,
propose
further
experiments
validate
model’s
predictions.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 18, 2025
Summary
The
function
of
HSFs,
known
otherwise
as
‘master
thermoregulators,’
in
plant
developmental
remains
largely
uninvestigated.
In
this
study,
we
strategically
analyze
SlHSFB3a
,
a
class
B
sub
member
HSF
transcription
factor
family,
uniquely
expresses
age-dependent
tomato
roots
and
improves
root
architecture
by
synchronizing
auxin
homeostasis.
This
data
demonstrates
overexpressed
transgenics
display
higher
lateral
(LR)
density
early
LR
emergence
improving
architecture.
Generation
CRISPR-Knockout
mutants
displayed
contrasting
phenotype,
confirming
’s
vital
role
growth.
manipulated
roots,
concentration
gradient
responses
oscillated
with
increase
number.
We
highlight
the
signal
transduction
mediated
activation
that
enhances
LRs.
directly
inhibits
repressors,
increases
flow
via
ARF7/LOB20
pathway
positively
modulates
Current Opinion in Cell Biology,
Год журнала:
2025,
Номер
95, С. 102527 - 102527
Опубликована: Май 16, 2025
This
review
explores
recent
emerging
insights
into
enhancer
action,
focusing
on
underexplored
aspects
such
as
the
physical
size
of
regulatory
elements,
stochasticity
transcription
factor
binding
and
chromatin
structure,
role
nonlinear
processes
in
reconciling
longstanding
discrepancies
between
theoretical
models
experimental
observations.
Together,
these
provide
a
nuanced
view
biology,
highlighting
complexity
gene
regulation
need
for
innovative
methodologies
to
further
decode
mechanisms.
