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
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.
Trends in Genetics,
Год журнала:
2024,
Номер
40(2), С. 160 - 174
Опубликована: Янв. 12, 2024
Recent
imaging
studies
have
captured
the
dynamics
of
regulatory
events
transcription
inside
living
cells.
These
include
factor
(TF)
DNA
binding,
chromatin
remodeling
and
modification,
enhancer-promoter
(E-P)
proximity,
cluster
formation,
preinitiation
complex
(PIC)
assembly.
Together,
these
molecular
culminate
in
stochastic
bursts
RNA
synthesis,
but
their
kinetic
relationship
remains
largely
unclear.
In
this
review,
we
compare
timescales
upstream
steps
(input)
with
kinetics
transcriptional
bursting
(output)
to
generate
mechanistic
models
single
We
highlight
open
questions
potential
technical
advances
guide
future
endeavors
toward
a
quantitative
understanding
regulation.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Фев. 1, 2025
Transcription
factors
(TFs)
such
as
RBPJ
in
Notch
signaling
bind
to
specific
DNA
sequences
regulate
transcription.
How
TF-DNA
binding
kinetics
and
cofactor
interactions
modulate
gene
regulation
is
mostly
unknown.
We
determine
the
kinetics,
transcriptional
activity,
genome-wide
chromatin
occupation
of
mutant
variants
by
live-cell
single-molecule
tracking,
reporter
assays,
ChIP-Seq.
Importantly,
search
time
exceeds
its
residence
time,
indicating
kinetic
rather
than
thermodynamic
stability.
Impaired
RBPJ-DNA
Adams-Oliver-Syndrome
affect
both
target
site
association
dissociation,
while
impaired
mainly
alters
unspecific
binding.
Moreover,
our
data
point
possibility
that
contributes
specificity.
Findings
for
other
TFs
comparable
indicate
stability
might
prevail
vivo.
propose
an
effective
vivo
energy
landscape
instructive
visualization
mutation-induced
changes.
Biomolecules,
Год журнала:
2024,
Номер
14(2), С. 176 - 176
Опубликована: Фев. 1, 2024
Central
to
the
development
and
survival
of
all
organisms
is
regulation
gene
expression,
which
begins
with
process
transcription
catalyzed
by
RNA
polymerases.
During
protein-coding
genes,
general
factors
(GTFs)
work
alongside
polymerase
II
(Pol
II)
assemble
preinitiation
complex
at
start
site,
open
promoter
DNA,
initiate
synthesis
nascent
messenger
RNA,
transition
productive
elongation,
ultimately
terminate
transcription.
Through
these
different
stages
transcription,
Pol
dynamically
phosphorylated
C-terminal
tail
its
largest
subunit,
serving
as
a
control
mechanism
for
elongation
signaling/binding
platform
co-transcriptional
factors.
The
large
number
core
protein
participating
in
fundamental
steps
add
dense
layers
that
contribute
complexity
temporal
spatial
expression
within
any
given
cell
type.
system
highly
conserved
across
levels
eukaryotes;
however,
most
information
here
will
focus
on
human
system.
This
review
walks
through
various
from
assembly
termination,
highlighting
functions
mechanisms
machinery
participates
each
stage.
Agronomy,
Год журнала:
2024,
Номер
14(10), С. 2421 - 2421
Опубликована: Окт. 19, 2024
Plants
encounter
various
stresses
in
their
natural
environments
and
can
effectively
respond
to
only
one
stress
at
a
time.
Through
complex
gene
network,
transcription
factors
(TFs)
such
as
WRKY
TFs
regulate
diverse
array
of
responses.
The
clarification
the
structural
characteristics
proteins,
along
with
recent
advancements
molecular
dynamics
simulations,
has
shed
light
on
formation,
stability,
interactions
DNA–protein
complexes.
This
provided
novel
viewpoint
regarding
control
TFs.
investigation
superfamilies,
encompassing
historical
development,
diversity,
evolutionary
patterns,
become
feasible
due
transcriptome
approach’s
capacity
provide
extensive
comprehensive
transcripts.
significance
lies
pivotal
role
within
several
signaling
cascades
regulatory
networks
that
influence
plant
defense
present
review
summarizes
functional
aspects
high-volume
sequence
data
from
different
species
studied
date.
Moreover,
comparative
analysis
approach
was
utilized
determine
functions
identified
response
both
abiotic
biotic
stresses,
revealed
through
numerous
studies
species.
results
this
will
be
understanding
events
context
climate
change,
incorporating
new
scientific
evidence
propose
an
innovative
viewpoint.
ACS Synthetic Biology,
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 14, 2024
Enhancers
are
central
for
the
regulation
of
metazoan
transcription
but
have
proven
difficult
to
study,
primarily
due
a
myriad
interdependent
variables
shaping
their
activity.
Consequently,
synthetic
biology
has
emerged
as
main
approach
dissecting
mechanisms
enhancer
function.
We
start
by
reviewing
simple
highly
parallel
reporter
assays,
which
been
successful
in
quantifying
complexity
activator/coactivator
at
enhancers.
then
describe
studies
that
examine
how
enhancers
function
genomic
context
and
combination
with
other
enhancers,
revealing
they
activate
genes
through
variety
different
mechanisms,
working
together
system.
Here,
we
focus
on
can
quantify
dynamics
time.
end
considering
consequences
having
many
within
'local
environment',
believe
leads
correlated
gene
expression
likely
reports
general
principles
biology.
Current Opinion in Structural Biology,
Год журнала:
2024,
Номер
88, С. 102875 - 102875
Опубликована: Июль 10, 2024
Pioneering
transcription
factors
(TFs)
can
drive
cell
fate
changes
by
binding
their
DNA
motifs
in
a
repressive
chromatin
environment.
Recent
structures
illustrate
emerging
rules
for
nucleosome
engagement:
TFs
distort
the
nucleosomal
to
gain
access
or
employ
alternative
DNA-binding
modes
with
smaller
footprints,
they
preferentially
solvent-exposed
near
entry/exit
sites,
and
frequently
interact
histones.
The
extent
of
TF-histone
interactions,
turn,
depends
on
motif
location
nucleosome,
type
fold,
adjacent
domains
present.
interactions
phase
TF
relative
nucleosomes,
we
discuss
how
these
complex
surprisingly
diverse
between
nucleosomes
contribute
function.
