Transcription
activation
of
genes
by
estrogens
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
estrogen
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.
Current Opinion in Genetics & Development,
Journal Year:
2025,
Volume and Issue:
92, P. 102328 - 102328
Published: March 12, 2025
The
development
of
multicellular
organisms
relies
on
the
precise
coordination
molecular
events
across
multiple
spatial
and
temporal
scales.
Understanding
how
information
flows
from
interactions
to
cellular
processes
tissue
organization
during
is
crucial
for
explaining
remarkable
reproducibility
complex
organisms.
This
review
explores
chromatin-encoded
transduced
localized
transcriptional
global
gene
expression
patterns,
highlighting
challenge
bridging
these
We
discuss
recent
experimental
findings
theoretical
frameworks,
emphasizing
polymer
physics
as
a
tool
describing
relationship
between
chromatin
structure
dynamics
By
integrating
perspectives,
we
aim
clarify
regulation
coordinated
levels
biological
suggest
strategies
future
approaches.
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.
Journal of Biological Chemistry,
Journal Year:
2025,
Volume and Issue:
unknown, P. 108548 - 108548
Published: April 1, 2025
Liquid-liquid
phase
separation
is
a
fundamental
biophysical
process
in
which
biopolymers,
such
as
proteins,
nucleic
acids,
and
their
complexes,
spontaneously
demix
into
distinct
coexisting
phases.
This
phenomenon
drives
the
formation
of
membraneless
organelles-cellular
subcompartments
without
lipid
bilayer
that
perform
specialized
functions.
In
plants,
phase-separated
biomolecular
condensates
play
pivotal
roles
regulating
gene
expression,
from
genome
organization
to
transcriptional
post-transcriptional
processes.
addition,
governs
plant-specific
traits,
flowering
photosynthesis.
As
sessile
organisms,
plants
have
evolved
leverage
for
rapid
sensing
response
environmental
fluctuations
stress
conditions.
Recent
studies
highlight
critical
role
plant
adaptation,
particularly
abiotic
stress.
review
compiles
latest
research
on
biology,
providing
examples
diverse
functions
development,
responses.
We
propose
represents
conserved
dynamic
mechanism
enabling
adapt
efficiently
ever-changing
Deciphering
molecular
mechanisms
underlying
responses
opens
new
avenues
biotechnological
strategies
aimed
at
engineering
stress-resistant
crops.
These
advancements
significant
implications
agriculture,
addressing
crop
productivity
face
climate
change.
Accounts of Chemical Research,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 18, 2024
ConspectusThe
ability
of
genomic
DNA
to
adopt
non-canonical
secondary
structures
known
as
G-quadruplexes
(G4s)
under
physiological
conditions
has
been
recognized
for
its
potential
regulatory
function
various
biological
processes.
Among
those,
transcription
recently
emerged
a
key
process
that
can
be
heavily
affected
by
G4
formation,
particularly
when
these
form
at
gene
promoters.
While
the
presence
G4s
within
promoters
traditionally
associated
with
transcriptional
inhibition,
in
model
whereby
act
roadblocks
polymerase
elongation,
recent
genomics
experiments
have
revealed
role
is
more
complex
than
initially
anticipated.
Indeed,
earlier
studies
linking
G4-formation
and
mainly
relied
on
small-molecule
ligands
stabilize
promote
G4s,
which
might
lead
disruption
protein-DNA
interactions
local
environments
and,
therefore,
does
not
necessarily
reflect
endogenous
There
now
strong
evidence
pointing
toward
being
enhancement,
rather
repression,
through
multifaceted
mechanisms
such
recruitment
proteins,
molding
chromatin
architecture,
mode
phase
separation.In
this
Account,
we
explore
pivotal
findings
from
our
research
particular
subset
namely,
those
formed
between
distant
locations
or
independent
nucleic
acid
strands,
referred
multimolecular
(mG4s),
discuss
their
active
regulation.
We
present
suggesting
formation
mG4s
may
positively
regulate
inducing
phase-separation
selectively
recruiting
chromatin-remodeling
proteins.
Our
work
highlighted
how
mG4-forming
RNA
sequences
liquid-liquid
separation
(LLPS)
absence
any
protein.
This
discovery
provided
new
insights
into
mechanism
mG4
expression,
establishing
networks
based
distal
guanine-guanine
base
pairing
creates
liquid
droplets
interface
loops.
relevant
light
increasing
enhancers
drive
elevated
expression
genes.
Given
three-dimensional
nature
enhancers,
underscore
would
beneficial
promoting
transcription.
Moreover,
will
elaborate
repair
remodeling
protein
named
Cockayne
Syndrome
B
(CSB)
displays
astonishing
binding
selectivity
over
canonical
unimolecular
counterparts,
another
architecture
loops
sites.Altogether,
presented
Account
suggest
context
could
crucial
yet
underexplored
structural
feature
Whether
actively
are
mere
consequence
plasticity
remains
elucidated.
Still,
given
novel
offered
targeted
chemical
probes,
anticipate
further
fundamental
biology
regulated
provide
unprecedented
opportunities
development
therapeutic
agents
aimed
targeting
acids
fresh
perspective.
Biomolecules,
Journal Year:
2024,
Volume and Issue:
14(7), P. 875 - 875
Published: July 20, 2024
In
eukaryotic
cells,
gene
transcription
typically
occurs
in
discrete
periods
of
promoter
activity,
interspersed
with
intervals
inactivity.
This
pattern
deviates
from
simple
stochastic
events
and
warrants
a
closer
examination
the
molecular
interactions
that
activate
promoter.
Recent
studies
have
identified
factor
(TF)
clusters
as
key
precursors
to
transcriptional
bursting.
Often,
these
TF
form
at
chromatin
segments
are
physically
distant
promoter,
making
changes
conformation
crucial
for
promoter-TF
cluster
interactions.
this
review,
I
explore
formation
constituents
clusters,
examining
how
dynamic
interplay
between
architecture
clustering
influences
Additionally,
discuss
techniques
visualizing
provide
an
outlook
on
understanding
remaining
gaps
field.
Transcription
activation
of
genes
by
estrogens
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
estrogen
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.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Aug. 26, 2024
Abstract
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.
