ACS Chemical Biology,
Journal Year:
2022,
Volume and Issue:
18(4), P. 1027 - 1036
Published: March 17, 2022
Gene
transcription
does
not
only
require
writers
of
active
histone
modifications;
on-site
opposition
by
erasers
is
essential
for
many
genes.
Here,
we
propose
the
concept
dynamic
modifications
to
explain
this
conundrum.
We
highlight
requirement
HDACs
acetylation
balance
at
superenhancers,
and
KDM5A
H4K3me3
recycling
highly
gene
promoters.
that
post-translational
regulate
charge
biomolecular
condensate
formation
nucleosome
turnover
form
a
short-term
memory
informs
lock-and-step
checkpoints
chromatin
engagement
RNA
polymerase
II.
Genes & Development,
Journal Year:
2023,
Volume and Issue:
37(9-10), P. 354 - 376
Published: May 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."
Cell,
Journal Year:
2024,
Volume and Issue:
187(19), P. 5282 - 5297.e20
Published: Aug. 20, 2024
Biomolecular
condensates
assemble
in
living
cells
through
phase
separation
and
related
transitions.
An
underappreciated
feature
of
these
dynamic
molecular
assemblies
is
that
they
form
interfaces
with
other
cellular
structures,
including
membranes,
cytoskeleton,
DNA
RNA,
membraneless
compartments.
These
are
expected
to
give
rise
capillary
forces,
but
there
few
ways
quantifying
harnessing
forces
cells.
Here,
we
introduce
viscoelastic
chromatin
tethering
organization
(VECTOR),
which
uses
light-inducible
biomolecular
generate
at
targeted
loci.
VECTOR
can
be
utilized
programmably
reposition
genomic
loci
on
a
timescale
seconds
minutes,
quantitatively
revealing
local
heterogeneity
the
material
properties
chromatin.
synthetic
built
from
components
naturally
liquid-like
structures
cells,
highlighting
potential
role
for
native
do
work
reorganize
genome
impact
architecture.
Communications Biology,
Journal Year:
2024,
Volume and Issue:
7(1)
Published: Feb. 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.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 6, 2025
RNA
polymerase
II
(RNAPII)
is
regulated
by
sequence-specific
transcription
factors
(TFs)
and
the
pre-initiation
complex
(PIC):
TFIIA,
TFIIB,
TFIID,
TFIIE,
TFIIF,
TFIIH,
Mediator.
TFs
Mediator
contain
intrinsically-disordered
regions
(IDRs)
form
phase-separated
condensates,
but
how
IDRs
control
RNAPII
function
remains
poorly
understood.
Using
purified
PIC
factors,
we
developed
a
Real-time
In-vitro
Fluorescence
Transcription
assay
(RIFT)
for
second-by-second
visualization
of
at
hundreds
promoters
simultaneously.
We
show
rapid
activation
IDR-dependent,
without
condensate
formation.
For
example,
MED1-IDR
can
functionally
replace
native
TF,
activating
with
similar
(not
identical)
kinetics;
however,
squelches
as
condensate,
activates
single-protein.
cooperatively
activate
bursting
re-initiation
surprisingly,
drive
TF-promoter
recruitment,
TF-DNA
binding.
Collectively,
RIFT
addressed
questions
largely
intractable
cell-based
methods,
yielding
mechanistic
insights
about
IDRs,
enhancer-promoter
communication,
that
complement
live-cell
imaging
data.
Biomolecules,
Journal Year:
2024,
Volume and Issue:
14(2), P. 176 - 176
Published: Feb. 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.
