Genome biology,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: July 8, 2024
Abstract
Spatial
transcriptomics
technologies
permit
the
study
of
spatial
distribution
RNA
at
near-single-cell
resolution
genome-wide.
However,
feasibility
studying
allele-specific
expression
(ASE)
from
these
data
remains
uncharacterized.
Here,
we
introduce
spASE,
a
computational
framework
for
detecting
and
estimating
ASE.
To
tackle
challenges
presented
by
cell
type
mixtures
low
signal
to
noise
ratio,
implement
hierarchical
model
involving
additive
smoothing
splines.
We
apply
our
method
allele-resolved
Visium
Slide-seq
mouse
cerebellum
hippocampus
report
new
insight
into
landscape
type-specific
ASE
therein.
Fixing
cells
with
paraformaldehyde
(PFA)
is
an
essential
step
in
numerous
biological
techniques
as
it
thought
to
preserve
a
snapshot
of
biomolecular
transactions
living
cells.
Fixed-cell
imaging
such
immunofluorescence
have
been
widely
used
detect
liquid–liquid
phase
separation
(LLPS)
vivo.
Here,
we
compared
images,
before
and
after
fixation,
expressing
intrinsically
disordered
proteins
that
are
able
undergo
LLPS.
Surprisingly,
found
PFA
fixation
can
both
enhance
diminish
putative
LLPS
behaviors.
For
specific
proteins,
even
cause
their
droplet-like
puncta
artificially
appear
do
not
any
detectable
the
live
condition.
presence
glycine,
molecule
modulates
rates,
reverse
effect
from
enhancing
diminishing
appearance.
We
further
established
kinetic
model
context
dynamic
protein–protein
interactions.
Simulations
based
on
suggest
protein
localization
fixed
depends
intricate
balance
interaction
dynamics,
overall
rate
notably,
difference
between
rates
different
proteins.
Consistent
simulations,
live-cell
single-molecule
experiments
showed
fast
relative
dynamics
minimize
artifacts.
Our
work
reveals
changes
appearance
cells,
presents
caveat
studying
using
fixation-based
methods,
suggests
mechanism
underlying
artifact.
Cell Reports,
Journal Year:
2023,
Volume and Issue:
42(4), P. 112068 - 112068
Published: April 1, 2023
The
spatiotemporal
control
of
gene
expression
is
dependent
on
the
activity
cis-acting
regulatory
sequences,
called
enhancers,
which
regulate
target
genes
over
variable
genomic
distances
and,
often,
by
skipping
intermediate
promoters,
suggesting
mechanisms
that
enhancer-promoter
communication.
Recent
genomics
and
imaging
technologies
have
revealed
highly
complex
interaction
networks,
whereas
advanced
functional
studies
started
interrogating
forces
behind
physical
communication
among
multiple
enhancers
promoters.
In
this
review,
we
first
summarize
our
current
understanding
factors
involved
in
communication,
with
a
particular
focus
recent
papers
new
layers
complexities
to
old
questions.
second
part
subset
connected
"hubs"
discuss
their
potential
functions
signal
integration
regulation,
as
well
putative
might
determine
dynamics
assembly.
Molecular Cell,
Journal Year:
2024,
Volume and Issue:
84(7), P. 1271 - 1289.e12
Published: Feb. 21, 2024
Polycomb
repressive
complex
2
(PRC2)
is
reported
to
bind
many
RNAs
and
has
become
a
central
player
in
reports
of
how
long
non-coding
(lncRNAs)
regulate
gene
expression.
Yet,
there
growing
discrepancy
between
the
biochemical
evidence
supporting
specific
lncRNA-PRC2
interactions
functional
demonstrating
that
PRC2
often
dispensable
for
lncRNA
function.
Here,
we
revisit
RNA
binding
by
show
may
not
occur
vivo.
Using
denaturing
purification
vivo
crosslinked
RNA-protein
complexes
human
mouse
cell
lines,
observe
loss
detectable
chromatin-associated
proteins
previously
(CTCF,
YY1,
others),
despite
accurately
mapping
bona
fide
RNA-binding
sites
across
others
(SPEN,
TET2,
others).
Taken
together,
these
results
argue
critical
re-evaluation
broad
role
orchestrate
various
chromatin
regulatory
mechanisms.
Nature Structural & Molecular Biology,
Journal Year:
2023,
Volume and Issue:
30(8), P. 1216 - 1223
Published: June 8, 2023
Abstract
Subnuclear
compartmentalization
has
been
proposed
to
play
an
important
role
in
gene
regulation
by
segregating
active
and
inactive
parts
of
the
genome
distinct
physical
biochemical
environments.
During
X
chromosome
inactivation
(XCI),
noncoding
Xist
RNA
coats
chromosome,
triggers
silencing
forms
a
dense
body
heterochromatin
from
which
transcription
machinery
appears
be
excluded.
Phase
separation
involved
XCI,
might
explain
exclusion
preventing
its
diffusion
into
-coated
territory.
Here,
using
quantitative
fluorescence
microscopy
single-particle
tracking,
we
show
that
polymerase
II
(RNAPII)
freely
accesses
territory
during
initiation
XCI.
Instead,
apparent
depletion
RNAPII
is
due
loss
chromatin
stably
bound
fraction.
These
findings
indicate
initial
reflects
absence
actively
transcribing
RNAPII,
rather
than
consequence
putative
domain.
Chemical Reviews,
Journal Year:
2024,
Volume and Issue:
124(8), P. 4734 - 4777
Published: April 5, 2024
This
comprehensive
Review
delves
into
the
chemical
principles
governing
RNA-mediated
crowding
events,
commonly
referred
to
as
granules
or
biological
condensates.
We
explore
pivotal
role
played
by
RNA
sequence,
structure,
and
modifications
in
these
processes,
uncovering
their
correlation
with
phenomena
under
physiological
conditions.
Additionally,
we
investigate
instances
where
deviates
from
its
intended
function,
leading
pathological
consequences.
By
deepening
our
understanding
of
delicate
balance
that
governs
molecular
driven
implications
for
cellular
homeostasis,
aim
shed
light
on
this
intriguing
area
research.
Our
exploration
extends
methodologies
employed
decipher
composition
structural
intricacies
granules,
offering
a
overview
techniques
used
characterize
them,
including
relevant
computational
approaches.
Through
two
detailed
examples
highlighting
significance
noncoding
RNAs,
NEAT1
XIST,
formation
phase-separated
assemblies
influence
landscape,
emphasize
crucial
organization
function.
elucidating
underpinnings
crowding,
investigating
modifications,
structures,
exploring
both
aberrant
phase
separation
phenomena,
provides
multifaceted
world
