Research Square (Research Square),
Год журнала:
2022,
Номер
unknown
Опубликована: Июль 26, 2022
Abstract
How
enhancers
control
target
gene
expression
over
long
genomic
distances
remains
an
important
unsolved
problem.
Here
we
studied
enhancer-promoter
contact
architecture
and
communication
by
integrating
data
from
nucleosome-resolution
maps,
nascent
transcription,
perturbations
to
transcription-associated
proteins
thousands
of
candidate
enhancers.
Contact
frequency
between
functionally
validated
pairs
was
most
enriched
near
the
+1
+2
nucleosomes
at
promoters,
indicating
that
functional
spend
time
in
close
physical
proximity.
Blocking
RNA
polymerase
II
(Pol
II)
caused
major
disruptions
contacts.
Paused
Pol
occupancy
enzymatic
activity
poly
(ADP-ribose)
1
(PARP1)
stabilized
Based
on
our
findings,
propose
updated
model
couples
transcriptional
dynamics
communication.
Proceedings of the National Academy of Sciences,
Год журнала:
2023,
Номер
120(11)
Опубликована: Март 10, 2023
Cohesin
folds
mammalian
interphase
chromosomes
by
extruding
the
chromatin
fiber
into
numerous
loops.
"Loop
extrusion"
can
be
impeded
chromatin-bound
factors,
such
as
CTCF,
which
generates
characteristic
and
functional
organization
patterns.
It
has
been
proposed
that
transcription
relocalizes
or
interferes
with
cohesin
active
promoters
are
loading
sites.
However,
effects
of
on
have
not
reconciled
observations
extrusion
cohesin.
To
determine
how
modulates
extrusion,
we
studied
mouse
cells
in
could
alter
abundance,
dynamics,
localization
genetic
"knockouts"
regulators
CTCF
Wapl.
Through
Hi-C
experiments,
discovered
intricate,
cohesin-dependent
contact
patterns
near
genes.
Chromatin
around
genes
exhibited
hallmarks
interactions
between
transcribing
RNA
polymerases
(RNAPs)
cohesins.
These
reproduced
polymer
simulations
RNAPs
were
moving
barriers
to
obstructed,
slowed,
pushed
The
predicted
preferential
at
is
inconsistent
our
experimental
data.
Additional
ChIP-seq
experiments
showed
putative
loader
Nipbl
predominantly
enriched
promoters.
Therefore,
propose
preferentially
loaded
barrier
function
RNAP
accounts
for
accumulation
Altogether,
find
an
stationary,
but
rather,
translocates
Loop
might
interact
dynamically
generate
maintain
gene
regulatory
elements
shape
genomic
organization.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Янв. 8, 2022
Abstract
Cohesin
folds
mammalian
interphase
chromosomes
by
extruding
the
chromatin
fiber
into
numerous
loops.
“Loop
extrusion”
can
be
impeded
chromatin-bound
factors,
such
as
CTCF,
which
generates
characteristic
and
functional
organization
patterns.
It
has
been
proposed
that
transcription
relocalizes
or
interferes
with
cohesin,
active
promoters
are
cohesin
loading
sites.
However,
effects
of
on
have
not
reconciled
observations
extrusion
cohesin.
To
determine
how
modulates
extrusion,
we
studied
mouse
cells
in
could
alter
abundance,
dynamics,
localization
genetic
‘knockouts’
regulators
CTCF
Wapl.
Through
Hi-C
experiments,
discovered
intricate,
cohesin-dependent
contact
patterns
near
genes.
Chromatin
around
genes
exhibited
hallmarks
interactions
between
transcribing
RNA
polymerases
(RNAPs)
cohesins.
These
reproduced
polymer
simulations
RNAPs
were
“moving
barriers”
to
obstructed,
slowed,
pushed
The
predicted
preferential
at
is
inconsistent
our
experimental
data.
Additional
ChIP-seq
experiments
showed
putative
loader
Nipbl
predominantly
enriched
promoters.
Therefore,
propose
preferentially
loaded
barrier
function
RNAP
accounts
for
accumulation
Altogether,
find
a
new
type
stationary,
but
rather,
translocates
Loop
might
interact
dynamically
generate
maintain
gene
regulatory
elements
shape
genomic
organization.
Significance
Statement
critical
folding
genome
Extrusion
halted
proteins
bound
specific
loci,
chromosomal
domains
regulate
expression.
process
itself
modulate
thus
refolding
simulations,
show
act
loop-extruding
Unlike
stationary
barriers,
actively
relocalize
cohesins,
spatial
Our
model
predicts
explain
why
accumulates
provides
mechanism
clustering
transcription-extrusion
interactions,
contacts.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Июль 14, 2022
Although
enhancers
are
central
to
the
regulation
of
mammalian
gene
expression,
mechanisms
underlying
Enhancer-Promoter
(E-P)
interactions
remain
unclear.
Chromosome
conformation
capture
(3C)
methods
effectively
large-scale
3D
genome
structure
but
struggle
achieve
depth
necessary
resolve
fine-scale
E-P
interactions.
Here,
we
develop
Region
Capture
Micro-C
(RCMC)
by
combining
MNase-based
3C
with
a
tiling
region-capture
approach
and
generate
deepest
maps
reported
thus
far
only
modest
sequencing.
By
applying
RCMC
in
mouse
embryonic
stem
cells
reaching
genome-wide
equivalent
∼200
billion
unique
contacts,
reveals
previously
unresolvable
patterns
highly
nested
focal
interactions,
which
term
microcompartments.
Microcompartments
frequently
connect
promoters
largely
robust
loss
loop
extrusion
inhibition
transcription.
We
therefore
propose
that
many
form
through
compartmentalization
mechanism,
may
explain
why
acute
cohesin
depletion
modestly
affects
global
expression.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Март 16, 2024
Abstract
Cohesin
is
a
ring-shaped
complex,
responsible
for
establishing
sister
chromatid
cohesion
and
forming
topologically
associating
domains
(TADs)
chromatin
loops.
Loss-of-function
mutations
in
cohesin
subunits
its
regulatory
factors
can
cause
Cornelia
de
Lange
syndrome
(CdLS).
Because
dysregulated
gene
expression
was
observed
CdLS,
it
has
long
been
thought
that
plays
role
transcription.
Here,
we
investigated
the
effect
of
acute
depletion
on
transcription
small
number
genes
exhibited
differential
expression.
Analysis
RNA
polymerase
II
(Pol
II)
distribution
revealed
reduced
Pol
promoter
binding
pausing
simultaneously
at
majority
genes.
This
implies
most
genes,
two
decreases
counterbalance
each
other,
resulting
unchanged
Additionally,
find
loss
increased
super
elongation
complex
(SEC),
which
mediates
release
from
paused
state.
Moreover,
reduction
caused
by
no
longer
when
SEC
inhibited.
These
observations
suggest
regulates
restricting
recruitment
to
promoters.
Together,
our
study
demonstrates
involvement
transcriptional
regulation,
particularly
pause
release.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Июль 8, 2022
Abstract
How
enhancers
control
target
gene
expression
over
long
genomic
distances
remains
an
important
unsolved
problem.
Here
we
studied
enhancer-promoter
contact
architecture
and
communication
by
integrating
data
from
nucleosome-resolution
maps,
nascent
transcription,
perturbations
to
transcription-associated
proteins
thousands
of
candidate
enhancers.
Contact
frequency
between
functionally
validated
pairs
was
most
enriched
near
the
+1
+2
nucleosomes
at
promoters,
indicating
that
functional
spend
time
in
close
physical
proximity.
Blocking
RNA
polymerase
II
(Pol
II)
caused
major
disruptions
contacts.
Paused
Pol
occupancy
enzymatic
activity
poly
(ADP-ribose)
1
(PARP1)
stabilized
Based
on
our
findings,
propose
updated
model
couples
transcriptional
dynamics
communication.
The
enhancer-promoter
looping
model,
in
which
enhancers
activate
their
target
genes
via
physical
contact,
has
long
dominated
the
field
of
gene
regulation.
However,
ubiquity
this
model
been
questioned
due
to
evidence
alternative
mechanisms
and
lack
its
systematic
validation,
primarily
owing
absence
suitable
experimental
techniques.
In
study,
we
present
a
new
MNase-based
proximity
ligation
method
called
MChIP-C,
allowing
for
measurement
protein-mediated
chromatin
interactions
at
single-nucleosome
resolution
on
genome-wide
scale.
By
applying
MChIP-C
study
H3K4me3
promoter-centered
K562
cells,
found
that
it
had
greatly
improved
sensitivity
compared
restriction
endonuclease-based
C-methods.
This
allowed
us
identify
EP300
histone
acetyltransferase
SWI/SNF
remodeling
complex
as
potential
candidates
establishing
and/or
maintaining
interactions.
Finally,
leveraging
data
from
published
CRISPRi
screens,
most
functionally-verified
do
physically
interact
with
cognate
promoters,
supporting
model.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2022,
Номер
unknown
Опубликована: Ноя. 15, 2022
Abstract
Chromatin
is
an
essential
component
of
nuclear
mechanical
response
and
shape
that
maintains
compartmentalization
function.
The
biophysical
properties
chromatin
alter
stability,
but
little
known
about
whether
or
how
major
genomic
functions
can
impact
the
integrity
nucleus.
We
hypothesized
transcription
might
affect
cell
rupture
through
its
effects
on
structure
dynamics.
To
test
this
idea,
we
inhibited
with
RNA
polymerase
II
inhibitor
alpha-amanitin
in
wild
type
cells
perturbed
present
increased
blebbing.
Transcription
inhibition
suppresses
blebbing
for
several
types,
perturbations,
inhibitors.
Furthermore,
necessary
robust
bleb
formation,
stabilization,
bleb-based
ruptures.
These
morphological
appear
to
occur
a
novel
pathway,
since
does
not
either
histone
modification
state
rigidity,
which
typically
control
find
active/phosphorylated
pol
Ser5,
marking
initiation,
enriched
blebs
relative
DNA.
Thus,
initiation
hallmark
blebs.
Polymer
simulations
suggest
motor
activity
within
chromatin,
such
as
II,
generate
active
forces
deform
periphery,
deformations
depend
Our
data
provide
evidence
function
impacts
suggests
mechanism,
separate
distinct
from
regulating
large-scale