bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2022,
Volume and Issue:
unknown
Published: July 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.
Nature Communications,
Journal Year:
2022,
Volume and Issue:
13(1)
Published: April 19, 2022
Abstract
Enhancers
and
promoters
predominantly
interact
within
large-scale
topologically
associating
domains
(TADs),
which
are
formed
by
loop
extrusion
mediated
cohesin
CTCF.
However,
it
is
unclear
whether
complex
chromatin
structures
exist
at
sub-kilobase-scale
to
what
extent
fine-scale
regulatory
interactions
depend
on
extrusion.
To
address
these
questions,
we
present
an
MNase-based
chromosome
conformation
capture
(3C)
approach,
has
enabled
us
generate
the
most
detailed
local
interaction
data
date
(20
bp
resolution)
precisely
investigate
effects
of
CTCF
depletion
architecture.
Our
reveal
that
cis
-regulatory
elements
have
distinct
internal
nano-scale
structures,
insulation
dependent
CTCF,
but
independent
cohesin.
In
contrast,
find
causes
a
subtle
reduction
in
longer-range
enhancer-promoter
can
cause
rewiring
contacts.
Together,
our
show
not
essential
for
interactions,
contributes
their
robustness
specificity
precise
regulation
gene
expression.
Nature Structural & Molecular Biology,
Journal Year:
2022,
Volume and Issue:
30(1), P. 38 - 51
Published: Dec. 22, 2022
Abstract
The
relationships
between
chromosomal
compartmentalization,
chromatin
state
and
function
are
poorly
understood.
Here
by
profiling
long-range
contact
frequencies
in
HCT116
colon
cancer
cells,
we
distinguish
three
silent
states,
comprising
two
types
of
heterochromatin
a
enriched
for
H3K9me2
H2A.Z
that
exhibits
neutral
three-dimensional
interaction
preferences
which,
to
our
knowledge,
has
not
previously
been
characterized.
We
find
marked
H3K9me3,
HP1α
HP1β
correlates
with
strong
compartmentalization.
demonstrate
disruption
DNA
methyltransferase
activity
greatly
remodels
genome
compartmentalization
whereby
domains
lose
H3K9me3-HP1α/β
binding
acquire
the
neutrally
interacting
while
retaining
late
replication
timing.
Furthermore,
show
is
permissive
loop
extrusion
cohesin
but
refractory
CTCF
binding.
Together,
work
reveals
dynamic
structural
organizational
diversity
portion
establishes
connections
regulation
chromosome
organization,
including
an
interplay
methylation,
extrusion.
Cell,
Journal Year:
2023,
Volume and Issue:
186(26), P. 5826 - 5839.e18
Published: Dec. 1, 2023
Super-enhancers
are
compound
regulatory
elements
that
control
expression
of
key
cell
identity
genes.
They
recruit
high
levels
tissue-specific
transcription
factors
and
co-activators
such
as
the
Mediator
complex
contact
target
gene
promoters
with
frequency.
Most
super-enhancers
contain
multiple
constituent
elements,
but
it
is
unclear
whether
these
have
distinct
roles
in
activating
expression.
Here,
by
rebuilding
endogenous
multipartite
α-globin
super-enhancer,
we
show
contains
bioinformatically
equivalent
functionally
element
types:
classical
enhancers
facilitator
elements.
Facilitators
no
intrinsic
enhancer
activity,
yet
their
absence,
unable
to
fully
upregulate
Without
facilitators,
exhibit
reduced
recruitment,
RNA
transcription,
enhancer-promoter
interactions.
interchangeable
display
functional
hierarchy
based
on
position
within
a
enhancer.
thus
play
an
important
role
potentiating
activity
ensuring
robust
activation
Epigenetics,
Journal Year:
2023,
Volume and Issue:
18(1)
Published: March 5, 2023
DNA
methylation,
one
of
the
best
characterized
epigenetic
marks
in
human
genome,
plays
a
pivotal
role
gene
transcription
regulation
and
other
biological
processes
humans.
On
top
that,
methylome
undergoes
profound
changes
cancer
disorders.
However,
large-scale
population-based
studies
are
limited
by
high
costs
need
for
considerable
expertise
data
analysis
whole-genome
bisulphite-sequencing
methodologies.
Following
success
EPIC
methylation
microarray,
newly
developed
Infinium
HumanMethylationEPIC
version
2.0
(900K
v2)
is
now
available.
This
new
array
contains
more
than
900,000
CpG
probes
covering
genome
excluding
masked
from
previous
version.
The
900K
v2
microarray
adds
200,000
extra
cis-regulatory
regions
such
as
enhancers,
super-enhancers
CTCF
binding
regions.
Herein,
we
have
technically
biologically
validated
to
show
its
reproducibility
consistency
among
technical
replicates
with
extracted
FFPE
tissue.
In
addition,
hybridized
primary
normal
tumoural
tissues
cell
lines
different
sources
tested
robustness
when
analysing
profiles.
validation
highlights
improvements
offered
demonstrates
versatility
this
updated
tool
characterizing
health
disease.
Nature Structural & Molecular Biology,
Journal Year:
2023,
Volume and Issue:
30(7), P. 991 - 1000
Published: July 1, 2023
Abstract
Enhancer-mediated
gene
activation
generally
requires
physical
proximity
between
enhancers
and
their
target
promoters.
However,
the
molecular
mechanisms
by
which
interactions
promoters
are
formed
not
well
understood.
Here,
we
investigate
function
of
Mediator
complex
in
regulation
enhancer-promoter
interactions,
combining
rapid
protein
depletion
high-resolution
MNase-based
chromosome
conformation
capture
approaches.
We
show
that
leads
to
reduced
interaction
frequencies,
associated
with
a
strong
decrease
expression.
In
addition,
find
increased
CTCF-binding
sites
upon
depletion.
These
changes
chromatin
architecture
redistribution
Cohesin
on
reduction
occupancy
at
enhancers.
Together,
our
results
indicate
complexes
contribute
provide
insights
into
communication
is
regulated.