Cell Reports,
Journal Year:
2022,
Volume and Issue:
41(5), P. 111567 - 111567
Published: Nov. 1, 2022
To
infer
potential
causal
relationships
between
3D
chromatin
structure,
enhancers,
and
gene
transcription,
we
mapped
each
feature
in
a
genome-wide
fashion
across
eight
narrowly
spaced
time
points
of
macrophage
activation.
Enhancers
genes
connected
by
loops
exhibit
stronger
correlations
histone
H3K27
acetylation
expression
than
can
be
explained
genomic
distance
or
physical
proximity
alone.
At
these
looped
enhancer-promoter
pairs,
changes
at
distal
enhancers
precede
expression.
Changes
directional
bias
differential
loop
anchors;
gained
are
associated
with
increased
oriented
away
from
the
center
loop,
lost
often
accompanied
high
levels
transcription
within
boundaries
themselves.
These
results
consistent
reciprocal
relationship
where
facilitate
connecting
promoters
to
whereas
impede
formation.
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(5), P. 867 - 882.e5
Published: Jan. 30, 2024
The
structural
maintenance
of
chromosomes
(SMC)
protein
complexes—cohesin,
condensin,
and
the
Smc5/6
complex
(Smc5/6)—are
essential
for
chromosome
function.
At
molecular
level,
these
complexes
fold
DNA
by
loop
extrusion.
Accordingly,
cohesin
creates
loops
in
interphase,
condensin
compacts
mitotic
chromosomes.
However,
role
Smc5/6's
recently
discovered
extrusion
activity
is
unknown.
Here,
we
uncover
that
associates
with
transcription-induced
positively
supercoiled
at
cohesin-dependent
boundaries
on
budding
yeast
(Saccharomyces
cerevisiae)
Mechanistically,
single-molecule
imaging
reveals
dimers
specifically
recognize
tip
plectonemes
efficiently
initiate
to
gather
into
a
large
plectonemic
loop.
Finally,
Hi-C
analysis
shows
links
chromosomal
regions
containing
positive
supercoiling
cis.
Altogether,
our
findings
indicate
controls
three-dimensional
organization
recognizing
initiating
DNA.
Science,
Journal Year:
2025,
Volume and Issue:
387(6734)
Published: Feb. 6, 2025
In
eukaryotes,
DNA-associated
protein
complexes
coevolve
with
genomic
sequences
to
orchestrate
chromatin
folding.
We
investigate
the
relationship
between
DNA
sequence
and
spontaneous
loading
activity
of
components
in
absence
coevolution.
Using
bacterial
genomes
integrated
into
Saccharomyces
cerevisiae
,
which
diverged
from
yeast
more
than
2
billion
years
ago,
we
show
that
nucleosomes,
cohesins,
associated
transcriptional
machinery
can
lead
formation
two
different
archetypes,
one
transcribed
other
silent,
independently
heterochromatin
formation.
These
archetypes
also
form
on
eukaryotic
exogenous
sequences,
depend
composition,
be
predicted
using
neural
networks
trained
native
genome.
They
do
not
mix
nucleus,
leading
a
bipartite
nuclear
compartmentalization,
reminiscent
organization
vertebrate
nuclei.
Development,
Journal Year:
2022,
Volume and Issue:
149(11)
Published: June 1, 2022
ABSTRACT
Enhancers
control
the
establishment
of
spatiotemporal
gene
expression
patterns
throughout
development.
Over
past
decade,
development
new
technologies
has
improved
our
capacity
to
link
enhancers
with
their
target
genes
based
on
colocalization
within
same
topological
domains.
However,
mechanisms
that
regulate
how
specifically
activate
some
but
not
others
a
given
domain
remain
unclear.
In
this
Review,
we
discuss
recent
insights
into
factors
controlling
enhancer
specificity,
including
genetic
composition
and
promoters,
linear
3D
distance
between
genes,
cell-type
specific
chromatin
landscapes.
We
also
elucidating
molecular
principles
specificity
might
help
us
better
understand
predict
pathological
consequences
human
genetic,
epigenetic
structural
variants.
