Current Opinion in Cell Biology,
Journal Year:
2022,
Volume and Issue:
74, P. 37 - 46
Published: Jan. 20, 2022
The
genome
of
an
early
embryo
undergoes
significant
remodelling
at
the
epigenetic,
transcriptional,
and
structural
levels.
New
technological
developments
have
made
it
possible
to
study
3D
organisation
in
zygote
many
different
species.
Recent
studies
human
embryos,
zebrafish,
medaka,
Xenopus
revealed
that,
similar
previous
results
mouse
Drosophila,
zygotic
is
unstructured
prior
activation.
While
these
show
that
topologically
associating
domains
are
established
coincident
with
activation
across
species,
other
structures
more
varied
timing.
Here,
we
review
recent
examining
timing
mechanisms
establishment
embryo,
discuss
similarities
differences
between
Investigating
chromatin
conformation
embryos
has
potential
reveal
novel
organisation.
Science,
Journal Year:
2023,
Volume and Issue:
380(6652), P. 1357 - 1362
Published: June 29, 2023
Chromosomes
in
the
eukaryotic
nucleus
are
highly
compacted.
However,
for
many
functional
processes,
including
transcription
initiation,
pairwise
motion
of
distal
chromosomal
elements
such
as
enhancers
and
promoters
is
essential
necessitates
dynamic
fluidity.
Here,
we
used
a
live-imaging
assay
to
simultaneously
measure
positions
pairs
their
transcriptional
output
while
systematically
varying
genomic
separation
between
these
two
DNA
loci.
Our
analysis
reveals
coexistence
compact
globular
organization
fast
subdiffusive
dynamics.
These
combined
features
cause
an
anomalous
scaling
polymer
relaxation
times
with
leading
long-ranged
correlations.
Thus,
encounter
loci
much
less
dependent
on
distance
than
predicted
by
existing
models,
potential
consequences
gene
expression.
Nature Genetics,
Journal Year:
2024,
Volume and Issue:
56(4), P. 686 - 696
Published: March 11, 2024
Abstract
To
regulate
expression,
enhancers
must
come
in
proximity
to
their
target
gene.
However,
the
relationship
between
timing
of
enhancer–promoter
(E–P)
and
activity
remains
unclear,
with
examples
uncoupled,
anticorrelated
correlated
interactions.
assess
this,
we
selected
600
characterized
or
promoters
tissue-specific
Drosophila
embryos
performed
Capture-C
FACS-purified
myogenic
neurogenic
cells
during
specification
tissue
differentiation.
This
enabled
direct
comparison
E–P
transitioning
from
OFF-to-ON
ON-to-OFF
states
across
developmental
conditions.
showed
remarkably
similar
topologies
specified
muscle
neuronal
cells,
which
are
uncoupled
activity.
During
differentiation,
many
new
distal
interactions
emerge
where
changes
reflect
The
mode
regulation
therefore
appears
change
as
embryogenesis
proceeds,
largely
permissive
cell-fate
more
instructive
terminal
when
is
coupled
activation.
Science Advances,
Journal Year:
2022,
Volume and Issue:
8(19)
Published: May 13, 2022
Boundaries
in
animal
genomes
delimit
contact
domains
with
enhanced
internal
frequencies
and
have
debated
functions
limiting
regulatory
cross-talk
between
guiding
enhancers
to
target
promoters.
Most
mammalian
boundaries
form
by
stalling
of
chromosomal
loop-extruding
cohesin
CTCF,
but
most
Drosophila
CTCF
independently.
However,
how
CTCF-independent
function
remains
largely
unexplored.
Here,
we
assess
genome
folding
developmental
gene
expression
fly
embryos
lacking
the
ubiquitous
boundary-associated
factor
Cp190.
We
find
that
sequence-specific
DNA
binding
proteins
such
as
Su(Hw)
directly
interact
recruit
Cp190
promoter-distal
boundaries.
is
essential
for
early
development
prevents
specific
loci
pattern
embryo.
was,
contrast,
dispensable
long-range
enhancer-promoter
communication
at
tested
loci.
thus
currently
major
player
boundary
formation
function,
revealing
diverse
mechanisms
evolved
partition
into
independent
domains.
Nature Communications,
Journal Year:
2022,
Volume and Issue:
13(1)
Published: April 12, 2022
Chromosomes
are
hierarchically
folded
within
cell
nuclei
into
territories,
domains
and
subdomains,
but
the
functional
importance
evolutionary
dynamics
of
these
hierarchies
poorly
defined.
Here,
we
comprehensively
profile
genome
organizations
five
Anopheles
mosquito
species
show
how
different
levels
chromatin
architecture
influence
each
other.
Patterns
observed
on
Hi-C
maps
associated
with
known
cytological
structures,
epigenetic
profiles,
gene
expression
levels.
Evolutionary
analysis
reveals
conservation
synteny
blocks
for
tens
millions
years
enrichment
breakpoints
in
regions
increased
genomic
insulation.
However,
in-depth
shows
a
confounding
effect
density
both
insulation
distribution
breakpoints,
suggesting
limited
causal
relationship
between
At
level
individual
loci,
identify
specific,
extremely
long-ranged
looping
interactions,
conserved
~100
million
years.
We
demonstrate
that
mechanisms
underlying
contacts
differ
from
previously
described
Polycomb-dependent
interactions
clustering
active
chromatin.
Science Advances,
Journal Year:
2023,
Volume and Issue:
9(5)
Published: Feb. 3, 2023
The
boundaries
of
topologically
associating
domains
(TADs)
are
delimited
by
insulators
and/or
active
promoters;
however,
how
they
initially
established
during
embryogenesis
remains
unclear.
Here,
we
examined
this
the
first
hours
Drosophila
embryogenesis.
DNA-FISH
confirms
that
intra-TAD
pairwise
proximity
is
zygotic
genome
activation
(ZGA)
but
with
extensive
cell-to-cell
heterogeneity.
Most
newly
formed
occupied
combinations
CTCF,
BEAF-32,
CP190.
Depleting
each
insulator
individually
from
chromatin
revealed
TADs
can
still
establish,
although
lower
insulation,
a
subset
(~10%)
being
more
dependent
on
specific
insulators.
Some
weakened
have
aberrant
gene
expression
due
to
unconstrained
enhancer
activity.
However,
majority
misexpressed
genes
no
obvious
direct
relationship
changes
in
domain-boundary
insulation.
Deletion
an
promoter
(thereby
blocking
transcription)
at
one
boundary
had
greater
impact
than
deleting
insulator-bound
region
itself.
This
suggests
cross-talk
between
and
promoters
transcription
might
reinforce
domain
insulation
