Genome Research,
Год журнала:
2023,
Номер
33(4), С. 572 - 586
Опубликована: Апрель 1, 2023
Epigenetic
modifications
undergo
drastic
erasure
and
reestablishment
after
fertilization.
This
reprogramming
is
required
for
proper
embryonic
development
cell
differentiation.
In
mammals,
some
histone
are
not
completely
reprogrammed
play
critical
roles
in
later
development.
contrast,
nonmammalian
vertebrates,
most
thought
to
be
more
intensively
erased
reestablished
by
the
stage
of
zygotic
genome
activation
(ZGA).
However,
that
escape
vertebrates
their
potential
functional
remain
unknown.
Here,
we
quantitatively
comprehensively
analyzed
modification
dynamics
during
epigenetic
Japanese
killifish,
medaka
(
Oryzias
latipes
)
embryos.
Our
data
revealed
H3K27ac,
H3K27me3,
H3K9me3
complete
reprogramming,
whereas
H3K4
methylation
cleavage
stage.
Furthermore,
experimentally
showed
such
retained
at
early
stages:
(i)
H3K27ac
premarks
promoters
stage,
inhibition
acetyltransferases
disrupts
patterning
H3K27
CpG-dense
promoters,
but
does
affect
chromatin
accessibility
ZGA;
(ii)
globally
specifically
telomeric
regions,
which
maintenance
genomic
stability
These
results
expand
understanding
diversity
conservation
unveil
previously
uncharacterized
functions
reprogramming.
Nature Communications,
Год журнала:
2021,
Номер
12(1)
Опубликована: Март 1, 2021
Abstract
In
eukaryotes,
DNA
is
packed
inside
the
cell
nucleus
in
form
of
chromatin,
which
consists
DNA,
proteins
such
as
histones,
and
RNA.
Euchromatin,
permissive
for
transcription,
spatially
organized
into
transcriptionally
inactive
domains
interspersed
with
pockets
transcriptional
activity.
While
transcription
RNA
have
been
implicated
euchromatin
organization,
it
remains
unclear
how
their
interplay
forms
maintains
pockets.
Here
we
combine
theory
experiment
to
analyze
dynamics
organization
pluripotent
zebrafish
cells
exit
mitosis
begin
transcription.
We
show
that
accumulation
induces
formation
displace
chromatin.
propose
accumulating
recruits
RNA-binding
together
tend
separate
from
euchromatin.
Full
phase
separation
prevented
because
tethered
transcribed
through
polymerases.
Instead,
smaller
scale
microphases
emerge
do
not
grow
further
typical
pattern
organization.
Science,
Год журнала:
2023,
Номер
381(6653), С. 92 - 100
Опубликована: Июль 6, 2023
Nanoscale
chromatin
organization
regulates
gene
expression.
Although
is
notably
reprogrammed
during
zygotic
genome
activation
(ZGA),
the
of
regulatory
factors
this
universal
process
remains
unclear.
In
work,
we
developed
expansion
microscopy
(ChromExM)
to
visualize
chromatin,
transcription,
and
transcription
in
vivo.
ChromExM
embryos
ZGA
revealed
how
pioneer
factor
Nanog
interacts
with
nucleosomes
RNA
polymerase
II
(Pol
II),
providing
direct
visualization
transcriptional
elongation
as
string-like
nanostructures.
Blocking
led
more
Pol
particles
clustered
around
Nanog,
stalled
at
promoters
Nanog-bound
enhancers.
This
a
new
model
termed
"kiss
kick",
which
enhancer-promoter
contacts
are
transient
released
by
elongation.
Our
results
demonstrate
that
broadly
applicable
study
nanoscale
nuclear
organization.
PLoS Genetics,
Год журнала:
2020,
Номер
16(1), С. e1008546 - e1008546
Опубликована: Янв. 15, 2020
In
many
organisms,
early
embryonic
development
is
driven
by
maternally
provided
factors
until
the
controlled
onset
of
transcription
during
zygotic
genome
activation.
The
regulation
chromatin
accessibility
and
its
relationship
to
gene
activity
this
transition
remain
poorly
understood.
Here,
we
generated
maps
with
ATAC-seq
from
activation
lineage
specification.
During
period,
increases
at
regulatory
elements.
This
increase
independent
RNA
polymerase
II-mediated
transcription,
exception
hypertranscribed
miR-430
locus.
Instead,
often
precedes
associated
genes.
Loss
maternal
Pou5f3,
Sox19b,
Nanog,
which
are
known
be
required
for
zebrafish
activation,
results
in
decreased
Importantly,
regions,
especially
when
established
Sox19b
predictive
future
transcription.
Our
show
that
Nanog
open
up
prime
genes
zebrafish.
Annual Review of Genomics and Human Genetics,
Год журнала:
2021,
Номер
22(1), С. 147 - 170
Опубликована: Март 30, 2021
Nucleosomes
wrap
DNA
and
impede
access
for
the
machinery
of
transcription.
The
core
histones
that
constitute
nucleosomes
are
subject
to
a
diversity
posttranslational
modifications,
or
marks,
impact
transcription
genes.
Their
functions
have
sometimes
been
difficult
infer
because
enzymes
write
read
them
complex,
multifunctional
proteins.
Here,
we
examine
evidence
marks
argue
major
perform
fairly
small
number
roles
in
either
promoting
preventing
it.
Acetylations
phosphorylations
on
histone
disrupt
histone–DNA
contacts
and/or
destabilize
promote
Ubiquitylations
stimulate
methylations
provide
scaffold
formation
silencing
complexes
resistance
those
complexes,
carry
memory
transcriptional
state.
Tail
deconstruct
particular
contexts.
We
speculate
these
simple
form
basis
regulation
by
marks.
