Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Дек. 27, 2024
Although
epigenetic
modification
has
long
been
recognized
as
a
vital
force
influencing
gene
regulation
in
plants,
the
dynamics
of
chromatin
structure
implicated
intertwined
transcriptional
duplicated
genes
polyploids
have
yet
to
be
understood.
Here,
we
document
dynamic
organization
two
subgenomes
allotetraploid
cotton
(Gossypium
hirsutum)
by
generating
3D
genomic,
epigenomic
and
transcriptomic
datasets
from
12
major
tissues/developmental
stages
covering
life
cycle.
We
systematically
identify
subset
that
are
closely
associated
with
specific
tissue
functions.
Interestingly,
these
exhibit
not
only
higher
specificity
but
also
more
pronounced
homoeologous
bias.
comprehensively
elucidate
intricate
process
subgenomic
collaboration
divergence
across
various
tissues.
A
comparison
among
tissues
reveals
widespread
differences
reorganization
genome
structures,
Dt
subgenome
exhibiting
extent
status
than
At
subgenome.
Moreover,
construct
comprehensive
atlas
putative
functional
elements
discover
37
cis-regulatory
(CREs)
selection
signals
acquired
during
domestication
improvement.
These
data
analyses
publicly
available
research
community
through
web
portal.
In
summary,
this
study
provides
abundant
resources
depicts
regulatory
architecture
genome,
which
thereby
facilitates
understanding
biological
processes
guides
breeding.
This
describes
cotton,
an
focus
on
genomic
at
throughout
Nature Structural & Molecular Biology,
Год журнала:
2023,
Номер
30(7), С. 991 - 1000
Опубликована: Июль 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.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Июль 15, 2023
Abstract
The
first
activation
of
gene
expression
during
development
(zygotic
genome
activation,
ZGA)
is
accompanied
by
massive
changes
in
chromosome
organization.
connection
between
these
two
processes
remains
unknown.
Using
Hi-C
for
zebrafish
embryos,
we
found
that
folding
starts
establishing
“fountains”,
novel
elements
organization,
emerging
selectively
at
enhancers
upon
ZGA.
polymer
simulations,
demonstrate
fountains
can
emerge
as
sites
targeted
cohesin
loading
and
require
two-sided,
yet
desynchronized,
loop
extrusion.
Specific
loss
pioneer
transcription
factors
drive
ZGA
reveals
a
causal
enhancer
activity
fountain
formation.
Finally,
show
early
Medaka
Xenopus
embryos;
moreover,
cohesin-dependent
pattern
on
mouse
embryonic
stem
cells.
Taken
together,
are
the
enhancer-specific
organization;
they
constitute
starting
points
development,
likely
serving
loading.
Science,
Год журнала:
2024,
Номер
383(6687), С. 1122 - 1130
Опубликована: Март 7, 2024
Eukaryotic
genomes
are
organized
by
loop
extrusion
and
sister
chromatid
cohesion,
both
mediated
the
multimeric
cohesin
protein
complex.
Understanding
how
holds
DNAs
together,
loss
of
cohesion
causes
age-related
infertility
in
females,
requires
knowledge
as
to
cohesin's
stoichiometry
vivo.
Using
quantitative
super-resolution
imaging,
we
identified
two
discrete
populations
chromatin-bound
postreplicative
human
cells.
Whereas
most
complexes
appear
dimeric,
that
localized
sites
associated
with
sororin
was
exclusively
monomeric.
The
monomeric
sororin:cohesin
demonstrates
is
conferred
individual
rings,
a
key
prediction
proposal
arises
from
co-entrapment
DNAs.
Current Opinion in Genetics & Development,
Год журнала:
2024,
Номер
86, С. 102198 - 102198
Опубликована: Апрель 24, 2024
Genomes
are
organised
through
hierarchical
structures,
ranging
from
local
kilobase-scale
cis-regulatory
contacts
to
large
chromosome
territories.
Most
notably,
(sub)-compartments
partition
chromosomes
according
transcriptional
activity,
while
topologically
associating
domains
(TADs)
define
landscapes.
The
inactive
X
in
mammals
has
provided
unique
insights
into
the
regulation
and
function
of
three-dimensional
(3D)
genome.
Concurrent
with
silencing
majority
genes
major
alterations
its
chromatin
state,
undergoes
profound
spatial
rearrangements
at
multiple
scales.
These
include
emergence
megadomains,
compartment
structure
loss
TADs.
Moreover,
Xist
locus,
which
orchestrates
X-chromosome
inactivation,
key
regulatory
domains.
This
review
provides
an
overview
recent
control
these
structural
contextualises
them
within
a
broader
understanding
3D
genome
organisation.
Biochemical Society Transactions,
Год журнала:
2024,
Номер
52(2), С. 793 - 802
Опубликована: Март 7, 2024
Eukaryotic
genomes
are
compacted
and
organized
into
distinct
three-dimensional
(3D)
structures,
which
range
from
small-scale
nucleosome
arrays
to
large-scale
chromatin
domains.
These
structures
play
an
important
role
in
the
regulation
of
transcription
other
nuclear
processes.
The
molecular
mechanisms
that
drive
formation
across
scales
relationship
between
structure
function
remain
incompletely
understood.
Because
processes
involved
complex
interconnected,
it
is
often
challenging
dissect
underlying
principles
environment.
Therefore,
vitro
reconstitution
systems
provide
a
valuable
approach
gain
insight
by
formed
determine
cause-consequence
relationships
involved.
In
this
review,
we
give
overview
approaches
have
been
used
study
how
they
increased
our
understanding
these
structures.
We
start
discussing
studies
given
positioning.
Next,
discuss
recent
efforts
reconstitute
larger-scale
domains
loops
resulting
insights
genome
organization.
conclude
with
outlook
on
potential
future
applications
may
contribute
answering
open
questions
concerning
architecture.
Cellular and Molecular Life Sciences,
Год журнала:
2025,
Номер
82(1)
Опубликована: Фев. 20, 2025
Liquid–liquid
phase
separation
(LLPS),
driven
by
dynamic,
low-affinity
multivalent
interactions
of
proteins
and
RNA,
results
in
the
formation
macromolecular
condensates
on
chromatin.
These
structures
are
likely
to
provide
high
local
concentrations
effector
factors
responsible
for
various
processes
including
transcriptional
regulation
DNA
repair.
In
particular,
enhancers,
super-enhancers,
promoters
serve
as
platforms
condensate
assembly.
current
paradigm,
enhancer-promoter
(EP)
interaction
could
be
interpreted
a
result
enhancer-
promoter-based
contact/fusion.
There
is
increasing
evidence
that
spatial
juxtaposition
enhancers
provided
loop
extrusion
(LE)
SMC
complexes.
Here,
we
propose
may
act
barriers
LE,
thereby
contributing
nuclear
contacts
between
regulatory
genomic
elements.
Annals of the New York Academy of Sciences,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 3, 2025
Abstract
During
zygotic
genome
activation
(ZGA)
and
early
development,
hierarchical
levels
of
chromatin
structure
undergo
remarkable
perturbations:
changes
in
the
nuclear‐to‐cytoplasmic
ratio
various
components;
accessibility;
histone
exchange;
formation
3D
structures
such
as
loops,
topologically
associated
domains,
compartments.
Here,
we
review
peculiarities,
variability,
emergence
structural
features
during
ZGA
different
organisms.
Focusing
on
newly
found
called
fountains
,
describe
prerequisites
for
cohesin
loading
DNA
possible
mechanisms
organization
development.
Fountains
resulting
from
asymmetric
bidirectional
extrusion
spread
cohesin‐loading
points
a
CTCF‐independent
manner.
We
discuss
that
may
not
possess
specific
functions,
unlike
conventional
structures,
could
be
other
biological
processes
where
occurs.
