Characterization of Rationally Designed CRISPR/Cas9-Based DNA Methyltransferases with Distinct Methyltransferase and Gene Silencing Activities in Human Cell Lines and Primary Human T Cells
ACS Synthetic Biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 3, 2025
Nuclease-deactivated
Cas
(dCas)
proteins
can
be
used
to
recruit
epigenetic
effectors,
and
this
class
of
editing
technologies
has
revolutionized
the
ability
synthetically
control
mammalian
epigenome
transcriptome.
DNA
methylation
is
one
most
important
well-characterized
modifications
in
mammals,
while
many
different
forms
dCas-based
methyltransferases
(dCas-DNMTs)
have
been
developed
for
programmable
methylation,
these
tools
are
frequently
poorly
tolerated
and/or
lowly
expressed
cell
types.
Further,
use
dCas-DNMTs
largely
restricted
lines,
which
limits
mechanistic
insights
karyotypically
normal
contexts
hampers
translational
utility
longer
term.
Here,
we
extend
previous
into
rational
design
catalytic
core
DNMT3A
methyltransferase
test
three
dCas9-DNMT3A/3L
variants
across
human
lines
primary
donor-derived
T
cells.
We
find
that
mutations
within
stabilize
expression
fusion
Jurkat
cells
without
sacrificing
or
gene-silencing
performance.
also
show
rationally
engineered
alter
profiles
at
loci
targeted
with
Finally,
leverage
transcriptionally
repressive
effects
functionally
link
a
key
immunomodulatory
transcription
factor
cytokine
secretion
Overall,
our
work
expands
synthetic
biology
toolkit
provides
roadmap
DNMTs
Язык: Английский
Divergence in cellular markers observed in single-cell transcriptomics datasets between cultured primary trabecular meshwork cells and tissues
Scientific Data,
Год журнала:
2025,
Номер
12(1)
Опубликована: Фев. 14, 2025
Abstract
The
trabecular
meshwork
within
the
outflow
apparatus
is
critical
in
maintaining
intraocular
pressure
homeostasis.
In
vitro
studies
employing
primary
cell
cultures
of
human
(hTM)
have
conventionally
served
as
surrogates
for
investigating
pathobiology
TM
dysfunction.
Despite
its
abundant
use,
translation
outcomes
from
to
ex
vivo
and/or
remains
a
challenge.
Given
heterogeneity,
performing
single-cell
RNA
sequencing
comparing
hTM
tissue
may
provide
important
insights
on
cellular
identity
and
translatability,
such
an
approach
has
not
been
reported
before.
this
study,
we
assembled
total
14
samples
across
passages
1–4,
including
4
individuals
diagnosed
with
glaucoma.
This
dataset
offers
comprehensive
transcriptomic
resource
scRNA-seq
data
study
global
changes
gene
expression
comparison
cells
situ
.
We
performed
extensive
preprocessing
quality
control,
allowing
research
community
access
utilize
public
resource.
Язык: Английский
Unraveling the metabolic‒epigenetic nexus: a new frontier in cardiovascular disease treatment
Cell Death and Disease,
Год журнала:
2025,
Номер
16(1)
Опубликована: Март 18, 2025
Abstract
Cardiovascular
diseases
are
the
leading
causes
of
death
worldwide.
However,
there
still
shortcomings
in
currently
employed
treatment
methods
for
these
diseases.
Therefore,
exploring
molecular
mechanisms
underlying
cardiovascular
is
an
important
avenue
developing
new
strategies.
Previous
studies
have
confirmed
that
metabolic
and
epigenetic
alterations
often
involved
across
patients.
Moreover,
factors
interact
with
each
other
affect
progression
a
coordinated
manner.
Lactylation
novel
posttranslational
modification
(PTM)
links
metabolism
epigenetics
affects
disease
progression.
analyzing
crosstalk
between
cellular
expected
to
provide
insights
development
The
purpose
this
review
describe
relationship
heart
such
as
failure,
myocardial
infarction,
atherosclerosis,
focus
on
acylation
methylation,
propose
potential
therapeutic
measures.
Язык: Английский
Replication-coupled inheritance of chromatin states
Cell Insight,
Год журнала:
2024,
Номер
3(6), С. 100195 - 100195
Опубликована: Авг. 23, 2024
During
the
development
of
eukaryote,
faithful
inheritance
chromatin
states
is
central
to
maintenance
cell
fate.
DNA
replication
poses
a
significant
challenge
for
state
because
every
nucleosome
in
genome
disrupted
as
fork
passes.
It
has
been
found
that
many
factors
including
polymerases,
histone
chaperones,
well
as,
RNA
Pol
II
and
modifying
enzymes
coordinate
spatially
temporally
maintain
epigenome
during
this
progress.
In
review,
we
provide
summary
detailed
mechanisms
replication-coupled
assembly
post-replication
maturation,
highlight
these
processes,
discuss
future
directions
challenges
field.
Язык: Английский
Role of epigenetics and alterations in RNA metabolism in leukodystrophies
Wiley Interdisciplinary Reviews - RNA,
Год журнала:
2024,
Номер
15(3)
Опубликована: Май 1, 2024
Abstract
Leukodystrophies
are
a
class
of
rare
heterogeneous
disorders
which
affect
the
white
matter
brain,
ultimately
leading
to
disruption
in
brain
development
and
damaging
effect
on
cognitive,
motor
social‐communicative
development.
These
present
great
clinical
heterogeneity,
along
with
phenotypic
overlap
this
could
be
partially
due
contributions
from
environmental
stimuli.
It
is
context
that
there
need
investigate
what
other
factors
may
contribute
both
disease
insurgence
phenotypical
novel
evidence
raising
attention
toward
study
epigenetics
transcription
mechanisms
can
influence
phenotype
beyond
genetics.
Modulation
machinery
including
histone
modifications,
DNA
methylation
non‐coding
RNAs
dysregulation,
crucial
players
these
disorders,
moreover
an
aberrant
RNA
maturation
process
has
been
linked
leukodystrophies.
Here,
we
provide
overview
hoping
supply
closer
step
analysis
leukodystrophies
not
only
as
genetically
determined
but
also
added
level
complexity
where
epigenetic
dysregulation
key
relevance.
This
article
categorized
under:
Regulatory
RNAs/RNAi/Riboswitches
>
Disease
Development
Язык: Английский
Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells
Journal of Biological Methods,
Год журнала:
2024,
Номер
11(2), С. e99010015 - e99010015
Опубликована: Июль 10, 2024
Spatiotemporal
regulation
of
gene
expression
is
essential
for
maintaining
cellular
homeostasis
throughout
kidney
development
and
disease
progression.
Transcription
factors
(TFs)
epigenetic
modifications
play
pivotal
roles
in
controlling
expression.
Profiling
chromatin
across
the
genome,
along
with
distribution
target
by
TFs
specific
cell
types,
crucial
understanding
dynamic
changes
Here,
we
presented
a
comprehensive
workflow
epigenomic,
cistromic,
transcriptomic
analyses
primary
tubular
cells.
Specifically,
our
methodologies
included
isolation
epithelial
cells,
RNA
extraction,
assay
transposase-accessible
using
sequencing,
ultra-low-input
micrococcal
nuclease-based
native
immunoprecipitation,
cleavage
under
targets
release
nuclease,
subsequent
bioinformatic
analysis.
This
protocol
provides
methodological
framework
investigating
diseases.
Язык: Английский
Epigenomic anomalies in induced pluripotent stem cells from Alzheimer disease cases
Anthony Flamier,
Alisar Katbe,
Dounya Serhani
и другие.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 30, 2024
SUMMARY
Reprogramming
of
adult
somatic
cells
into
induced
pluripotent
stem
(iPSCs)
resets
the
aging
clock.
However,
primed
iPSCs
can
retain
cell-of-origin
epigenomic
marks,
especially
those
linked
to
heterochromatin
and
lamina-associated
regions.
Here
we
show
that
produced
from
dermal
fibroblasts
late-onset
sporadic
Alzheimer’s
disease
(AD)
cases
anomalies
supersede
developmental
defects
neurodegeneration.
When
compared
elderly
controls,
AD
reduced
BMI1
expression,
lower
H3K9me3
levels,
an
altered
DNA
methylome.
Gene
Ontology
analysis
differentially
methylated
regions
(DMRs)
reveals
terms
cell-cell
adhesion
synapse,
with
cognitive
resilience-associated
MEF2
family
transcription
factors
being
most
enriched
at
DMRs.
Upon
noggin
exposure,
lesser
efficient
neural
induction
forebrain
specification,
together
increased
ZIC2,
ZIC5
WNT-related
gene
expression.
Long-term
neuronal
cultures
present
a
dedifferentiation
loss-of-cell
identity
phenotype.
Despite
these
anomalies,
generate
cortical
neurons
in
normal
proportion
readily
form
cerebral
organoids
developing
amyloid
Tau
pathology.
overexpression
mitigates
tau
accumulation,
fragmentation,
G4
induction.
These
findings
implicate
reprogramming
resistant
or
uncharacterized
genetic
alterations
working
trans
on
epigenome
pathophysiology.
Язык: Английский
Nano-based perivascular intervention sustains a nine-month long-term suppression of intimal hyperplasia in vein grafts
Bioactive Materials,
Год журнала:
2024,
Номер
44, С. 82 - 96
Опубликована: Окт. 13, 2024
Язык: Английский
Epigenetic restoration of differentiation competency via reversal of epiblast regionalisation
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 28, 2024
Abstract
Although
the
epiblast
in
embryo
has
capacity
to
generate
all
tissues
of
body,
its
vitro
counterparts
often
exhibit
differentiation
biases,
posing
significant
challenges
for
both
basic
research
and
translational
applications
involving
pluripotent
stem
cells
(PSCs).
The
origins
these
biases
remain
incompletely
understood.
In
this
study,
we
identify
PSC
as
arising
from
fluctuations
repressive
activating
histone
posttranslational
modifications,
leading
acquisition
a
caudal
epiblast-like
phenotype.
We
present
novel
approach
overcome
bias
using
chemical
chromatin
restoration
(CHR)
treatment.
This
method
restores
transcriptional
programs,
accessibility,
modification
profiles,
potential,
effectively
recapitulating
competent
anterior
state.
Furthermore,
propose
that
high
bivalency
state
is
defining
feature
human
epiblast.
suggest
marks
drive
regionalization,
ultimately
shaping
cellular
responses
cues.
Язык: Английский