Advanced Science,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 7, 2025
Abstract
The
dynamics
of
chromatin
conformation
involve
continuous
and
reversible
changes
within
the
nucleus
a
cell,
which
participate
in
regulating
processes
such
as
gene
expression,
DNA
replication,
damage
repair.
Here,
SEE
is
introduced,
an
artificial
intelligence
(AI)
method
that
utilizes
autoencoder
transformer
techniques
to
analyze
using
single‐cell
RNA
sequencing
data
limited
number
Hi‐C
maps.
employed
investigate
across
different
scales,
enabling
detection
(i)
rearrangements
topologically
associating
domains
(TADs),
(ii)
oscillations
interactions
at
loci.
Additionally,
facilitates
interpretation
disease‐associated
single‐nucleotide
polymorphisms
(SNPs)
by
leveraging
dynamic
features
conformation.
Overall,
offers
single‐cell,
high‐resolution
approach
analyzing
both
developmental
disease
contexts.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 22, 2024
Abstract
Comprehensive
analysis
of
chromatin
architecture
is
crucial
for
understanding
the
gene
regulatory
programs
during
development
and
in
disease
pathogenesis,
yet
current
methods
often
inadequately
address
unique
challenges
presented
by
heterogeneous
tissue
samples.
Here,
we
introduce
Droplet
Hi-C,
which
employs
a
commercial
microfluidic
device
high-throughput,
single-cell
conformation
profiling
droplets.
Using
mapped
at
resolution
from
mouse
cortex
analyzed
major
cortical
cell
types.
Additionally,
used
this
technique
to
detect
copy
number
variation
(CNV),
structural
variations
(SVs)
extrachromosomal
DNA
(ecDNA)
cancer
cells,
revealing
clonal
dynamics
other
oncogenic
events
treatment.
We
further
refined
allow
joint
transcriptome
single
facilitating
more
comprehensive
exploration
links
between
expression
both
normal
tissues
tumors.
Thus,
Hi-C
not
only
addresses
critical
gaps
but
also
emerges
as
versatile
tool
enhancing
our
regulation
health
disease.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
Abstract
Accurately
detecting
enhancer-promoter
loops
from
genome-wide
interaction
data,
such
as
Hi-C,
is
crucial
for
understanding
gene
regulation.
Current
normalization
methods,
Iterative
Correction
and
Eigenvector
decomposition
(ICE),
are
commonly
used
to
remove
biases
in
Hi-C
data
prior
chromatin
loop
detection.
However,
while
structural
or
CTCF-associated
signals
retained,
often
greatly
diminished
after
ICE
similar
making
these
regulatory
harder
detect.
To
address
this
limitation,
we
developed
Raichu,
a
novel
method
normalizing
contact
data.
Raichu
identifies
nearly
twice
many
ICE,
recovering
almost
all
detected
by
revealing
thousands
of
additional
missed
ICE.
With
its
enhanced
sensitivity
loops,
detects
more
biologically
meaningful
differential
between
conditions
the
same
cell
type.
Furthermore,
performs
consistently
across
different
sequencing
depths
platforms,
including
HiChIP,
single-cell
it
versatile
tool
uncovering
new
insights
into
three-
dimensional
(3D)
genomic
organization
transcriptional
Drug Testing and Analysis,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 5, 2025
ABSTRACT
Since
the
early
20th
century,
concept
of
doping
was
first
introduced.
To
achieve
better
athletic
performance,
chemical
substances
were
used.
By
mid‐20th
it
became
gradually
recognized
that
illegal
use
can
seriously
endangered
athletes'
health
and
compromised
fairness
sports
competitions.
Over
past
30
years,
World
Anti‐Doping
Agency
(WADA)
has
established
corresponding
rules
regulations
to
prohibit
athletes
from
using
or
restrict
certain
drugs,
isotope,
chromatography,
mass
spectrometry
techniques
accredited
detect
substances.
With
development
gene
editing
technology,
many
genetic
diseases
have
been
effectively
treated,
but
enabled
by
same
also
potential
pose
a
threat
in
form
doping.
WADA
explicitly
indicated
Prohibited
List
as
prohibited
method
(M3)
approved
qPCR
detection.
However,
easily
evade
detection,
if
target
genes'
upstream
regulatory
elements
are
considered,
task
more
challenging.
Hi‐C
experiment
driven
3D
genome
through
perspectives
such
topologically
associating
domain
(TAD)
chromatin
loop,
provides
comprehensive
in‐depth
understanding
regulation
expression,
thereby
preventing
level
In
this
work,
we
will
explore
different
perspective
analyzing
recent
studies
on
related
genes
under
genome.
Advanced Science,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 7, 2025
Abstract
The
dynamics
of
chromatin
conformation
involve
continuous
and
reversible
changes
within
the
nucleus
a
cell,
which
participate
in
regulating
processes
such
as
gene
expression,
DNA
replication,
damage
repair.
Here,
SEE
is
introduced,
an
artificial
intelligence
(AI)
method
that
utilizes
autoencoder
transformer
techniques
to
analyze
using
single‐cell
RNA
sequencing
data
limited
number
Hi‐C
maps.
employed
investigate
across
different
scales,
enabling
detection
(i)
rearrangements
topologically
associating
domains
(TADs),
(ii)
oscillations
interactions
at
loci.
Additionally,
facilitates
interpretation
disease‐associated
single‐nucleotide
polymorphisms
(SNPs)
by
leveraging
dynamic
features
conformation.
Overall,
offers
single‐cell,
high‐resolution
approach
analyzing
both
developmental
disease
contexts.