bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 22, 2024
Abstract
DNA
methylation
clocks
have
been
widely
used
for
accurate
age
prediction,
but
most
studies
carried
out
on
mammals.
Here
we
present
a
clock
the
aquatic
frog
Xenopus
tropicalis
,
model
organism
in
developmental
biology
and
genomics.
The
clock,
trained
targeted
bisulfite
sequencing
data,
achieved
cross-validation
median
absolute
error
of
0.70
years.
To
construct
collected
data
from
192
frogs
at
genomic
regions
containing
CpG
sites
previously
shown
to
age-associated
.
We
found
that
with
levels
significantly
increasing
or
decreasing
are
enriched
heterochromatic
marked
H4K20me3
H3K9me3.
positively
bivalent
chromatin
gene
bodies
H3K36me3,
tend
be
proximal
lowly
expressed
genes.
These
epigenetic
features
aging
similar
those
mammals,
suggesting
evolutionary
conservation
mechanisms.
Our
enables
future
experiments
leverage
unique
properties
amphibians.
Nucleic Acids Research,
Год журнала:
2022,
Номер
51(2), С. 501 - 516
Опубликована: Авг. 5, 2022
Abstract
Individual
cells
are
basic
units
of
life.
Despite
extensive
efforts
to
characterize
the
cellular
heterogeneity
different
organisms,
cross-species
comparisons
landscape
dynamics
have
not
been
achieved.
Here,
we
applied
single-cell
RNA
sequencing
(scRNA-seq)
map
organism-level
cell
landscapes
at
multiple
life
stages
for
mice,
zebrafish
and
Drosophila.
By
integrating
comprehensive
dataset
>
2.6
million
single
cells,
constructed
a
identified
signatures
common
pathways
that
changed
throughout
span.
We
structural
inflammation
mitochondrial
dysfunction
as
most
hallmarks
organism
aging,
found
pharmacological
activation
metabolism
alleviated
aging
phenotypes
in
mice.
The
with
other
published
datasets
were
stored
an
integrated
online
portal—Cell
Landscape.
Our
work
provides
valuable
resource
studying
lineage
development,
maturation
aging.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Окт. 14, 2023
The
growing
number
of
available
single-cell
gene
expression
datasets
from
different
species
creates
opportunities
to
explore
evolutionary
relationships
between
cell
types
across
species.
Cross-species
integration
RNA-sequencing
data
has
been
particularly
informative
in
this
context.
However,
order
do
so
robustly
it
is
essential
have
rigorous
benchmarking
and
appropriate
guidelines
ensure
that
results
truly
reflect
biology.
Here,
we
benchmark
28
combinations
homology
mapping
methods
algorithms
a
variety
biological
settings.
We
examine
the
capability
each
strategy
perform
species-mixing
known
homologous
preserve
heterogeneity
using
9
established
metrics.
also
develop
new
biology
conservation
metric
address
maintenance
type
distinguishability.
Overall,
scANVI,
scVI
SeuratV4
achieve
balance
conservation.
For
evolutionarily
distant
species,
including
in-paralogs
beneficial.
SAMap
outperforms
when
integrating
whole-body
atlases
with
challenging
annotation.
provide
our
freely
cross-species
assessment
pipeline
help
analyse
algorithms.
Signal Transduction and Targeted Therapy,
Год журнала:
2022,
Номер
7(1)
Опубликована: Окт. 2, 2022
Abstract
The
germline
cells
are
essential
for
the
propagation
of
human
beings,
thus
survival
mankind.
stem
cells,
as
a
unique
cell
type,
generate
various
states
germ
and
then
differentiate
into
specialized
spermatozoa
ova,
producing
offspring,
while
self-renew
to
more
cells.
Abnormal
development
often
causes
severe
diseases
in
humans,
including
infertility
cancer.
Primordial
(PGCs)
first
emerge
during
early
embryonic
development,
migrate
gentile
ridge,
join
formation
gonads.
In
males,
they
spermatogonial
which
give
rise
via
meiosis
from
onset
puberty,
females,
female
(FGSCs)
retain
stemness
ovary
initiate
oocytes.
cell-like
(PGCLCs)
can
be
induced
vitro
or
pluripotent
this
review,
we
focus
on
current
advances
these
adult
PGCLCs
provide
an
overview
molecular
mechanisms
underlying
differentiation
outline
their
physiological
functions,
pathological
implications,
clinical
applications.
Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology,
Год журнала:
2024,
Номер
15(1)
Опубликована: Авг. 2, 2024
Abstract
Understanding
biological
mechanisms
is
fundamental
for
improving
animal
production
and
health
to
meet
the
growing
demand
high-quality
protein.
As
an
emerging
biotechnology,
single-cell
transcriptomics
has
been
gradually
applied
in
diverse
aspects
of
research,
offering
effective
method
study
gene
expression
high-throughput
single
cells
different
tissues/organs
animals.
In
unprecedented
manner,
researchers
have
identified
cell
types/subtypes
their
marker
genes,
inferred
cellular
fate
trajectories,
revealed
cell‒cell
interactions
animals
using
transcriptomics.
this
paper,
we
introduce
development
technology
review
processes,
advancements,
applications
research.
We
summarize
recent
efforts
obtain
a
more
profound
understanding
nutrition
health,
reproductive
performance,
genetics,
disease
models
livestock
species.
Moreover,
practical
experience
accumulated
based
on
large
number
cases
highlighted
provide
reference
determining
key
factors
(e.g.,
sample
size,
clustering,
type
annotation)
analysis.
also
discuss
limitations
outlook
current
stage.
This
paper
describes
comprehensive
progress
novel
insights
sustainable
advancements
agricultural
productivity
health.
The
specialized
cell
types
of
the
mucociliary
epithelium
(MCE)
lining
respiratory
tract
enable
continuous
airway
clearing,
with
its
defects
leading
to
chronic
diseases.
molecular
mechanisms
driving
fate
acquisition
and
temporal
specialization
during
epithelial
development
remain
largely
unknown.
Here,
we
profile
developing
Xenopus
MCE
from
pluripotent
mature
stages
by
single-cell
transcriptomics,
identifying
multipotent
early
progenitors
that
execute
multilineage
cues
before
specializing
into
late-stage
ionocytes
goblet
basal
cells.
Combining
in
silico
lineage
inference,
situ
hybridization,
multiplexed
RNA
imaging,
capture
initial
bifurcation
multiciliated
chart
type
emergence
progression
types.
Comparative
analysis
nine
atlases
reveals
an
evolutionary
conserved
transcriptional
module
ciliated
cells,
whereas
secretory
distinct
function-specific
programs
across
vertebrates.
We
uncover
a
nonhierarchical
model
alongside
data
resource
for
understanding
biology.
Journal of Advanced Research,
Год журнала:
2024,
Номер
unknown
Опубликована: Май 1, 2024
Understanding
the
sex
determination
mechanisms
in
birds
has
great
significance
for
biological
sciences
and
production
poultry
industry.
Sex
chickens
is
a
complex
process
that
involves
fate
decisions
of
supporting
cells
such
as
granulosa
or
Sertoli
cells.
However,
systematic
understanding
genetic
regulation
cell
commitment
underlying
still
lacking.
We
aimed
to
dissect
molecular
characteristics
associated
with
gonads
chicken
embryos.
Single-nucleus
RNA-seq
(snRNA-seq)
ATAC-seq
(snATAC-seq)
analysis
were
conducted
on
female
male
at
embryonic
day
3.5
(E3.5),
E4.5,
E5.5.
Here,
we
provided
time-course
transcriptional
chromatin
accessible
profiling
during
single-cell
resolution.
uncovered
differences
composition
developmental
trajectories
between
found
divergence
transcription
accessibility
gonadal
first
emerged
Furthermore,
revealed
key
cell-type-specific
factors
(TFs)
regulatory
networks
drive
lineage
commitment.
signaling
pathways,
dominated
by
BMP
signaling,
are
preferentially
activated
males
development.
Further
pseudotime
indicated
regulated
mainly
TEAD
gene
family
driven
DMRT1
regulons.
Cross-species
suggested
high
conservation
both
types
cell-lineage-specific
TFs
across
six
vertebrates.
Overall,
our
study
will
contribute
accelerating
development
manipulation
technology
industry
application
unique
model
studying
decisions.
