Cell Genomics,
Journal Year:
2024,
Volume and Issue:
4(2), P. 100498 - 100498
Published: Feb. 1, 2024
Long
interspersed
element
1
(L1)
retrotransposons
are
implicated
in
human
disease
and
evolution.
Their
global
activity
is
repressed
by
DNA
methylation,
but
deciphering
the
regulation
of
individual
copies
has
been
challenging.
Here,
we
combine
short-
long-read
sequencing
to
unveil
L1
methylation
heterogeneity
across
cell
types,
families,
loci
elucidate
key
principles
involved.
We
find
that
youngest
primate
families
specifically
hypomethylated
pluripotent
stem
cells
placenta
not
most
tumors.
Locally,
intronic
intimately
associated
with
gene
transcription.
Conversely,
state
can
propagate
proximal
region
up
300
bp.
This
phenomenon
accompanied
binding
specific
transcription
factors,
which
drive
expression
chimeric
transcripts.
Finally,
hypomethylation
alone
typically
insufficient
trigger
due
redundant
silencing
pathways.
Our
results
illuminate
epigenetic
transcriptional
interplay
between
their
host
genome.
Cell Research,
Journal Year:
2018,
Volume and Issue:
28(12), P. 1141 - 1157
Published: Oct. 12, 2018
Human
adult
spermatogenesis
balances
spermatogonial
stem
cell
(SSC)
self-renewal
and
differentiation,
alongside
complex
germ
cell-niche
interactions,
to
ensure
long-term
fertility
faithful
genome
propagation.
Here,
we
performed
single-cell
RNA
sequencing
of
~6500
testicular
cells
from
young
adults.
We
found
five
niche/somatic
types
(Leydig,
myoid,
Sertoli,
endothelial,
macrophage),
observed
germline-niche
interactions
key
human-mouse
differences.
Spermatogenesis,
including
meiosis,
was
reconstructed
computationally,
revealing
sequential
coding,
non-coding,
repeat-element
transcriptional
signatures.
Interestingly,
identified
discrete
transcriptional/developmental
states,
a
novel
early
SSC
state,
termed
State
0.
Epigenetic
features
nascent
transcription
analyses
suggested
developmental
plasticity
within
States.
To
understand
the
origin
0,
profiled
infants,
distinct
similarities
between
0
infant
SSCs.
Overall,
our
datasets
describe
epigenetic
signatures
normal
human
testis,
provide
new
insights
into
transitions
plasticity.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2021,
Volume and Issue:
unknown
Published: May 5, 2021
Abstract
We
present
STARsolo
,
a
comprehensive
turnkey
solution
for
quantifying
gene
expression
in
single-cell/nucleus
RNA-seq
data,
built
into
aligner
STAR
.
Using
simulated
data
that
closely
resembles
realistic
scRNA-seq,
we
demonstrate
is
highly
accurate
and
significantly
outperforms
pseudoalignment-to-transcriptome
tools.
can
replicate
the
results
of,
but
considerably
faster
than
CellRanger
currently
most
widely
used
tool
pre-processing
scRNA-seq
data.
In
addition
to
uniquely
mapped
reads,
takes
account
of
multi-gene
necessary
detect
certain
classes
biologically
important
genes.
It
has
flexible
cell
barcode
processing
scheme,
compatible
with
many
established
protocols,
extendable
emerging
technologies.
quantify
transcriptomic
features
beyond
expression,
which
illustrate
by
analyzing
cell-type-specific
alternative
splicing
Tabula
Muris
project.
Genome Research,
Journal Year:
2019,
Volume and Issue:
29(4), P. 697 - 709
Published: March 11, 2019
Aging
is
accompanied
by
the
functional
decline
of
tissues.
However,
a
systematic
study
epigenomic
and
transcriptomic
changes
across
tissues
during
aging
missing.
Here,
we
generated
chromatin
maps
transcriptomes
from
four
one
cell
type
young,
middle-aged,
old
mice-yielding
143
high-quality
data
sets.
We
focused
on
marks
linked
to
gene
expression
regulation
identity:
histone
H3
trimethylation
at
lysine
4
(H3K4me3),
mark
enriched
promoters,
acetylation
27
(H3K27ac),
active
enhancers.
Epigenomic
landscapes
could
easily
distinguish
between
ages,
machine-learning
analysis
showed
that
specific
states
predict
transcriptional
aging.
Analysis
sets
all
identified
recurrent
age-related
in
key
processes,
including
up-regulation
immune
system
response
pathways
such
as
interferon
response.
The
pathway
with
age
was
increased
transcription
remodeling
endogenous
retroviral
sequences.
Pathways
misregulated
mouse
tissues,
notably
innate
pathways,
were
also
other
vertebrate
species-African
turquoise
killifish,
rat,
humans-indicating
common
signatures
species.
To
date,
our
set
represents
largest
multitissue
for
This
resource
identifies
are
characteristic
young
which
be
leveraged
restore
aspects
youthful
functionality
