Extrachromosomal
circular
DNA
(eccDNA),
an
extrachromosomal
structured
DNA,
is
extensively
found
in
eukaryotes.
Investigating
eccDNA
at
the
single-cell
level
crucial
for
understanding
cellular
heterogeneity,
evolution,
development,
and
specific
functions.
However,
high-throughput
identification
methods
are
complex,
lack
of
mature,
widely
applicable
technologies
has
resulted
limited
resources.
To
address
this
gap,
we
built
scEccDNAdb,
a
database
based
on
whole-genome
sequencing
data.
It
contains
3
195
464
entries
from
human
mouse
samples,
with
annotations
including
oncogenes,
typical
enhancers,
super-enhancers,
CCCTC-binding
factor-binding
sites,
single
nucleotide
polymorphisms,
chromatin
accessibility,
expression
quantitative
trait
loci,
transcription
factor
binding
motifs,
structural
variants.
Additionally,
it
provides
nine
online
analysis
visualization
tools,
which
enable
creation
publication-quality
figures
through
user-uploaded
files.
Overall,
scEccDNAdb
comprehensive
analyzing
data
across
diverse
cell
types,
tissues,
species.
Database
URL:
https://lcbb.swjtu.edu.cn/scEccDNAdb/.
Briefings in Bioinformatics,
Год журнала:
2024,
Номер
25(2)
Опубликована: Янв. 22, 2024
Abstract
Extrachromosomal
circular
DNA
(eccDNA)
is
currently
attracting
considerable
attention
from
researchers
due
to
its
significant
impact
on
tumor
biogenesis.
High-throughput
sequencing
(HTS)
methods
for
eccDNA
identification
are
continually
evolving.
However,
an
efficient
pipeline
the
integrative
and
comprehensive
analysis
of
obtained
HTS
data
still
lacking.
Here,
we
introduce
eccDNA-pipe,
accessible
software
package
that
offers
a
user-friendly
conducting
starting
raw
data.
This
dataset
includes
various
techniques
such
as
whole-genome
(WGS),
Circle-seq
Circulome-seq,
through
short-read
or
long-read
sequencing.
eccDNA-pipe
presents
solution
both
upstream
downstream
analysis,
encompassing
quality
control
in
tasks
length
distribution
differential
genes
enriched
with
visualization
structures.
Notably,
automatically
generates
high-quality
publication-ready
plots.
In
summary,
provides
customized
research.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Окт. 24, 2024
Extrachromosomal
circular
DNA
(eccDNA)
is
crucial
in
oncogene
amplification,
gene
transcription
regulation,
and
intratumor
heterogeneity.
While
various
analysis
pipelines
experimental
methods
have
been
developed
for
eccDNA
identification,
their
detection
efficiencies
not
systematically
assessed.
To
address
this,
we
evaluate
the
performance
of
7
using
seven
simulated
datasets,
terms
accuracy,
identity,
duplication
rate,
computational
resource
consumption.
We
also
compare
efficiency
through
twenty-one
real
sequencing
datasets.
Here,
show
that
Circle-Map
Circle_finder
(bwa-mem-samblaster)
outperform
other
short-read
pipelines.
However,
exhibits
notable
redundancy
its
outcomes.
CReSIL
most
effective
pipeline
long-read
data
at
depths
higher
than
10X.
Moreover,
sequencing-based
Circle-Seq
shows
superior
detecting
copy
number-amplified
over
10
kb
length.
These
results
offer
valuable
insights
researchers
choosing
suitable
research.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Март 28, 2025
Chromosomal
instability
(CIN)
is
pervasive
in
human
tumours
and
often
leads
to
structural
or
numerical
chromosomal
aberrations.
Somatic
variants
(SVs)
are
intimately
related
copy
number
alterations
but
the
two
types
of
variant
studied
independently.
Additionally,
despite
numerous
studies
on
detecting
various
SV
patterns,
there
still
no
general
quantitative
models
generation.
To
address
this
issue,
we
develop
a
computational
cell-cycle
model
for
generation
SVs
from
end-joining
repair
replication
after
double-strand
break
formation.
Our
provides
information
relationship
between
breakage
fusion
bridge
cycle,
chromothripsis,
seismic
amplification,
extra-chromosomal
circular
DNA.
Given
whole-genome
sequencing
data,
also
allows
us
infer
important
parameters
with
Bayesian
inference.
framework
unifies
disparate
genomic
patterns
resulted
CIN,
null
mutational
SV,
reveals
deeper
insights
into
impact
genome
rearrangement
tumour
evolution.
Extrachromosomal
circular
DNAs
(eccDNAs)
are
a
type
of
originating
from
but
independent
chromosomal
DNAs.
Nowadays,
with
the
rapid
development
sequencing
and
bioinformatics,
accuracy
eccDNAs
detection
has
significantly
improved.
This
advancement
consequently
enhanced
feasibility
exploring
biological
characteristics
functions
eccDNAs.
review
elucidates
potential
mechanisms
eccDNA
generation,
existing
methods
for
their
analysis,
basic
features.
Furthermore,
it
focuses
on
in
regulating
gene
expression
under
both
physiological
pathological
conditions.
Additionally,
summarizes
clinical
implications
human
cancers
health.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Янв. 4, 2024
Abstract
Chromosomal
instability
(CIN)
is
pervasive
in
human
tumours
and
often
leads
to
structural
or
numerical
chromosomal
aberrations.
Somatic
variants
(SVs)
are
intimately
related
copy
number
alterations
but
the
two
types
of
variant
studied
independently.
In
addition,
despite
numerous
studies
on
detecting
various
SV
patterns,
there
still
no
general
quantitative
models
generation.
To
address
this
issue,
we
develop
a
computational
cell-cycle
model
for
generation
SVs
from
end-joining
repair
replication
after
double
strand
break
formation.
Our
provides
information
relationship
between
breakage
fusion
bridge
cycle,
chromothripsis,
seismic
amplification,
extra-chromosomal
circular
DNA.
Given
single-cell
whole-genome
sequencing
data,
also
allows
us
infer
important
parameters
with
Bayesian
inference.
framework
unifies
disparate
genomic
patterns
resulted
CIN,
null
mutational
SV,
reveals
new
insights
into
impact
genome
rearrangement
tumour
evolution.
Frontiers in Genetics,
Год журнала:
2024,
Номер
15
Опубликована: Апрель 29, 2024
Human
extrachromosomal
circular
DNA,
or
eccDNA,
has
been
the
topic
of
extensive
investigation
in
last
decade
due
to
its
prominent
regulatory
role
development
disorders
including
cancer.
With
rapid
advancement
experimental,
sequencing
and
computational
technology,
millions
eccDNA
records
are
now
accessible.
Unfortunately,
literature
databases
only
provide
snippets
this
information,
preventing
us
from
fully
understanding
eccDNAs.
Researchers
frequently
struggle
with
process
selecting
algorithms
tools
examine
eccDNAs
interest.
To
explain
underlying
formation
mechanisms
five
basic
classes
eccDNAs,
we
categorized
their
characteristics
functions
summarized
eight
biogenesis
theories.
Most
significantly,
created
a
clear
procedure
help
selection
suitable
techniques
thoroughly
examined
most
recent
experimental
bioinformatics
methodologies
data
resources
for
identifying,
measuring
analyzing
sequences.
In
conclusion,
highlighted
current
obstacles
prospective
paths
research,
specifically
discussing
probable
uses
molecular
diagnostics
clinical
prediction,
an
emphasis
on
potential
contribution
novel
strategies.
Frontiers in Molecular Neuroscience,
Год журнала:
2023,
Номер
16
Опубликована: Дек. 6, 2023
Stimuli
that
stimulate
neurons
elicit
transcription
of
immediate-early
genes,
a
process
which
requires
local
sites
chromosomal
DNA
to
form
double-strand
breaks
(DSBs)
generated
by
topoisomerase
IIb
within
few
minutes,
followed
repair
hours.
Wakefulness,
exploring
novel
environment,
and
contextual
fear
conditioning
also
turn-on
synaptic
genes
requiring
DSBs
repair.
It
has
been
reported
(in
non-neuronal
cells)
extrachromosomal
circular
can
at
as
the
are
repaired.
I
propose
activated
may
generate
DNAs
during
DSB
sites,
thus
creating
long-lasting
"markers"
activity
pattern
contain
sequences
from
their
origin
regulate
long-term
gene
expression.
Although
population
is
diverse
overall
associated
with
pathology,
subclass
small
("microDNAs,"
∼100-400
bases
long),
largely
derives
unique
genomic
attractive
features
act
stable,
mobile
expression
in
sequence-specific
manner.
Circular
be
templates
for
RNAs,
particularly
inhibitory
siRNAs,
RNAs
other
non-coding
interact
microRNAs.
These
translation
involved
plasticity,
learning
memory.
Another
possible
fate
inserted
stably
into
chromosomes
after
new
response
subsequent
activation
events.
Thus,
insertions
activity-induced
tend
inactivate
them
aid
homeostatic
regulation
avoid
over-excitation,
well
providing
"counter"
neuron's
history.
Moreover,
release
secretory
exosomes
transferred
recipient
cells
Mobile
packaged
exosomes,
released
an
activity-dependent
manner,
cells,
where
they
regulatory
possibly
incorporated
chromosomes.
Finally,
aging
neurodegenerative
diseases
(including
Alzheimer's
disease)
increase
neurons.
will
become
important
future
assess
how
pathology-associated
relate
DNAs,
whether
latter
potentially
contribute
pathogenesis.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 3, 2023
Abstract
Extrachromosomal
circular
DNA
(eccDNA)
is
crucial
in
oncogene
amplification,
gene
transcription
regulation,
and
intratumor
heterogeneity.
While
various
analysis
pipelines
experimental
methods
have
been
developed
for
eccDNA
identification,
their
detection
efficiencies
not
systematically
assessed.
To
address
this,
we
evaluated
the
performance
of
7
using
three
simulated
datasets,
terms
accuracy,
similarity,
duplication
rate,
computational
resource
consumption.
We
also
compared
efficiency
through
twenty-one
real
sequencing
datasets.
Our
results
identified
Circle-Map
CReSIL
as
most
effective
short-read
long-read
data,
respectively.
Moreover,
third-generation
sequencing-based
Circle-Seq
showed
superior
detecting
copy
number-amplified
over
10
kb
length.
These
offer
valuable
insights
researchers
choosing
suitable
research.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июль 22, 2024
Abstract
Extrachromosomal
circular
DNA
(eccDNA),
an
extrachromosomal
structured
DNA,
is
extensively
found
in
eukaryotes.
Exploring
eccDNA
at
the
single-cell
level
contributes
to
understanding
heterogeneity,
evolution,
development,
and
specific
functions
within
cells.
Nevertheless,
high-throughput
identification
methods
for
are
complex,
currently
mature
widely
applicable
technologies
lacking.
Those
factors
have
led
a
scarcity
of
resources
studying
level.
Therefore,
using
available
whole-genome
sequencing
(WGS)
data,
we
constructed
comprehensive
database
named
scEccDNAdb
(
https://lcbb.swjtu.edu.cn/scEccDNAdb/
).
Presently,
comprises
3,195,464
entries
from
both
disease/health
human
mouse
samples,
which
provides
annotations
including
oncogenes,
typical
enhancers,
super-enhancers,
CTCF
binding
sites,
SNPs,
chromatin
accessibility,
eQTLs,
transcription
factor
motifs,
SVs.
Additionally,
it
nine
online
analysis
visualization
tools,
facilitating
generation
publication-quality
figures
through
upload
customized
files.
Overall,
represents
first
known
us
exploring
analyzing
data
diverse
cell
types,
tissues,
species.
Graphical
abstract